@prefix biotools: . @prefix bsc: . @prefix bsct: . @prefix dcterms: . @prefix edam: . @prefix sc: . @prefix schema: . @prefix xsd: . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3325, edam:topic_3365, edam:topic_3473 ; sc:citation , , , , "pmcid:PMC3042601", "pmcid:PMC3498066", "pmcid:PMC4617611", "pmcid:PMC4750478", "pubmed:20981092", "pubmed:23128226", "pubmed:26432245", "pubmed:26432246" ; sc: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." ; sc:featureList edam:operation_0306, edam:operation_3196, edam:operation_3202, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "1000Genomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.internationalgenome.org" ; biotools:primaryContact "Auton A" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2305, edam:format_2306, edam:format_3003, edam:format_3007 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102 ; sc:author "Ensembl team" ; sc:description "Map your data to the current assembly." ; sc:featureList edam:operation_2944 ; sc:name "1000Genomes assembly converter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2572, edam:format_3016 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Ensembl Genomes team" ; sc:citation , "pmcid:PMC3340611", "pubmed:22543379" ; sc:description "Get a subset of data from a BAM or VCF file." ; sc:featureList edam:operation_2121 ; sc:name "1000Genomes data slicer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3345 ; sc:author "Ensembl team" ; sc:citation ; sc:description "Convert a set of Ensembl IDs from a previous release into their current equivalents." ; sc:featureList edam:operation_3282 ; sc:name "1000Genomes ID history converter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199 ; sc:author "Ensembl Genomes team", "Resequencing Informatics" ; sc:citation , "pmcid:PMC2894800", "pubmed:20459805" ; sc:contributor "Resequencing Informatics" ; sc:description "Identify variation patterns in a chromosomal region of interest for different individuals." ; sc:featureList edam:operation_3504 ; sc:name "1000Genomes Variation Pattern Finder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199 ; sc:author "Ensembl Genomes team", "Resequencing Informatics" ; sc:contributor "Resequencing Informatics" ; sc: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." ; sc:featureList edam:operation_0335 ; sc:name "1000Genomes VCF2PED" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC10865685", "pubmed:38350858" ; sc:description "An intuitive and efficient tool for filtering VCF files." ; sc:featureList edam:operation_3227, edam:operation_3675, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "123VCF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://project123vcf.sourceforge.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0593, edam:topic_0749 ; sc:citation ; sc:description "Tool to evaluate 13C chemical shift assignments of RNA." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "13Check_RNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BIOS-IMASL/13Check_RNA" ; biotools:primaryContact "A. A. Icazatti", "J. A. Vila" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pmcid:PMC4495292", "pubmed:25735772" ; sc:description "Webserver that predicts 14-3-3-binding sites by combining predictions from three different classifiers: ANN, PSSM and SVM." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "14-3-3-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.compbio.dundee.ac.uk/1433pred" ; biotools:primaryContact "The Barton Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0659, edam:topic_2229, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC9580931", "pubmed:36304264" ; sc:description "16S-ITGDB is an integrated database for improving taxonomic classification of 16S ribosomal RNA (rRNA) sequences." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3460 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "16S-ITGDB" ; sc:url "https://github.com/yphsieh/ItgDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0659, edam:topic_3474 ; sc:citation , "pmcid:PMC4315456", "pubmed:25646627" ; sc: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." ; sc:featureList edam:operation_3460 ; sc:name "16S classifier" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://metabiosys.iiserb.ac.in/16Sclassifier/application.php" ; biotools:primaryContact "MetaBioSys Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3301 ; sc:citation , "pmcid:PMC5751400", "pubmed:29297318" ; sc:description "Comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing." ; sc:featureList edam:operation_2454 ; sc:name "16sPIP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://16spip.mypathogen.cn/" ; biotools:primaryContact "Wen Zhang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2885, edam:topic_3673 ; sc: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." ; sc:featureList edam:operation_3840 ; sc:name "1928 Diagnostics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.1928diagnostics.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305 ; sc:citation ; sc: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." ; sc:featureList edam:operation_2428, edam:operation_3283, edam:operation_3503 ; sc:license "MIT" ; sc:name "19andMe" ; sc:softwareHelp ; sc:url "https://19andme.covid19.mathematica.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Demonstrates Professor Grigoryan's illustration of geometrical interpretation of the 1-D DFT." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Geometrical interpretation of the 1-D DFT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29788-geometrical-interpretation-of-the-1-d-dft" ; biotools:primaryContact "Michael Chan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC8180056", "pubmed:34090332" ; sc:description "Mapping-free variant detection from DNA-seq data of matched samples." ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3227, edam:operation_3436, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "2-kupl" ; sc:url "https://github.com/yunfengwang0317/2-kupl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3324, edam:topic_3673 ; sc:citation , "pmcid:PMC8769043", "pubmed:33406042" ; sc:description "2019nCoVAS is a web service for different analyses including transmission, genome, and psychological stress." ; sc:featureList edam:operation_0324, edam:operation_2403, edam:operation_2426 ; sc:name "2019nCoVAS" ; sc:url "http://www.combio-lezhang.online/2019ncov/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_3175, edam:topic_3474 ; sc:citation , "pmcid:PMC5167163", "pubmed:27911828" ; sc:description "2020plus classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene from small somatic variants by using Random Forests." ; sc:featureList edam:operation_0276, edam:operation_0313, edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "2020plus" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v1.2.2" ; sc:url "https://github.com/KarchinLab/2020plus" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1475 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2992 ; sc:encodingFormat edam:format_3547 ; sc:name "Protein structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_1317 ; sc: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." ; sc:featureList edam:operation_2486 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "2DProts" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://2dprots.ncbr.muni.cz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0736, edam:topic_3542 ; sc:citation , "pmcid:PMC6602421", "pubmed:31114904" ; sc:description "Webserver for the comparison of secondary structure algorithms and the secondary structure of protein structures." ; sc:featureList edam:operation_0267, edam:operation_0319, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "2StrucCompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://2struccompare.cryst.bbk.ac.uk/index.php" ; biotools:primaryContact "Elliot Drew", "Robert W. Janes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3318, edam:topic_3520 ; sc:citation , , "pmcid:PMC5103804", "pmcid:PMC8832274", "pubmed:27634801", "pubmed:35084336" ; sc: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." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "2B-Alert Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://2b-alert-web.bhsai.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3474 ; sc: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." ; sc:featureList edam:operation_3443, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:name "2D Image cepstral analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/51004-2d-image-cepstral-analysis" ; biotools:primaryContact "Pavel Paunov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154 ; sc:citation , "pubmed:20696175" ; sc:description "Web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids." ; sc:featureList edam:operation_0337, edam:operation_2479 ; sc:name "2D-MH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/pplot/2D-MH" ; biotools:primaryContact "Xiao Lab", "Xuan Xiao" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1519 ; sc:name "Peptide molecular weights" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2373 ; sc:name "Spot ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2091 ; sc:name "Accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1528 ; sc:name "Protein isoelectric point" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1528 ; sc:name "Protein isoelectric point" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0942 ; sc:name "2D PAGE image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:12923769" ; sc:description "2D-PAGE database." ; sc:featureList edam:operation_0224 ; sc:name "2D-PAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Siena, Italy" ; sc:softwareHelp ; sc:url "http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi" ; biotools:primaryContact "Luca Bini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0623, edam:topic_3542 ; sc:citation ; sc:description "Web server for protein secondary structure visualization." ; sc:featureList edam:operation_0468, edam:operation_0470, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "2dSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.lcqb.upmc.fr/2dss/" ; biotools:primaryContact "Juliana S.. Bernardes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Algorithms for 2D AR and 2D ARMA parameters estimation." ; sc:isAccessibleForFree true ; sc:name "2D AR and 2D ARMA parameters estimation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29360-2d-ar-and-2d-arma-parameters-estimation" ; biotools:primaryContact "Simona Maggio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:32307725" ; sc:description "2DE-pattern is a database containing data on proteins/isoforms/proteoforms profiles." ; sc:featureList edam:operation_2421 ; sc:name "2DE-pattern" ; sc:url "http://2de-pattern.pnpi.nrcki.ru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_2229, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC7267828", "pubmed:32108864" ; sc: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. 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The goal of 3DGV is to build fully immersive VR genome browser where the user can seamlessly interact." ; sc:featureList edam:operation_0570, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "3D Genome Viewer (3DGV)" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3dgv.cs.mcgill.ca/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3421 ; sc:citation , "pmcid:PMC6325541", "pubmed:30627639" ; sc:description "Script that analyzes microglia morphology from 3D data. Outputs include cell and territorial volume, branch length, and number of branch and end points." ; sc:featureList edam:operation_3450, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "3DMorph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ElisaYork/3DMorph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3315, edam:topic_3384 ; sc:citation ; sc:description """3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. 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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""" ; sc:featureList edam:operation_0531, edam:operation_2935, edam:operation_3223, edam:operation_3563 ; sc:isAccessibleForFree true ; sc:name "3SRP" ; sc:operatingSystem "Linux" ; sc:provider "BiRD bioinformatics facility" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3320, edam:topic_3517 ; sc:citation , "pmcid:PMC8728222", "pubmed:34432052" ; sc:description "An atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues." ; sc:featureList edam:operation_2943, edam:operation_3196, edam:operation_3208, edam:operation_3232, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "3 aQTL-atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://wlcb.oit.uci.edu/3aQTLatlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0798, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0310, edam:operation_3472, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "3CAC" ; sc:url "https://github.com/Shamir-Lab/3CAC" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC8665754", "pubmed:34270679" ; sc:description "Pathogenicity prediction of human variants using multitask learning with evolutionary constraints." ; sc:featureList edam:operation_0331, edam:operation_3227, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "3Cnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zenodo.org/record/4716879#.YIO-xqkzZH1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3304 ; sc:citation , "pubmed:31449837" ; sc: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." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "3d-SPADE" ; sc:url "https://elephant.readthedocs.io/en/latest/reference/spade.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2275 ; sc:citation ; sc:description "The 3D-Beacons Network provides unified programmatic access to experimentally determined and predicted structure models." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "3D-Beacons" ; sc:softwareHelp , , ; sc:softwareVersion "1.0.0" ; sc:url "https://3d-beacons.org" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_1476, edam:format_3464, edam:format_3874 ; sc:name "Trajectory data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0092, edam:topic_3510, edam:topic_3892 ; sc:author "Adam Hospital" ; sc:citation , , "pmcid:PMC6736963", "pmcid:PMC7284151", "pubmed:31506435", "pubmed:32566135" ; sc:contributor "Genís Bayarri" ; sc: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). 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It is a plugin for Medical Imaging Interaction Toolkit (https://www.mitk.org/)." ; sc:featureList edam:operation_3552 ; sc:name "3D-Cell-Annotator" ; sc:url "http://www.3D-cell-annotator.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3344, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:description "An interactive tool for users to browse through sagittal, axial and coronal views of CT/MRI images." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "3D CT MRI images interactive sliding viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29134-3d-ct-mri-images-interactive-sliding-viewer" ; biotools:primaryContact "Gang Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0097, edam:topic_0593, edam:topic_1317 ; sc:author ; sc:citation , "pmcid:PMC2703913", "pubmed:19417072" ; sc: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." ; sc:featureList edam:operation_0570, edam:operation_2476, edam:operation_2481 ; sc:isAccessibleForFree true ; sc:name "3D-DART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://milou.science.uu.nl/services/3DDART/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3344, edam:topic_3382 ; sc:description "Generate in 3D the diffusion gradient vector field as in Xu and Prince 1998" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "3D Diffusion gradient" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/31994-diffusion-gradient-vector-field-in-3d" ; biotools:primaryContact "Khaled Khairy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0654 ; sc:citation , "pmcid:PMC5635820", "pubmed:28336562" ; sc:description "3D de novo assembly (3D-DNA) is a pipeline for de novo assembly using HiC." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:license "MIT" ; sc:name "3d-dna" ; sc:url "https://github.com/aidenlab/3d-dna" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_0602, edam:topic_2258, edam:topic_3314 ; sc:citation , "pmcid:PMC5342320", "pubmed:28125221" ; sc:description "Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine." ; sc:featureList edam:operation_2406, edam:operation_2414, edam:operation_3646 ; sc:name "3D-e-Chem-VM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3d-e-chem.github.io/3D-e-Chem-VM/" ; biotools:primaryContact "C. De. Graaf", "Ross Mcguire", "S. Verhoeven" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0157, edam:topic_3534 ; sc:citation , "pmcid:PMC2808867", "pubmed:19767616" ; sc: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." ; sc:featureList edam:operation_0321, edam:operation_0478, edam:operation_2997, edam:operation_3561 ; sc:name "3D-Footprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://floresta.eead.csic.es/3dfootprint" ; biotools:primaryContact "3D-Footprint Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3344, edam:topic_3382 ; sc:description "A toolbox for performing image registrations on 4D RTOG files or any other volumetric image." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "3D Free Form Image Registration Toolbox (GUI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.5.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/21017-3d-free-form-image-registration-toolbox-gui" ; biotools:primaryContact "Daniel Markel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0821, edam:topic_2275, edam:topic_2814 ; sc:citation , "pmcid:PMC2447717", "pubmed:18515349" ; sc: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." ; sc:featureList edam:operation_0320, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_2487 ; sc:name "3D-Fun" ; sc:url "http://3dfun.bioinfo.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3175, edam:topic_3176, edam:topic_3940 ; sc:citation , "pmcid:PMC7319547", "pubmed:32442297" ; sc: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.""" ; sc:featureList edam:operation_0481, edam:operation_0570, edam:operation_3196 ; sc:name "3D-GNOME" ; sc:softwareVersion "2.0" ; sc:url "https://3dgnome.cent.uw.edu.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "MATLAB script for converting a image stack into a 3D array." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "3D image stacker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/38788-3d-image-stack-viewer" ; biotools:primaryContact "boyexex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation , , , "pmcid:PMC168910", "pmcid:PMC168911", "pubmed:12761065", "pubmed:12824309", "pubmed:12824423" ; sc:description "3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach." ; sc:featureList edam:operation_0267, edam:operation_0268, edam:operation_0474, edam:operation_0477 ; sc:name "3D-Jury" ; sc:url "http://meta.bioinfo.pl/submit_wizard.pl" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1520 ; sc:name "Peptide hydrophobic moment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1522 ; sc:name "Protein sequence hydropathy plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Computations of joint angles and displacements, moments and forces (lower / upper limb)" ; sc:featureList edam:operation_0407 ; sc:isAccessibleForFree true ; sc:name "3D Kinematics and Inverse Dynamics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/58021-3d-kinematics-and-inverse-dynamics" ; biotools:primaryContact "Raphael Dumas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0128, edam:topic_0157, edam:topic_0602 ; sc:citation , "pmcid:PMC1933210", "pubmed:17517763" ; sc:description "Tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes." ; sc:featureList edam:operation_0474, edam:operation_2406, edam:operation_2479, edam:operation_2492, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "3D-partner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gemdock.life.nctu.edu.tw/3d-partner/" ; biotools:primaryContact "Jinn-Moon Yang", "Yu-Shu Lo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3383, edam:topic_3384, edam:topic_3452, edam:topic_3954 ; sc:citation , "pmcid:PMC7082691", "pubmed:32211292" ; sc:description """3D photoacoustic visualization studio. Bio Optics and Acoustics Laboratory.""" ; sc:featureList edam:operation_0297, edam:operation_0337, edam:operation_3443 ; sc:name "3D PHOVIS" ; sc:url "http://www.boa-lab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0160, edam:topic_0736 ; sc:citation "pubmed:10526371", "pubmed:10860755" ; sc:description "Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information." ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_0303, edam:operation_0474 ; sc:name "3D-pssm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html" ; biotools:primaryContact "Lawrence Kelley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_2275, edam:topic_3375 ; sc:citation , "pubmed:31595406" ; sc: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).""" ; sc:featureList edam:operation_0478, edam:operation_3435, edam:operation_3659 ; sc:name "3d-qsar" ; sc:url "http://www.3d-qsar.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC8594885", "pubmed:33345702" ; sc: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.""" ; sc:featureList edam:operation_0264, edam:operation_2939, edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:name "3D RNA-seq" ; sc:url "https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc: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." ; sc:featureList edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "3D Shepp-Logan Phantom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50974-3d-shepp-logan-phantom" ; biotools:primaryContact "Patrick Bolan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166 ; sc:citation , "pubmed:24573477" ; sc: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." ; sc:featureList edam:operation_2479, edam:operation_3351, edam:operation_3666 ; sc:name "3D-SURFER" ; sc:softwareHelp ; sc:url "http://kiharalab.org/3d-surfer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3444, edam:topic_3452, edam:topic_3954 ; sc:citation , "pmcid:PMC7822775", "pubmed:33057891" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:license "BSD-2-Clause" ; sc:name "3D-XGuide" ; sc:url "https://github.com/ExCaVI-Ulm/3D-XGuide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pmcid:PMC6747482", "pubmed:31450739" ; sc:description "An Web Server for RNA 3D structure prediction." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441 ; sc:name "3dRNA" ; sc:softwareVersion "v2.0" ; sc:url "http://biophy.hust.edu.cn/3dRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3382 ; sc:citation , "pubmed:34743262" ; sc:description "An interactive software for 3D segmentation and analysis of dendritic spines." ; sc:featureList edam:operation_3450, edam:operation_3799 ; sc:name "3D Spine Analysis Software (3dSpAn)" ; sc:softwareHelp ; sc:url "https://sites.google.com/view/3dSpAn/" ; biotools:primaryContact , , "Ewa Baczynska", "Nirmal Das" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3444 ; sc:description "This software contains 2D and 3D Shepp-Logan phantoms in both the image and Fourier domains." ; sc:isAccessibleForFree true ; sc:name "Three Dimensional Analytical Magnetic Resonance Imaging Phantom in the Fourier Domain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/15697-three-dimensional-analytical-magnetic-resonance-imaging-phantom-in-the-fourier-domain" ; biotools:primaryContact "Cheng Guan Koay" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1146 ; sc:name "EMDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0219, edam:topic_3047, edam:topic_3366 ; sc:author , "Joan Segura" ; sc:citation , , , ; sc: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." ; sc:featureList edam:operation_0564, edam:operation_0570, edam:operation_2422 ; sc:funder "CORBEL", "CSIC", "Comunidad de Madrid", "EOSC-Life", "Instituto de Salud Carlos III", "Spanish Ministry of Science and Innovation" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "3DBIONOTES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ES", "INB", "cnb.csic.es" ; sc:softwareHelp ; sc:softwareVersion "v3" ; sc:url "http://3dbionotes.cnb.csic.es/ws" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2229, edam:topic_3382, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC8748745", "pubmed:35013443" ; sc:description "A light and robust tool to do 3D cell instance segmentation for cell membrane images. It is useful when the cells clump together." ; sc:featureList edam:operation_3443, edam:operation_3552, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:name "3DCellSeg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AntonotnaWang/3DCellSeg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation , "pmcid:PMC3167051", "pubmed:21791532" ; sc: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." ; sc:featureList edam:operation_0295, edam:operation_0504 ; sc:name "3DCOMB" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.06" ; sc:url "http://ttic.uchicago.edu/~jinbo/software.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC7496221", "pubmed:32859248" ; sc: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""" ; sc:featureList edam:operation_0481, edam:operation_3222, edam:operation_3435 ; sc:license "MIT" ; sc:name "3DeFDR" ; sc:url "https://bitbucket.org/creminslab/5c3defdr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0611, edam:topic_3382, edam:topic_3385 ; sc:citation , "pmcid:PMC3692114", "pubmed:23671335" ; sc: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." ; sc:featureList edam:operation_0321, edam:operation_2406, edam:operation_3457 ; sc:name "3DEM Loupe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3demloupe.cnb.csic.es" ; biotools:primaryContact "3DEM Loupe Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3569 ; sc:citation ; sc:description "Robust computational infrastructure capable of supporting the automatic and standardised benchmarking of image processing applications for cryoEM." ; sc:featureList edam:operation_2428 ; sc:name "3DEMBenchmark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "cnb.csic.es" ; sc:softwareHelp ; sc:url "http://i2pc.cnb.csic.es/3dembenchmark/LoadHome.htm" ; biotools:primaryContact "Joan Segura" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_0769, edam:topic_2814, edam:topic_3400 ; sc:citation , "pmcid:PMC9162058", "pubmed:35664289" ; sc:description "The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space." ; sc:featureList edam:operation_0303, edam:operation_0474, edam:operation_0570, edam:operation_3663, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "3DFI" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/PombertLab/3DFI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0199, edam:topic_0621, edam:topic_3169, edam:topic_3912 ; sc:citation , "pmcid:PMC9252746", "pubmed:35639501" ; sc:description "A web-server to benchmark computational models for 3D Genomics." ; sc:featureList edam:operation_0475, edam:operation_2483, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "3DGenBench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://3dgenbench.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:35511112" ; sc:description "3D graph and text based neural network for drug-drug interaction prediction." ; sc:featureList edam:operation_3625, edam:operation_3927, edam:operation_4009 ; sc:license "Apache-2.0" ; sc:name "3DGT-DDI" ; sc:url "https://github.com/hehh77/3DGT-DDI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0128, edam:topic_0602, edam:topic_2275 ; sc:author "Joan Segura" ; sc:citation , "pmcid:PMC4775853", "pubmed:26772592" ; sc: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" ; sc:featureList edam:operation_2949, edam:operation_3350 ; sc:name "3DIANA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3diana.cnb.csic.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0602, edam:topic_0736 ; sc:citation , "pmcid:PMC3013799", "pubmed:20965963" ; sc: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." ; sc:featureList edam:operation_0246, edam:operation_0248, edam:operation_0303, edam:operation_2492, edam:operation_2949 ; sc:name "3DID database of 3D interacting domains" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3did.irbbarcelona.org/" ; biotools:primaryContact "Patrick Aloy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0204, edam:topic_0621, edam:topic_2640, edam:topic_3295 ; sc:citation , "pmcid:PMC7778885", "pubmed:33245777" ; sc: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.""" ; sc:featureList edam:operation_2429, edam:operation_3208, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "3DIV" ; sc:softwareHelp ; sc:url "http://3div.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_2814, edam:topic_3511, edam:topic_3534 ; sc:citation , "pmcid:PMC2896164", "pubmed:20513649" ; sc: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." ; sc:featureList edam:operation_0474, edam:operation_0482, edam:operation_2575 ; sc:name "3DLigandSite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sbg.bio.ic.ac.uk/3dligandsite" ; biotools:primaryContact "Mark Wass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0166 ; sc:citation , , , , "pmcid:PMC1866380", "pmcid:PMC1933223", "pmcid:PMC420233", "pubmed:15119965", "pubmed:16351754", "pubmed:17488847", "pubmed:9837739" ; sc:description "3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures." ; sc:featureList edam:operation_0245, edam:operation_0448, edam:operation_2406, edam:operation_2479, edam:operation_3767 ; sc:name "3dLOGO" ; sc:url "http://3dlogo.uniroma2.it/3dLOGO/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_2814, edam:topic_3120, edam:topic_3676 ; sc:citation , "pmcid:PMC11018535", "pubmed:38565273" ; sc:description "A command line tool for bio bank-scale mapping of variants to protein structures." ; sc:featureList edam:operation_0321, edam:operation_0331, edam:operation_0477, edam:operation_2429, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "3Dmapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/vicruiser/3Dmapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workbench" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3297, edam:topic_3306, edam:topic_3398, edam:topic_3569 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0250, edam:operation_0322, edam:operation_0477, edam:operation_2476 ; sc:name "3DMem-enzyme" ; sc:url "http://www.iceht.forth.gr/staff/burganos.html" ; biotools:primaryContact "Vassilios Burganos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3314, edam:topic_3382 ; sc:citation , , "pmcid:PMC4393526", "pmcid:PMC9416521", "pubmed:25505090", "pubmed:36035779" ; sc: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." ; sc:featureList edam:operation_0570 ; sc:license "BSD-3-Clause" ; sc:name "3Dmol.js" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3dmol.csb.pitt.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0166, edam:topic_0654, edam:topic_3382 ; sc:citation "pubmed:19906722" ; sc: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." ; sc:featureList edam:operation_0245, edam:operation_0339, edam:operation_0360, edam:operation_2442, edam:operation_3431 ; sc:name "3DNALandscapes" ; sc:url "http://dcp.rutgers.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3003 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3176, edam:topic_3656 ; sc:citation , "pmcid:PMC6029251", "pubmed:29334377" ; sc:description "A package of Python scripts that sensitively detects nested, hierarchical domains in HiC data." ; sc:featureList edam:operation_0279 ; sc:isAccessibleForFree true ; sc:name "3DNetMod" ; sc:softwareHelp ; sc:url "https://bitbucket.org/creminslab/3dnetmod_method_v1.0_10_06_17" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_3298, edam:topic_3500, edam:topic_3810 ; sc:citation , "pmcid:PMC8317184", "pubmed:34235898" ; sc:description "Application for two- and three-dimensional fish morphological phenotype extraction from point cloud analysis." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "3DPhenoFish" ; sc:url "https://github.com/lyh24k/3DPhenoFish/tree/master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3169, edam:topic_3940 ; sc:citation , "pmcid:PMC9750120", "pubmed:36355469" ; sc:description "An accessible simulation framework to model the interplay between chromatin and loop extrusion." ; sc:featureList edam:operation_0481 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "3DPolyS-LE" ; sc:operatingSystem "Linux" ; sc:url "https://gitlab.com/togop/3DPolyS-LE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation , "pmcid:PMC4316736", "pubmed:25664223" ; sc:description "3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view." ; sc:featureList edam:operation_3083 ; sc:name "3DProIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bicompute.appspot.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation , "pmcid:PMC5006309", "pubmed:26471454" ; sc:description "3DRobot is a program devoted for automated generation of diverse and well-packed protein structure decoys." ; sc:featureList edam:operation_2479 ; sc:name "3DRobot" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://zhanglab.ccmb.med.umich.edu/3DRobot" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_3650, edam:format_3875, edam:format_3885, edam:format_3910 ; sc:name "Trajectory data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1459 ; sc:encodingFormat edam:format_1476 ; sc:name "Nucleic acid structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2331 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0092, edam:topic_1317, edam:topic_3307, edam:topic_3892 ; sc:author "Genís Bayarri" ; sc:contributor ; sc:description "3DRS, a web-based tool to share interactive representations of 3D biomolecular structures and Molecular Dynamics trajectories" ; sc:featureList edam:operation_0570, edam:operation_3890 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "3DRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mmb.irbbarcelona.org/3dRS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_2885, edam:topic_3295, edam:topic_3940 ; sc:citation , "pmcid:PMC8728236", "pubmed:34723317" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_3227, edam:operation_3431, edam:operation_3661 ; sc:name "3DSNP" ; sc:softwareHelp , ; sc:url "https://omic.tech/3dsnpv2/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3344, edam:topic_3520 ; sc:description "A 3-dimensional quantification algorithm for LC–MS labeled profile data" ; sc:featureList edam:operation_0314, edam:operation_3755, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "3DSpectra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47904-3dspectra" ; biotools:primaryContact "Sara Nasso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation , "pmcid:PMC1538824", "pubmed:16844975" ; sc:description "Tool for superposing two or more protein structures that uses RASMOL for visualization, some browser configuration is necessary." ; sc:featureList edam:operation_0320, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_2406 ; sc:name "3DSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cluster.physics.iisc.ernet.in/3dss/options.html" ; biotools:primaryContact "K Sekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation , "pmcid:PMC3394331", "pubmed:22693215" ; sc: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." ; sc:featureList edam:operation_0389, edam:operation_0445, edam:operation_0477, edam:operation_2575, edam:operation_3222 ; sc:name "3DTF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gene-regulation.com/pub/programs/3dtf/" ; biotools:primaryContact "Denitsa Alamanova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0625, edam:topic_2533, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC10251577", "pubmed:37296383" ; sc:description "Tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D." ; sc:featureList edam:operation_0302, edam:operation_0331, edam:operation_0337, edam:operation_3227, edam:operation_3661 ; sc:license "MIT" ; sc:name "3DVizSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://analysistools.cancer.gov/3dvizsnp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation , "pubmed:21586519" ; sc: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." ; sc:featureList edam:operation_0282, edam:operation_0283, edam:operation_2421, edam:operation_2429 ; sc:name "3FunMap" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://statgen.psu.edu/software/3funmap.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3168, edam:topic_3315 ; sc:citation , "pmcid:PMC8934446", "pubmed:35307007" ; sc:description "Optimized Levenshtein distance for clustering third-generation sequencing data." ; sc:featureList edam:operation_0491, edam:operation_3096, edam:operation_3432 ; sc:license "Not licensed" ; sc:name "3GOLD" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/roblogan6/3GOLD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_2830, edam:topic_3930, edam:topic_3948 ; sc:citation ; sc:description """Prediction of potentially immunopathogenic SARS-CoV-2 epitopes via a novel immunoinformatic approach. 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Whittaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_2830 ; sc:citation , "pubmed:31410491" ; sc:description "A database for chemically defined antibodies." ; sc:featureList edam:operation_3431 ; sc:name "Antibodies Chemically Defined Database (ABCD)" ; sc:url "https://web.expasy.org/abcd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593 ; sc:citation , "pmcid:PMC6648237", "pubmed:31459783" ; sc:description "An R package to calculate equilibirum conditions with and without correction for ionic strength using Davies' equation." ; sc:name "ABCharge" ; sc:url "https://github.com/troelsring/ABCharge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Experimental Brain Computer Interface Software for the ModularEEG." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ABI software" ; sc:operatingSystem "Windows" ; sc:url "https://users.dcc.uchile.cl/~peortega/abi/" ; biotools:primaryContact "Jim Peters", "Pedro Ortega" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pubmed:31038664" ; sc:description "Adaptive boosting-based computational model for predicting potential miRNA-disease associations." ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ABMDA" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/githubcode007/ABMDA" ; biotools:primaryContact "Xing Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3408, edam:topic_3474 ; sc:citation , "pmcid:PMC6258961", "pubmed:30519191" ; sc:description "R Package for Calculating the Abnormal Blood Profile Score." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ABPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=ABPS" ; biotools:primaryContact "Frédéric Schütz" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1927, edam:format_1929, edam:format_1936 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3301 ; sc:author ; sc:description "Mass screening of contigs for antimicrobial resistance or virulence genes." ; sc:featureList edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ABRicate" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.9.8" ; sc:url "https://github.com/tseemann/abricate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885, edam:topic_3305, edam:topic_3500, edam:topic_3697 ; sc:citation , , "pmcid:PMC7478624", "pubmed:32320376" ; sc: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." ; sc:featureList edam:operation_3192, edam:operation_3659, edam:operation_3791, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "Accessory-based source attribution (AB_SA)" ; sc:url "https://github.com/lguillier/AB_SA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0632, edam:topic_3168 ; sc:citation ; sc:description "Allele CAlling proCedure for Illumina Amplicon sequencing data." ; sc:featureList edam:operation_0308, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ACACIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.com/psc_santos/ACACIA" ; biotools:primaryContact "Pablo S.C. Santos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC7049724", "pubmed:32034421" ; sc:description "ACCOST is a Python script that assigns statistical significance to differences in contact counts in Hi-C experiment." ; sc:license "Apache-2.0" ; sc:name "ACCOST" ; sc:url "https://bitbucket.org/noblelab/accost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC6307290", "pubmed:30587115" ; sc:description "Machine learning toolbox for clustering analysis and visualization." ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ACES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GrabherrGroup/ACES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_2275, edam:topic_3373 ; sc:citation , "pmcid:PMC6882193", "pubmed:33430982" ; sc:description "A free tool for drug repurposing using consensus inverse docking strategy." ; sc:featureList edam:operation_0337, edam:operation_0482, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "ACID" ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/ACID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091 ; sc:author ; sc:citation ; sc: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." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ACPP" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/brsaran/ACPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC6571645", "pubmed:31121946" ; sc:description "Computational Tool for the Prediction and Analysis of Anticancer Peptides." ; sc:featureList edam:operation_0252 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ACPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://codes.bio/acpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:31729528" ; sc:description "ACPred-Fuse is a web application that automatically can predict protein sequences with or without anticancer activity in peptide form." ; sc:featureList edam:operation_3092, edam:operation_3631, edam:operation_3767 ; sc:name "ACPred-Fuse" ; sc:url "http://server.malab.cn/ACPred-Fuse/Server.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3047, edam:topic_3474 ; sc:citation , "pmcid:PMC8212143", "pubmed:34179848" ; sc:description "A multi-scale resource of biological maps to study disease mechanisms." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_0533, edam:operation_2436, edam:operation_3927, edam:operation_3935 ; sc:name "Atlas of Cancer Signalling Network (ACSN)" ; sc:url "https://acsn.curie.fr/ACSN2/ACSN2.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:31359028" ; sc: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" ; sc:featureList edam:operation_3891 ; sc:name "ACTINN" ; sc:url "https://github.com/mafeiyang/ACTINN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3170, edam:topic_3334, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2499, edam:operation_3196, edam:operation_3658 ; sc:name "ACTOR" ; sc:url "https://github.com/mccabes292/actor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation , "pubmed:31813761" ; sc: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.""" ; sc:name "ACTman" ; sc:url "https://github.com/compsy/ACTman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3168 ; sc:citation , "pmcid:PMC6864362", "pubmed:31740563" ; sc: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.""" ; sc:featureList edam:operation_0491, edam:operation_3216, edam:operation_3802 ; sc:name "ADAPTABLE" ; sc:url "http://gec.u-picardie.fr/adaptable/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3474 ; sc:citation , "pmcid:PMC6612897", "pubmed:31510641" ; sc: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" ; sc:featureList edam:operation_3627, edam:operation_3803, edam:operation_3860 ; sc:name "ADAPTIVE" ; sc:url "http://www.bic.kyoto-u.ac.jp/pathway/tools/ADAPTIVE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Automated Deconvolution Augmentation of Profiles for Tissue Specific cells." ; sc:featureList edam:operation_2495, edam:operation_3237, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ADAPTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/ADAPTS" ; biotools:primaryContact "Samuel A. Danziger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0769, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31764991" ; sc: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""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3799 ; sc:license "LGPL-3.0" ; sc:name "ADDO" ; sc:url "https://github.com/LeileiCui/ADDO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0634 ; sc:citation , "pubmed:29360930" ; sc:description "Discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases." ; sc:featureList edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "ADEPTUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://adeptus.cs.tau.ac.il/home" ; biotools:primaryContact "Ron Shamir" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3334, edam:topic_3419 ; sc:citation , "pmcid:PMC8061253", "pubmed:31088588" ; sc:description "Risk calculator to predict ADHD in young adulthood." ; sc:featureList edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ADHD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ufrgs.br/prodah/adhd-calculator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation "pmcid:PMC6890416", "pubmed:31798351" ; sc: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.""" ; sc:name "ADMMBO" ; sc:url "https://github.com/SetarehAr/ADMMBO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0209, edam:topic_3377, edam:topic_3379, edam:topic_3474 ; sc:citation , , "pmcid:PMC7325315", "pubmed:31838499", "pubmed:31868917" ; sc:description "Broad-Spectrum Profiling of Drug Safety via Learning Complex Network." ; sc:featureList edam:operation_0478, edam:operation_2426, edam:operation_3435, edam:operation_3439 ; sc:name "ADRAlert" ; sc:url "http://www.bio-add.org/ADRAlert/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_3474 ; sc:citation , "pmcid:PMC6855565", "pubmed:31682632" ; sc:description "A novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences." ; sc:featureList edam:operation_2940, edam:operation_3352, edam:operation_3778 ; sc:name "ADS" ; sc:url "http://ekhidna2.biocenter.helsinki.fi/ADS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168, edam:topic_3303 ; sc:citation , "pmcid:PMC6376756", "pubmed:30764760" ; sc:description "Scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark." ; sc:featureList edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ADS-HCSpark" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/SCUT-CCNL/ADS-HCSpark.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7567505", "pubmed:31607216" ; sc: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." ; sc:featureList edam:operation_2495, edam:operation_3435 ; sc:name "Advanced Expression Survival Analysis (AESA)" ; sc:url "http://innovebioinfo.com/Databases/TCGA_Mutation_ExpressionDB/Mutationdb_Search5.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3169, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0531, edam:operation_2938, edam:operation_3435, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "AFCMHeatMap" ; sc:url "https://mohammadtarek.shinyapps.io/AFCMHeatMap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0208, edam:topic_0625, edam:topic_2830 ; sc:citation , "pubmed:31722398" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3431 ; sc:name "The Allele Frequency Net Database (AFND)" ; sc:url "http://www.allelefrequencies.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description """Another Gff Analysis Toolkit (AGAT) Suite of tools to handle gene annotations in any GTF/GFF format.""" ; sc:featureList edam:operation_0362, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AGAT" ; sc:softwareHelp ; sc:softwareVersion "v0.1.0" ; sc:url "https://github.com/NBISweden/AGAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0621, edam:topic_0736, edam:topic_3912 ; sc:citation , "pubmed:31741225" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_3096 ; sc:name "AGONOTES" ; sc:url "http://i.uestc.edu.cn/agonotes/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3399, edam:topic_3697 ; sc:citation , "pmcid:PMC6727555", "pubmed:31488068" ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "AGS ACN" ; sc:url "https://github.com/pereiramemo/AGS-and-ACN-tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC6533287", "pubmed:31123286" ; sc:description "Anti-Inflamamtory Compounds Database for drug discovery." ; sc:featureList edam:operation_2939, edam:operation_3431, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "AICD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://956023.ichengyun.net/AICD/index.php" ; biotools:primaryContact "Biaoyan Du", "Jiangyong Gu", "Zaoyuan Kuang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6886511", "pubmed:31694868" ; sc: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""" ; sc:featureList edam:operation_0264, edam:operation_0524, edam:operation_3800 ; sc:name "AIDE" ; sc:url "https://github.com/Vivianstats/AIDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3173, edam:topic_3474 ; sc:citation , "pmcid:PMC6781298", "pubmed:31590652" ; sc: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)""" ; sc:featureList edam:operation_0417, edam:operation_0438, edam:operation_3443 ; sc:name "AIKYATAN" ; sc:url "https://bitbucket.org/cellsandmachines/aikyatan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3474, edam:topic_3676 ; sc:citation , "pubmed:31141141" ; sc:description "Assessing concordance among human, in silico predictions and functional assays on genetic variant classification." ; sc:featureList edam:operation_3225, edam:operation_3431, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AIVAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TopGene/AIvar" ; biotools:primaryContact "Jianfeng Sang", "Jiaqi Luo", "Yujian Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:31112088" ; sc:description "Interactive calculator for Artificial Intelligence (AI) Thyroid Imaging Reporting and Data System (TI-RADS)." ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "AI TI-RADS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://deckard.duhs.duke.edu/~ai-ti-rads" ; biotools:primaryContact "Mateusz Buda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_3168 ; sc:citation , "pubmed:31689201" ; sc:description "Jointly integrating VCF-based variants and OWL-based biomedical ontologies in MongoDB." ; sc:featureList edam:operation_3227 ; sc:name "AJIA" ; sc:url "https://github.com/lyotvincent/AJIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC6948815", "pubmed:31877126" ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3557 ; sc:name "ALACD" ; sc:url "https://github.com/wangyc82/ALACD-v1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3271 ; sc:name "Gene tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0194, edam:topic_3944 ; sc:citation , "pmcid:PMC5664098", "pubmed:28961181" ; sc:description "Rapid detection of candidate horizontal gene transfers across the tree of life." ; sc:featureList edam:operation_2403, edam:operation_2451 ; sc:isAccessibleForFree true ; sc:name "ALIENNESS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://alienness.sophia.inra.fr/cgi/index.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC6686235", "pubmed:31391091" ; sc: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" ; sc:featureList edam:operation_3501 ; sc:name "ALOHA" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31391091" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3474 ; sc:citation , "pmcid:PMC6612814", "pubmed:31510706" ; sc: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-" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3891 ; sc:name "ALS" ; sc:url "https://github.com/byin-cwi/ALS-Deeplearning" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3421, edam:topic_3452 ; sc:citation , "pubmed:31435950" ; sc: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" ; sc:name "ALTIS" ; sc:url "http://lids.ic.unicamp.br/downloads" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6491633", "pubmed:31068967" ; sc:description "Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis." ; sc:featureList edam:operation_3677, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AMDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/xyz5074/AMDA" ; biotools:primaryContact "Xiang Zhan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3068, edam:topic_3676 ; sc:citation ; sc:description "A web application for automatic mendelian literature evaluation." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3226 ; sc:name "AMELIE" ; sc:url "http://AMELIE.stanford.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_2330 ; sc:name "Trajectory data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , "pmcid:PMC8545331", "pubmed:33821950" ; sc: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.""" ; sc:featureList edam:operation_2426, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "AMICI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AMICI-dev/AMICI" ; biotools:primaryContact , "Fabian Fröhlich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3366, edam:topic_3572, edam:topic_3697 ; sc:citation , "pmcid:PMC6883642", "pubmed:31779604" ; sc: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""" ; sc:featureList edam:operation_2436, edam:operation_3083, edam:operation_3803 ; sc:license "MIT" ; sc:name "AMON" ; sc:url "https://github.com/lozuponelab/AMON" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3324, edam:topic_3572 ; sc:author ; sc:citation ; sc:contributor ; sc:description "An R Package for Working with Antimicrobial Resistance Data." ; sc:featureList edam:operation_3482 ; sc:license "GPL-2.0" ; sc:name "AMR" ; sc:url "https://msberends.github.io/AMR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0749, edam:topic_2828 ; sc:citation , "pmcid:PMC6688666", "pubmed:31397323" ; sc: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" ; sc:featureList edam:operation_3552 ; sc:name "AMi" ; sc:url "https://doi.org/10.1107/S2053230X19009853" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3304, edam:topic_3474 ; sc:citation , "pubmed:31103790" ; sc:description "Attentive neural cell instance segmentation." ; sc:featureList edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ANCIS-Pytorch" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/yijingru/ANCIS-Pytorch" ; biotools:primaryContact "Daniel J. Hoeppner", "Dimitris N. Metaxas", "Jingru Yi", "Menglin Jiang", "Pengxiang Wu", "Qiaoying Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0736, edam:topic_3306 ; sc:citation , "pmcid:PMC6547486", "pubmed:31159742" ; sc:description "Atomic angle- and distance-dependent statistical potential for protein structure quality assessment." ; sc:featureList edam:operation_0249, edam:operation_0321, edam:operation_0476 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ANDIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://qbp.hzau.edu.cn/ANDIS/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_2330 ; sc:name "Evidence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_2332 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Ontology", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0085, edam:topic_0089, edam:topic_0194, edam:topic_0219, edam:topic_2229, edam:topic_3064, edam:topic_3065, edam:topic_3308, edam:topic_3383, edam:topic_3679 ; sc:citation , , , , ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0292, edam:operation_0336, edam:operation_0362, edam:operation_0567, edam:operation_2478, edam:operation_2495, edam:operation_3208, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ANISEED" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:softwareVersion "2019" ; sc:url "https://www.aniseed.fr" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC6694624", "pubmed:31412762" ; sc: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" ; sc:featureList edam:operation_3501 ; sc:name "ANMF" ; sc:url "https://github.com/MortySn/ANMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3474 ; sc:citation , "pmcid:PMC6505829", "pubmed:31067238" ; sc:description "Flux prediction using artificial neural network (ANN) for the upper part of glycolysis." ; sc:featureList edam:operation_3435, edam:operation_3439, edam:operation_3715 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ANN-Glycolysis-Flux-Prediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DSIMB/ANN-Glycolysis-Flux-Prediction" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching." ; sc:featureList edam:operation_3627, edam:operation_3755, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ANN-SoLo" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/bittremieux/ANN-SoLo" ; biotools:primaryContact "Wout Bittremieux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3174 ; sc:citation , "pmcid:PMC7299298", "pubmed:30649171" ; sc:description "Analysis and Performance Assessment of Label-free Proteome Quantification." ; sc:featureList edam:operation_3634, edam:operation_3638, edam:operation_3639 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ANPELA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://idrblab.cn/anpela/" ; biotools:primaryContact "Feng Zhu", "Jianbo Fu", "Jing Tang", "Yunxia Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "AOE (All Of gene Expression) - an integrated index for public gene expression databases." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AOE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://aoe.dbcls.jp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3343 ; sc:citation , "pmcid:PMC6791490", "pubmed:31487205" ; sc: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" ; sc:name "AOP" ; sc:url "https://aopwiki.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3314 ; sc:citation , "pubmed:31453632" ; sc: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" ; sc:featureList edam:operation_3216 ; sc:name "AOPERA" ; sc:url "https://igbb.github.io/AOPERA_HTML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC6759716", "pubmed:31620433" ; sc: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)""" ; sc:featureList edam:operation_0267, edam:operation_0335, edam:operation_0418 ; sc:name "AOPs-SVM" ; sc:url "http://server.malab.cn/AOPs-SVM/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3382 ; sc:citation , "pubmed:31684366" ; sc:description "A Python package for adaptive optics modelling and analysis." ; sc:featureList edam:operation_3443 ; sc:license "LGPL-3.0" ; sc:name "AOtools" ; sc:url "https://github.com/AOtools/aotools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31247716" ; sc:description "Proteotypic peptide prediction tool by taking the peptide digestibility into consideration." ; sc:featureList edam:operation_0252, edam:operation_0418, edam:operation_2929 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AP3" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://fugroup.amss.ac.cn/software/AP3/AP3.html" ; biotools:primaryContact "Cheng Chang", "Zhiqiang Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6943053", "pubmed:31586392" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_3196 ; sc:name "APAatlas" ; sc:url "https://hanlab.uth.edu/apa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3173 ; sc:citation ; sc:description "APEC (Accessibility Pattern based Epigenomic Clustering) - single cell epigenomic clustering based on accessibility pattern." ; sc:featureList edam:operation_3192, edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "APEC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/QuKunLab/APEC" ; biotools:primaryContact "Bin Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3416, edam:topic_3489 ; sc:citation , "pmcid:PMC6822468", "pubmed:31666054" ; sc: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." ; sc:name "APHIRM toolkit" ; sc:url "http://www.aphirm.org.au" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:31609085" ; sc: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""" ; sc:featureList edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "APIS" ; sc:url "https://cran.r-project.org/package=APIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3500 ; sc:citation , "pubmed:27153658" ; sc:description "APproximate PArallel and stochastic GrAph querying TOol for biological networks." ; sc:featureList edam:operation_0224, edam:operation_0495 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APPAGATO" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://profs.scienze.univr.it/~bombieri/APPAGATO/" ; biotools:primaryContact "Federico Busato", "Nicola Bombieri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2229, edam:topic_2640, edam:topic_3168 ; sc:citation ; sc: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/""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3501 ; sc:name "APSiC" ; sc:url "https://apsic.shinyapps.io/APSiC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2429, edam:operation_3192, edam:operation_3799 ; sc:name "AQRNA-seq" ; sc:url "https://github.com/dedonlab/aqrnaseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602 ; sc:citation , "pubmed:28334160" ; sc:description "Tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein." ; sc:featureList edam:operation_0387, edam:operation_2950, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:name "AQUA-DUCT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://www.aquaduct.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3332, edam:topic_3489 ; sc:citation , "pubmed:31603259" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_2476 ; sc:name "AQUA-MER" ; sc:url "https://aquamer.ornl.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0749, edam:topic_3534 ; sc:citation , "pmcid:PMC6718341", "pubmed:31141211" ; sc:description "Active and Regulatory site Prediction (AR‐Pred) to identify protein regulatory and functional binding sites." ; sc:featureList edam:operation_2464, edam:operation_3896, edam:operation_3903 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "AR-Pred" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/sambitmishra0628/AR-PRED_source" ; biotools:primaryContact "Sambit Mishra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6778075", "pubmed:31586139" ; sc: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""" ; sc:featureList edam:operation_3283, edam:operation_3443, edam:operation_3553 ; sc:license "MIT" ; sc:name "ARA" ; sc:url "https://github.com/animgoeth/ARA-CNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3575, edam:topic_3673 ; sc:citation ; sc: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)" ; sc:featureList edam:operation_3196, edam:operation_3431, edam:operation_3482 ; sc:name "ARDaP" ; sc:url "http://github.com/dsarov/ARDaP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3174 ; sc:citation , "pubmed:31054477" ; sc:description "Antibiotic Resistance Gene Analyzer." ; sc:featureList edam:operation_0308, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ARGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mem.rcees.ac.cn:8083/" ; biotools:primaryContact "Ye Deng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3855 ; sc:citation , "pmcid:PMC6643886", "pubmed:31088905" ; sc:description "ARMOR (Automated Reproducible MOdular RNA-seq) Workflow for Preprocessing and Differential Analysis of RNA-seq Data." ; sc:featureList edam:operation_2428, edam:operation_3192, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ARMOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/csoneson/ARMOR" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2269, edam:topic_3318, edam:topic_3421 ; sc:citation , "pmcid:PMC6868867", "pubmed:31752856" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3659 ; sc:name "ASA-PS" ; sc:url "https://s-spire-clintools.shinyapps.io/ASA_PS_Estimator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_3305, edam:topic_3390, edam:topic_3474 ; sc:citation , "pmcid:PMC6950225", "pubmed:31847188" ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_3359, edam:operation_3891 ; sc:name "ASA24" ; sc:url "https://epi.grants.cancer.gov/asa24/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_2545, edam:format_2546, edam:format_2572, edam:format_3590 ; sc:name "DNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3301 ; sc:author ; sc:citation ; sc:description "ASA³P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates." ; sc:featureList edam:operation_0323, edam:operation_0362, edam:operation_0524, edam:operation_3216, edam:operation_3460, edam:operation_3461, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ASA3P" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.3.0" ; sc:url "https://github.com/oschwengers/asap" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3419, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC6890833", "pubmed:31827430" ; sc:description """A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data. This repository contains the implementation of ASD-DiagNet algorithm""" ; sc:featureList edam:operation_3359, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "ASD-DiagNet" ; sc:url "https://github.com/pcdslab/ASD-DiagNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_1317, edam:topic_2640, edam:topic_3360, edam:topic_3382, edam:topic_3400, edam:topic_3500 ; sc:citation , , "pmcid:PMC6917801", "pmcid:PMC9525007", "pubmed:31848351", "pubmed:35972352" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ASHLAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://labsyspharm.github.io/ashlar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6709372", "pubmed:31462970" ; sc: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" ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_3800 ; sc:name "ASJA" ; sc:url "https://github.com/HuangLab-Fudan/ASJA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_0623, edam:topic_0637, edam:topic_3300 ; sc:citation ; sc: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:""" ; sc:featureList edam:operation_0291, edam:operation_3644 ; sc:name "ASM-Clust" ; sc:url "https://github.com/dspeth/ASM_clust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0610, edam:topic_3500 ; sc:citation , "pmcid:PMC6488576", "pubmed:31036810" ; sc:description "Animal Social Networks Repository - repository of interaction data from published studies of wild, captive, and domesticated animals." ; sc:featureList edam:operation_3562, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ASNR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bansallab.github.io/asnr/" ; biotools:primaryContact "Shweta Bansal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_0780, edam:topic_3168, edam:topic_3512 ; sc:citation , "pubmed:31843802" ; sc:description "An online database for exploring over 2,000 Arabidopsis small RNA libraries." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3435 ; sc:name "ASRD" ; sc:url "http://ipf.sustech.edu.cn/pub/asrd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0820, edam:topic_3324, edam:topic_3384 ; sc:citation , "pubmed:31609612" ; sc: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""" ; sc:name "ATBdiscrimination" ; sc:url "http://lishuyan.lzu.edu.cn/ATB/ATBdiscrimination.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0209, edam:topic_3474 ; sc:citation , "pmcid:PMC6739564", "pubmed:31543820" ; sc: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\"" ; sc:featureList edam:operation_3502 ; sc:license "GPL-3.0" ; sc:name "ATC-NLSP" ; sc:url "https://github.com/dqwei-lab/ATC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:31368481" ; sc: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.." ; sc:featureList edam:operation_0277, edam:operation_3439, edam:operation_3562 ; sc:license "GPL-2.0" ; sc:name "ATEN" ; sc:url "https://github.com/ningshi/ATEN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3421, edam:topic_3474 ; sc:citation , "pubmed:31468306" ; sc: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" ; sc:name "AUPA" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31468306" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3517, edam:topic_3810 ; sc:citation , "pmcid:PMC6444607", "pubmed:30940067" ; sc:description "Automatic adaptive LASSO for genome-wide prediction." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "AUTALASSO" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/patwa67/AUTALASSO" ; biotools:primaryContact "Patrik Waldmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0218, edam:topic_3474 ; sc:citation , "pmcid:PMC7301356", "pubmed:31467448" ; sc: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" ; sc:featureList edam:operation_2422, edam:operation_3227, edam:operation_3431 ; sc:name "AVADA" ; sc:url "http://bejerano.stanford.edu/AVADA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC6767648", "pubmed:31564248" ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3501 ; sc:name "AVA,Dx" ; sc:url "https://bromberglab.org/project/avadx/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_2830 ; sc:citation , "pmcid:PMC6728052", "pubmed:31442220" ; sc:description "An web application that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains." ; sc:featureList edam:operation_3202, edam:operation_3216 ; sc:name "AbLIFT" ; sc:url "http://AbLIFT.weizmann.ac.il" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602 ; sc:citation , "pubmed:27663497" ; sc: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." ; sc:featureList edam:operation_0362, edam:operation_2495, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AcCNET" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/valflanza/accnet" ; biotools:primaryContact "Val F. Lanza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0798, edam:topic_3474, edam:topic_3810 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0253, edam:operation_3092, edam:operation_3096 ; sc:name "AcRanker" ; sc:url "https://github.com/amina01/AcRanker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0632, edam:topic_0821, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC6908459", "pubmed:31832668" ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3460 ; sc:name "AcetoBase" ; sc:url "https://acetobase.molbio.slu.se" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_2640, edam:topic_3175 ; sc:citation , "pmcid:PMC3564258", "pubmed:23340843" ; sc: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." ; sc:featureList edam:operation_2415, edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ActiveDriver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0.0" ; sc:url "http://reimandlab.org/software/activedriver/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3315 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3478, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "AdTree" ; sc:url "https://github.com/tudelft3d/adtree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "An R package for data Adaptive Robust Estimation in Linear Regression with Application in GTEx Gene Expressions." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "AdaReg" ; sc:url "https://github.com/mwgrassgreen/AdaReg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3407 ; sc:citation , "pubmed:31648087" ; sc: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""" ; sc:featureList edam:operation_2421 ; sc:name "AdditiveChem" ; sc:url "http://www.rxnfinder.org/additivechem/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:citation , "pmcid:PMC6710032", "pubmed:31450236" ; sc: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" ; sc:name "AdequacyModel" ; sc:url "https://github.com/prdm0/AdequacyModel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation , "pubmed:30875428" ; sc:description "R-based tool to support topic discovery for systematic and literature reviews." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Adjutant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/amcrisan/Adjutant" ; biotools:primaryContact "Anamaria Crisan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3304 ; sc: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." ; sc:name "Adult Fruitfly Brain Atlas" ; sc:url "https://fruitfly.tefor.net/#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6891986", "pubmed:31801606" ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3472, edam:operation_3659 ; sc:name "Afann" ; sc:url "https://github.com/GeniusTang/Afann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3305 ; sc:citation , "pmcid:PMC6529631", "pubmed:31113894" ; sc:description "framework for the analysis of Aspergillus fumigatus isolates based on their microsatellite profile." ; sc:featureList edam:operation_3196, edam:operation_3797 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AfumID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://afumid.shinyapps.io/afumID" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3292, edam:topic_3315, edam:topic_3368 ; sc:citation , "pubmed:31599925" ; sc: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""" ; sc:featureList edam:operation_0331, edam:operation_2426, edam:operation_3436, edam:operation_3659 ; sc:name "AggreRATE-Pred" ; sc:url "http://www.iitm.ac.in/bioinfo/aggrerate-pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0130, edam:topic_0199 ; sc:citation , "pubmed:30825368" ; sc:description "Package for structure-based prediction of protein aggregation properties and rational design of protein solubility." ; sc:featureList edam:operation_0244, edam:operation_0409, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Aggrescan3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://biocomp.chem.uw.edu.pl/A3D/" ; biotools:primaryContact "Michal Jamroz", "Rafael Zambran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3810 ; sc:description "The RDF Knowledge-based Database for plant molecular networks." ; sc:name "AgroLD" ; sc:url "http://agrold.southgreen.fr/agrold/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3810 ; sc:description "Browser for ontologies for agricultural science based on NBCO BioPortal." ; sc:name "AgroPortal" ; sc:url "http://agroportal.lirmm.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6437997", "pubmed:30917859" ; sc:description "Tool introducing a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data." ; sc:featureList edam:operation_2495, edam:operation_3200, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Alevin" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://salmon.readthedocs.io/en/latest/alevin.html#references" ; biotools:primaryContact "A. Srivastava", "Rob Patro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0622, edam:topic_3293, edam:topic_3500 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3182, edam:operation_3198, edam:operation_3209 ; sc:license "MIT" ; sc:name "AliTV" ; sc:url "https://github.com/AliTVTeam/AliTV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3360 ; sc:citation , , "pmcid:PMC7141867", "pubmed:31750888" ; sc:description "Allele-Frequency-based Imputation of Tumor Purity from High-Depth Sequencing Data." ; sc:featureList edam:operation_3227, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "All-FIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KhiabanianLab/All-FIT" ; biotools:primaryContact "Khiabanian Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3421, edam:topic_3912 ; sc:citation , "pmcid:PMC6694686", "pubmed:31416467" ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_3096, edam:operation_3197 ; sc:license "MIT" ; sc:name "AlleleAnalyzer" ; sc:url "https://github.com/keoughkath/AlleleAnalyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC6602569", "pubmed:31069394" ; sc:description "Method for the identification and analysis of cancer driver targets." ; sc:featureList edam:operation_0331, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AlloDriver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mdl.shsmu.edu.cn/ALD" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0654, edam:topic_0780, edam:topic_3295 ; sc:citation , "pmcid:PMC7539454", "pubmed:33023650" ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3204, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "AlphaBeta" ; sc:url "http://bioconductor.org/packages/3.10/bioc/html/AlphaBeta.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pmcid:PMC7520044", "pubmed:32467963" ; sc: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." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3454, edam:operation_3557 ; sc:name "AlphaFamImpute" ; sc:url "http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31634848" ; sc:description "A method for sequence discovery with deep reinforcement learning." ; sc:featureList edam:operation_3695 ; sc:name "AlphaSeq" ; sc:url "https://github.com/lynshao/AlphaSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3673 ; sc:citation , "pmcid:PMC6639938", "pubmed:31360240" ; sc: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)" ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "AluMine" ; sc:provider ; sc:url "https://github.com/bioinfo-ut/AluMine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6411622", "pubmed:30906832" ; sc:description "R package for copy number variation calling and cancer risk prediction with next-generation sequencing data." ; sc:isAccessibleForFree true ; sc:name "AluScanCNV2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hutaobo/AluScanCNV2" ; biotools:primaryContact "Taobo Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3050, edam:topic_3301 ; sc:citation , "pmcid:PMC6460834", "pubmed:30910089" ; sc:description "Text mining tool for extracting information about microbial biodiversity in food." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AlvisIR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Bibliome/alvisir" ; biotools:primaryContact "Robert Bossy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3365, edam:topic_3489 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "Alyx" ; sc:softwareHelp ; sc:url "https://github.com/cortex-lab/alyx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3342 ; sc:citation , "pmcid:PMC6679440", "pubmed:31375105" ; sc: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" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3227 ; sc:name "AmpliSolve" ; sc:url "https://github.com/dkleftogi/AmpliSolve" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3168, edam:topic_3174, edam:topic_3316 ; sc:citation , "pmcid:PMC6901069", "pubmed:31816087" ; sc: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""" ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3460 ; sc:name "AmpliconTagger" ; sc:url "http://jtremblay.github.io/amplicontagger.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:citation , "pmcid:PMC6324066", "pubmed:30247677" ; sc: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)." ; sc:featureList edam:operation_0226 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "AmtDB" ; sc:operatingSystem "Linux" ; sc:provider "Institute of Molecular Genetics AS CR" ; sc:softwareHelp ; sc:softwareVersion "v1.007" ; sc:url "https://amtdb.org" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3337, edam:topic_3407 ; sc:citation , "pubmed:31094220" ; sc:description "Collection of amyloidoses and other clinical disorders related to amyloid deposition." ; sc:featureList edam:operation_3431, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AmyCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.biol.uoa.gr/amyco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3068, edam:topic_3489 ; sc:citation , "pmcid:PMC6790968", "pubmed:31608948" ; sc:description "A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_3778 ; sc:license "MIT" ; sc:name "Anabel" ; sc:url "https://skscience.org/anabel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0780, edam:topic_3452 ; sc:citation , "pmcid:PMC6395764", "pubmed:30816109" ; sc:description "Software package for quantitative analysis of plant ER architecture and dynamics." ; sc:featureList edam:operation_3216, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "AnalyzER" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1" ; sc:url "https://markfricker.org/77-2/software/er-network-analysis/" ; biotools:primaryContact "Dr M.D. Fricker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation , "pmcid:PMC6360811", "pubmed:30567711" ; sc:description "Package for trans-cell type prediction of transcription factor binding sites." ; sc:featureList edam:operation_0417, edam:operation_0445, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "Anchor" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GuanLab/Anchor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305 ; sc:citation , "pmcid:PMC6929553", "pubmed:31106350" ; sc: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." ; sc:featureList edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Anchored Multiplier Calculator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://anchoredmultiplier.ucsf.edu/" ; biotools:primaryContact "Paul D. Wesson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3673 ; sc:citation , "pmcid:PMC6580570", "pubmed:31208319" ; sc:description "Web-based exploration of numerical chromosomal variation in single cells." ; sc:featureList edam:operation_1812, edam:operation_3233, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Aneuvis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dpique.shinyapps.io/aneuvis/" ; biotools:primaryContact "Daniel Pique" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3500, edam:topic_3518, edam:topic_3673 ; sc:citation , "pmcid:PMC6943029", "pubmed:31584087" ; sc:description "A comprehensive database with multiple animal reference panels for genotype imputation." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3557, edam:operation_3661 ; sc:name "Animal-ImputeDB" ; sc:url "http://gong_lab.hzau.edu.cn/Animal_ImputeDB" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_3867 ; sc:name "Trajectory data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3892 ; sc:citation , "pmcid:PMC6482212", "pubmed:31058167" ; sc: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." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Anncolvar" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "v0.2", "v0.3", "v0.4", "v0.5", "v0.6" ; sc:url "https://github.com/spiwokv/anncolvar" ; biotools:primaryContact "Vojtech Spiwok" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0821 ; sc:citation , "pmcid:PMC6511854", "pubmed:31081040" ; sc:description "Interactive, functionally annotated bacterial tree of life that integrates taxonomic, phylogenetic and functional annotation data." ; sc:featureList edam:operation_0558, edam:operation_0567, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "AnnoTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://annotree.uwaterloo.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0203, edam:topic_0219, edam:topic_3518 ; sc:citation , "pmcid:PMC6824123", "pubmed:31675914" ; sc: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""" ; sc:featureList edam:operation_0361, edam:operation_0558, edam:operation_2422, edam:operation_3553 ; sc:name "Annot" ; sc:softwareHelp , ; sc:url "https://gitlab.com/biotransistor/annot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_3053, edam:topic_3168, edam:topic_3175 ; sc:citation , , "pmcid:PMC8262758", "pubmed:29669011", "pubmed:34023905" ; sc:description "Integrated tool for annotation and ranking of structural variations." ; sc:featureList edam:operation_0226, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AnnotSV" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://lbgi.fr/AnnotSV/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3315, edam:topic_3474 ; sc:citation "pubmed:31797628" ; sc:description """Generative Adversarial Networks for Anonymizing Private Medical Data. Scikit-learn library package (version 0.18). Keras library package (version 2.0.6)""" ; sc:featureList edam:operation_3283 ; sc:name "AnomiGAN" ; sc:url "https://github.com/hobae/AnomiGAN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_3168 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0308, edam:operation_0309, edam:operation_0335 ; sc:name "AnthOligo" ; sc:url "http://antholigo.chop.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_0821, edam:topic_3303 ; sc:citation , "pubmed:31661960" ; sc: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""" ; sc:featureList edam:operation_0417, edam:operation_3860 ; sc:name "AntiBac-Pred" ; sc:url "http://www.way2drug.com/antibac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3336 ; sc:citation , "pmcid:PMC7523681", "pubmed:31418763" ; sc: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" ; sc:name "AntiHIV-Pred" ; sc:url "http://www.way2drug.com/hiv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0623, edam:topic_0749 ; sc:citation , "pmcid:PMC6748703", "pubmed:31529106" ; sc: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" ; sc:featureList edam:operation_2492 ; sc:name "ApicoTFdb" ; sc:url "http://bioinfo.icgeb.res.in/PtDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_2830, edam:topic_3297 ; sc:citation , "pmcid:PMC6602511", "pubmed:31069385" ; sc:description "Web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models." ; sc:featureList edam:operation_0272, edam:operation_0394, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AppA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mspc.bii.a-star.edu.sg/minhn/appa.html" ; biotools:primaryContact "Chandra S Verma", "Minh N Nguyen", "Pingyu Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3169, edam:topic_3170, edam:topic_3173 ; sc:citation , "pmcid:PMC6817610", "pubmed:31695717" ; sc: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""" ; sc:featureList edam:operation_2436, edam:operation_3439, edam:operation_3672 ; sc:name "AppleMDO" ; sc:url "http://bioinformatics.cau.edu.cn/AppleMDO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3673 ; sc:citation ; sc: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\")" ; sc:featureList edam:operation_0487, edam:operation_0525, edam:operation_3227 ; sc:name "Aquila_stLFR" ; sc:url "https://github.com/maiziex/Aquila_stLFR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_3557 ; sc:citation , "pmcid:PMC6446796", "pubmed:30679268" ; sc:description "Proteome-wide structure-based prediction of protein-protein interactions in Arabidopsis." ; sc:featureList edam:operation_0478, edam:operation_2497, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "Arabidopsis Interactions Viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bar.utoronto.ca/interactions2/" ; biotools:primaryContact "Nicholas Provart" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931, edam:format_2572, edam:format_2573, edam:format_3462 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3320, edam:topic_3512 ; sc: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." ; sc:featureList edam:operation_3199, edam:operation_3228 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Arriba" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/suhrig/arriba/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3673, edam:topic_3676 ; sc:citation , , "pmcid:PMC7677819", "pubmed:33208101" ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_3182 ; sc:name "ArrowSAM" ; sc:url "https://github.com/abs-tudelft/ArrowSAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3068, edam:topic_3673 ; sc:citation , "pmcid:PMC6905352", "pubmed:31825479" ; sc: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""" ; sc:featureList edam:operation_1812, edam:operation_3431, edam:operation_3436 ; sc:license "MIT" ; sc:name "Arteria" ; sc:url "https://arteria-project.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31373612" ; sc: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" ; sc:name "ArtiFuse" ; sc:url "https://github.com/TRON-Bioinformatics/ArtiFusion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780 ; sc:citation , "pubmed:27007138" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AsANet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "http://cab.unina.it/asanet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3399, edam:topic_3577 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3096, edam:operation_3431 ; sc:name "AsCRISPR" ; sc:url "http://www.genemed.tech/ascrispr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0780, edam:topic_3172 ; sc:citation , "pmcid:PMC6852159", "pubmed:31111606" ; sc:description "Whole-genome annotation and functional analyses based on RNA expression data." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AspWood" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://aspwood.popgenie.org/aspwood-v3.0/" ; biotools:primaryContact "Ewa Mellerowicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation , "pmcid:PMC6191160", "pubmed:27318204" ; sc:description "Web analytics tool for the detection of variants from an assembly." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Assemblytics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://assemblytics.com/" ; biotools:primaryContact "Maria Nattestad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pmcid:PMC7998711", "pubmed:31532487" ; sc: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" ; sc:featureList edam:operation_2454 ; sc:license "GPL-3.0" ; sc:name "AssessORF" ; sc:url "http://www.bioconductor.org/packages/release/bioc/html/AssessORF.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_3512 ; sc:citation , "pmcid:PMC6732846", "pubmed:31523128" ; sc: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" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3644 ; sc:name "Assexon" ; sc:url "https://github.com/yhadevol/Assexon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0634, edam:topic_3512 ; sc:citation , "pubmed:32079659" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3629 ; sc:name "AstroDot" ; sc:url "https://doi.org/10.1242/jcs.239756" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3591 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2333 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3474 ; sc:citation , "pmcid:PMC6858541", "pubmed:31570865" ; sc:description "An event-based tool for analyzing and quantifying calcium or glutamate imaging data." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Astrocyte Quantification and Analysis (AQuA)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yu-lab-vt/aqua" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_1775, edam:topic_3168 ; sc:citation , "pubmed:31562099" ; sc: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" ; sc:featureList edam:operation_1777 ; sc:name "AsyRW" ; sc:url "http://mlda.swu.edu.cn/codes.php?name=AsyRW" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6323297", "pubmed:30624648" ; sc:description "Database of fusion transcripts in Arabidopsis thaliana." ; sc:featureList edam:operation_0224, edam:operation_0495, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:name "AtFusionDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nipgr.ac.in/AtFusionDB/" ; biotools:primaryContact "Dr. Shailesh Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3169, edam:topic_3173, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0438, edam:operation_3222, edam:operation_3436 ; sc:name "AtacWorks" ; sc:url "https://github.com/clara-genomics/AtacWorks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3297, edam:topic_3300, edam:topic_3697 ; sc:citation , "pubmed:31535335" ; sc: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" ; sc:featureList edam:operation_0337 ; sc:name "Atacama Database" ; sc:url "https://www.atacamadb.cl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2269, edam:topic_2830 ; sc:citation , "pmcid:PMC6658830", "pubmed:31372196" ; sc: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" ; sc:name "AtbPpred" ; sc:url "http://thegleelab.org/AtbPpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC5581536", "pubmed:28875074" ; sc: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:""" ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3219, edam:operation_3472 ; sc:name "Atropos" ; sc:url "https://github.com/jdidion/atropos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC7610525", "pubmed:32690972" ; sc: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""" ; sc:featureList edam:operation_2428, edam:operation_3450, edam:operation_3799 ; sc:license "MIT" ; sc:name "Augur" ; sc:url "https://github.com/neurorestore/Augur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2830, edam:topic_3314 ; sc:citation , "pubmed:31545316" ; sc: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" ; sc:license "MIT" ; sc:name "Auto-CHO" ; sc:url "https://sites.google.com/view/auto-cho/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC6923820", "pubmed:31856727" ; sc:description "Integrate multi-omics data with biological interaction networks using Multi-view Factorization AutoEncoder (MAE)." ; sc:featureList edam:operation_2492, edam:operation_3439, edam:operation_3659 ; sc:license "MIT" ; sc:name "AutoEncoder" ; sc:url "https://github.com/BeautyOfWeb/Multiview-AutoEncoder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_2275 ; sc:citation , "pubmed:31436329" ; sc: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" ; sc:featureList edam:operation_0482, edam:operation_3216, edam:operation_3899 ; sc:name "AutoGridFR" ; sc:url "http://adfr.scripps.edu/AutoDockFR/agfr.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3168, edam:topic_3320 ; sc:citation , "pubmed:32442321" ; sc: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)" ; sc:featureList edam:operation_3225 ; sc:name "AutoPVS1" ; sc:url "http://autopvs1.genetics.bgi.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC7310949", "pubmed:32212641" ; sc:description "Autotuner is a used to identify proper parameters during metabolomics data processing." ; sc:featureList edam:operation_3215 ; sc:license "MIT" ; sc:name "AutoTuner" ; sc:url "https://github.com/crmclean/Autotuner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3361, edam:topic_3678 ; sc:citation ; sc: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." ; sc:license "MPL-2.0" ; sc:name "Autopilot" ; sc:url "https://github.com/wehr-lab/autopilot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3518, edam:topic_3810 ; sc:citation , "pmcid:PMC6498479", "pubmed:31046664" ; sc: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." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Axiom Analysis Suite" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://www.thermofisher.com/dk/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/axiom-analysis-suite.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3474 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "B-SOiD" ; sc:url "https://github.com/YttriLab/B-SOiD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3382, edam:topic_3855 ; sc:citation , "pubmed:31554957" ; sc: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" ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "BACMMAN" ; sc:softwareHelp ; sc:url "https://github.com/jeanollion/bacmman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3170, edam:topic_3517 ; sc:citation , "pmcid:PMC7523653", "pubmed:31702789" ; sc: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""" ; sc:featureList edam:operation_2436, edam:operation_3658, edam:operation_3659, edam:operation_3799 ; sc:name "BAGSE" ; sc:url "https://github.com/xqwen/bagse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3518 ; sc:citation , "pubmed:27153667" ; sc:description "Tool that determines if two BAM files came from the same sample or patient by comparing common SNP positions." ; sc:featureList edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "BAM-matcher" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/sacgf/bam-matcher/src/master/" ; biotools:primaryContact "Paul P.S. Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6456731", "pubmed:30967541" ; sc:description "Bayesian mixture model for single-cell sequencing (BAMM-SC) method for clustering droplet-based single cell transcriptomic data from population studies." ; sc:featureList edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "BAMM-SC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/lichen-lab/BAMMSC" ; biotools:primaryContact "Li Chen", "Zhe Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6853765", "pubmed:31197312" ; sc:description "Automated checkup tool for matched sample pairs in NGS cohort." ; sc:featureList edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "BAMixChecker" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/heinc1010/BAMixChecker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation , "pmcid:PMC7075019", "pubmed:32178699" ; sc: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" ; sc:featureList edam:operation_0264, edam:operation_3223, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "BANDITS" ; sc:url "https://bioconductor.org/packages/BANDITS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6683345", "pubmed:31387612" ; sc: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" ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3200 ; sc:license "GPL-3.0" ; sc:name "BART-Seq" ; sc:url "https://github.com/theislab/bartSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0593, edam:topic_3538 ; sc:citation , "pmcid:PMC6290515", "pubmed:30537929" ; sc:description "Tool for high-throughput analysis of intrinsic disorder patterns in homologous proteins." ; sc:featureList edam:operation_0250, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BASILIScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://basilisc.com/" ; biotools:primaryContact "M. Barski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC7145713", "pubmed:31665503" ; sc: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""" ; sc:featureList edam:operation_0463, edam:operation_2495, edam:operation_3435 ; sc:name "BBCancer" ; sc:url "http://bbcancer.renlab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091 ; sc:author ; sc:citation , "pubmed:29695703" ; sc:description "BCIgePred (Linear B cell IgE Epitope Predictor) is a perl based open source tool for the prediction of Linear B-cell IgE epitopes." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BCIgEPred" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/brsaran/BCIgePred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3047, edam:topic_3172, edam:topic_3343 ; sc:citation , "pubmed:31593245" ; sc: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.)""" ; sc:featureList edam:operation_3564 ; sc:name "BCSExplorer" ; sc:url "http://www.rxnfinder.org/bcsexplorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0121, edam:topic_2828 ; sc:citation , "pmcid:PMC7523644", "pubmed:31603511" ; sc: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""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0410, edam:operation_0420, edam:operation_3454 ; sc:name "BCrystal" ; sc:url "https://github.com/raghvendra5688/BCrystal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3407, edam:topic_3474 ; sc:citation ; sc:description "Prediction of Homolytic Bond Dissociation Enthalpies for Organic Molecules at near Chemical Accuracy with Sub-Second Computational Cost." ; sc:featureList edam:operation_0394, edam:operation_0417, edam:operation_3439 ; sc:name "BDE" ; sc:url "https://ml.nrel.gov/bde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3168, edam:topic_3343 ; sc:citation , "pmcid:PMC6818255", "pubmed:30635653" ; sc: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." ; sc:featureList edam:operation_3192, edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "BEAN-counter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/csbio/BEAN-counter" ; biotools:primaryContact "Myers Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3063 ; sc:citation , "pmcid:PMC6602520", "pubmed:31114876" ; sc:description "Tool for Biomedical Entity Expansion, Ranking, and Exploration." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "BEERE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://discovery.informatics.uab.edu/beere/" ; biotools:primaryContact "Jake Y Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_3855 ; sc:citation , "pmcid:PMC6301338", "pubmed:30576488" ; sc:description "Environment for exploration and analysis of networks encoded in Biological Expression Language." ; sc:featureList edam:operation_1812, edam:operation_3083, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BEL Commons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bel-commons.scai.fraunhofer.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6691531", "pubmed:31405383" ; sc: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" ; sc:featureList edam:operation_3680, edam:operation_3800 ; sc:license "MIT" ; sc:name "BERMUDA" ; sc:url "https://github.com/txWang/BERMUDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168, edam:topic_3512, edam:topic_3912 ; sc:citation , "pmcid:PMC6806563", "pubmed:31647030" ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_3096, edam:operation_3461 ; sc:license "MIT" ; sc:name "BEable-GPS" ; sc:url "http://www.picb.ac.cn/rnomics/BEable-GPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320, edam:topic_3523 ; sc:citation , "pmcid:PMC6704634", "pubmed:31438847" ; sc: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" ; sc:featureList edam:operation_3223 ; sc:name "BGSC" ; sc:url "https://github.com/GrosseLab/BGSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3125, edam:topic_3534 ; sc:citation , "pubmed:31553288" ; sc: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" ; sc:featureList edam:operation_0482, edam:operation_2575 ; sc:name "BGSVM-NUC" ; sc:url "http://202.119.84.36:3079/BGSVM-NUC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation ; sc:description "An integrated Web-database for bovine sequencing variations and selective signatures." ; sc:featureList edam:operation_0487, edam:operation_2421, edam:operation_2422, edam:operation_3196, edam:operation_3208 ; sc:name "Bovine Genome Variation Database (BGVD)" ; sc:url "http://animal.nwsuaf.edu.cn/code/index.php/BosVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation , "pubmed:30718882" ; sc:description "BItsliced Genomic Signature Index (BIGSI) searches a collection of raw (fastq/bam), contigs or assembly for genes, variant alleles and arbitrary sequence." ; sc:featureList edam:operation_3211, edam:operation_3431, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BIGSI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.bigsi.io/" ; biotools:primaryContact "Phelim Bradley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749 ; sc:citation , "pmcid:PMC6734328", "pubmed:31500560" ; sc: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'" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:license "GPL-3.0" ; sc:name "BINDER" ; sc:url "http://github.com/ptrcksn/BINDER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2269 ; sc:citation , "pmcid:PMC7999138", "pubmed:31368479" ; sc: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)" ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3227 ; sc:name "BIRD" ; sc:url "http://www.geneprediction.org/bird" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology term" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3669 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Training material" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Resource metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1731 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Ontology concept definition" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0949 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Workflow metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3063, edam:topic_3298, edam:topic_3382 ; sc:contributor , , , , , "Chong Zhang" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_3761 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "BIII (BioImage Informatics Index, biii.eu)" ; sc:provider "NEUBIAS Network of Bioimage Analysts" ; sc:softwareHelp , , , , ; sc:url "https://biii.eu" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , , "pubmed:33040404" ; sc: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" ; sc:name "BISON" ; sc:url "http://nist.mni.mcgill.ca/?p=2148" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3316 ; sc:citation , "pmcid:PMC6923898", "pubmed:31861980" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3211, edam:operation_3680 ; sc:license "LGPL-3.0" ; sc:name "BISR-RNAseq" ; sc:url "https://code.bmi.osumc.edu/gadepalli.3/BISR-RNAseq-ICIBM2019" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_3512 ; sc:citation , , "pubmed:32492257" ; sc: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" ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "BITACORA" ; sc:url "http://www.ub.edu/softevol/bitacora" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC8285086", "pubmed:31359834" ; sc: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" ; sc:featureList edam:operation_3501, edam:operation_3557, edam:operation_3659 ; sc:name "BJASS" ; sc:url "https://github.com/yiucla/BJASS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602 ; sc:citation , "pubmed:31373347" ; sc:description "Basic Local Alignment for Networks Tool." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BLANT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/waynebhayes/BLANT" ; biotools:primaryContact "Wayne B. Hayes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3517, edam:topic_3810 ; sc:citation , "pmcid:PMC6365300", "pubmed:30535326" ; sc:description "Package for the next level of genome-wide association studies." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BLINK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Menggg/BLINK" ; biotools:primaryContact "Meng Huang", "Yao Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_2885, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6819473", "pubmed:31660858" ; sc: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""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3659 ; sc:name "BLMRM" ; sc:url "https://github.com/JingXieMIZZOU/BLMRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_3306, edam:topic_3314, edam:topic_3315 ; sc:citation , , , , , "pmcid:PMC5980761", "pubmed:29486559" ; sc: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""" ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3899 ; sc:license "MIT" ; sc:name "BLUES" ; sc:url "http://github.com/MobleyLab/blues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2840, edam:topic_3315, edam:topic_3360 ; sc:citation , "pubmed:31833558" ; sc:description "Determination of benchmark concentrations and their statistical uncertainty for cytotoxicity test data and functional in vitro assays." ; sc:featureList edam:operation_3435, edam:operation_3503, edam:operation_3799 ; sc:name "BMCeasy" ; sc:softwareHelp ; sc:url "http://invitrotox.uni-konstanz.de/BMC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3173 ; sc:citation , , "pmcid:PMC7049249", "pubmed:32097025" ; sc: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:" ; sc:featureList edam:operation_0224, edam:operation_3436, edam:operation_3501 ; sc:name "BMEG" ; sc:url "http://bmeg.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2640, edam:topic_3518 ; sc:citation , "pmcid:PMC4495295", "pubmed:25755273" ; sc:description "Software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BMRF-Net" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://sourceforge.net/projects/bmrfcjava/" ; biotools:primaryContact "Jianhua Xuan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3315 ; sc:citation , "pubmed:31035759" ; sc: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." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BMSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioeng.nus.edu.sg/engbio/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3810, edam:topic_3855 ; sc:citation , "pubmed:30819822" ; sc:description "R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction." ; sc:featureList edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "BMTME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=BMTME" ; biotools:primaryContact "Francisco Javier Luna-Vazquez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3377, edam:topic_3379 ; sc:citation , "pmcid:PMC6612853", "pubmed:31510658" ; sc: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" ; sc:name "BNNR" ; sc:url "https://github.com/BioinformaticsCSU/BNNR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0602 ; sc:citation , "pmcid:PMC6323831", "pubmed:30616557" ; sc: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." ; sc:featureList edam:operation_3280, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BO-LSTM" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/lasigeBioTM/BOLSTM" ; biotools:primaryContact "BioTM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3360 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BOCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lkorshoj/Block-Optical-Content-Scoring" ; biotools:primaryContact "Lee Korshoj" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308, edam:topic_3336 ; sc:citation , "pmcid:PMC6743792", "pubmed:31479446" ; sc: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]" ; sc:featureList edam:operation_2497, edam:operation_3501, edam:operation_3562 ; sc:name "BONITA" ; sc:url "https://github.com/thakar-lab/BONITA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0084 ; sc: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." ; sc:name "BOOSTER" ; sc:url "https://booster.pasteur.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3305, edam:topic_3324 ; sc:citation , , "pmcid:PMC7363093", "pubmed:32667952" ; sc:description """BORIS: R package for Bayesian Outbreak Reconstruction Inference and Simulation. Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates.""" ; sc:featureList edam:operation_0451, edam:operation_3660 ; sc:license "GPL-2.0" ; sc:name "BORIS" ; sc:url "https://github.com/sfires/BORIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3300, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC8485846", "pubmed:33216147" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_3359, edam:operation_3659 ; sc:license "MIT" ; sc:name "Brain Predictability toolbox" ; sc:softwareHelp ; sc:url "https://github.com/sahahn/BPt" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830 ; sc:citation ; sc:description "Software for reconstruction of B cell receptors (BCR) using short, paired-end single-cell RNA-sequencing." ; sc:featureList edam:operation_0230 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "BRAPeS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YosefLab/BRAPeS" ; biotools:primaryContact "Shaked Afik" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_3475 ; sc:name "Nucleic acid report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3320 ; sc:citation , , "pmcid:PMC5488362", "pubmed:28655331", "pubmed:30758827" ; sc:description "Bayesian method for estimating splicing isoform proportions from single cell RNA-seq data." ; sc:featureList edam:operation_2499, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BRIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://brie.readthedocs.io/en/latest/index.html" ; biotools:primaryContact "Yuanhua Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0659, edam:topic_3518 ; sc:citation , "pmcid:PMC6525352", "pubmed:31101000" ; sc:description "Systems biology web tool for microRNA and omics data integration." ; sc:featureList edam:operation_0463, edam:operation_1812, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BRM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cbb.pnnl.gov/brm/" ; biotools:primaryContact , "Katrina M. Waters" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2269, edam:topic_2885 ; sc:citation , "pubmed:31742317" ; sc:description "Block Regression Mapping (BRM) is a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing." ; sc:featureList edam:operation_0282, edam:operation_0283, edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "Block Regression Mapping (BRM)" ; sc:url "https://github.com/huanglikun/BRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3316, edam:topic_3336 ; sc:citation , "pubmed:31074975" ; sc:description "HPC Generic and Customizable Software Architecture for 3D Ligand-Based Virtual Screening of Large Molecular Databases." ; sc:featureList edam:operation_0482, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "BRUSELAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bio-hpc.ucam.edu/Bruselas/" ; biotools:primaryContact "Horacio Pérez-Sánchez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC6571488", "pubmed:31141611" ; sc:description "Web-based quantitative trait locus linkage analysis and bulk segregant analysis of yeast sequencing data." ; sc:featureList edam:operation_0282, edam:operation_1812, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BSA4Yeast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bsa4yeast.lcsb.uni.lu" ; biotools:primaryContact "Zhi Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0362, edam:operation_0435, edam:operation_2422 ; sc:name "BSGatlas" ; sc:url "http://rth.dk/resources/bsgatlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3068 ; sc:citation , "pmcid:PMC6805536", "pubmed:31640567" ; sc: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""" ; sc:featureList edam:operation_2238, edam:operation_3436 ; sc:name "BUGSnet" ; sc:url "https://bugsnetsoftware.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31073610" ; sc: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" ; sc:featureList edam:operation_3200, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "BUStools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://BUStools.github.io/" ; biotools:primaryContact "Lior Pachter", "Páll Melsted", "Vasilis Ntranos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation , , "pmcid:PMC7141418", "pubmed:32240182" ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3557 ; sc:name "BWGS" ; sc:url "https://cran.r-project.org/web/packages/BWGS/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_2269, edam:topic_3172, edam:topic_3517 ; sc:citation , "pubmed:31593215" ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3658, edam:operation_3659 ; sc:name "BWMR" ; sc:url "https://github.com/jiazhao97/BWMR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "BWView" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://uazu.net/bwview/" ; biotools:primaryContact "Jim Peters" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0736, edam:topic_0798, edam:topic_3324 ; sc:citation , "pmcid:PMC7145566", "pubmed:31665505" ; sc: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""" ; sc:featureList edam:operation_0418, edam:operation_0435, edam:operation_2421 ; sc:name "BacFITBase" ; sc:url "http://www.tartaglialab.com/bacfitbase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6924045", "pubmed:31856735" ; sc: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." ; sc:featureList edam:operation_0524, edam:operation_3196, edam:operation_3258 ; sc:name "BacHBerryEXP" ; sc:url "http://www.bachberryexp.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3305, edam:topic_3673 ; sc:citation , "pmcid:PMC6501397", "pubmed:31060512" ; sc:description "Pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing." ; sc:featureList edam:operation_1812, edam:operation_3227, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BacTag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://git.lumc.nl/l.khachatryan/BacTag" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC7027861", "pubmed:31693257" ; sc: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" ; sc:name "BactMAP" ; sc:url "https://veeninglab.com/bactmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC6562250", "pubmed:31099741" ; sc: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." ; sc:featureList edam:operation_0484, edam:operation_3216, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BactSNP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/IEkAdN/BactSNP" ; biotools:primaryContact "Takehiko Itoh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3373, edam:topic_3474 ; sc:citation , "pubmed:31521251" ; sc: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" ; sc:name "Bagging-SVM" ; sc:url "https://github.com/QUST-AIBBDRC/GA-Bagging-SVM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0781, edam:topic_3420 ; sc:citation ; sc:description "Robust and window-insensitive mixture model approaches for localizing balancing selection." ; sc:featureList edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BalLeRMix" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.personal.psu.edu/mxd60/ballermix.html" ; biotools:primaryContact "Michael DeGiorgio" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0797, edam:topic_3308, edam:topic_3810 ; sc:author ; sc:citation , , "pmcid:PMC3662865", "pubmed:22801500", "pubmed:23707967" ; sc:description "A Next-Generation Information System for Musa genomics" ; sc:featureList edam:operation_0338, edam:operation_2403, edam:operation_3208 ; sc:funder "ANR" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Banana Genome Hub" ; sc:softwareHelp , , ; sc:softwareVersion "v2" ; sc:url "https://banana-genome-hub.southgreen.fr/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pmcid:PMC6348988", "pubmed:30420522" ; sc:description "Software for analysis of nucleic acid structures and trajectories." ; sc:featureList edam:operation_0249, edam:operation_0279, edam:operation_2518 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Barnaba" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/srnas/barnaba" ; biotools:primaryContact "Small RNAs in silico" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3325, edam:topic_3673, edam:topic_3676 ; sc:author "Riku Katainen" ; sc:citation , , "pubmed:30323186" ; sc:description "Large-scale discovery tool for potential causative mutations in human coding and noncoding genome." ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "BasePlayer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://baseplayer.fi/" ; biotools:primaryContact "Riku Katainen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6343306", "pubmed:30669962" ; sc:description "Integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping." ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:name "BatMeth2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GuoliangLi-HZAU/BatMeth2" ; biotools:primaryContact "Guoliang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3308 ; sc:citation ; sc:description "A hierarchical Bayesian deconvolution model with stochastic search variable selection | Bayesian deconvolution model for intracellular component exploration (BayICE)" ; sc:featureList edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "BayICE" ; sc:url "https://github.com/AshTai/BayICE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_2640 ; sc:citation , "pmcid:PMC6454009", "pubmed:31001324" ; sc:description "Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts." ; sc:featureList edam:operation_0477, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:name "BayesPI-BAR2" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://folk.uio.no/junbaiw/BayesPI-BAR2/" ; biotools:primaryContact "Junbai Wang", "Kirill Batmanov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3379 ; sc:citation , "pmcid:PMC6711387", "pubmed:31456910" ; sc: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:" ; sc:featureList edam:operation_3454 ; sc:name "BayesianPredictiveFutility" ; sc:url "https://github.com/dungtsa/BayesianPredictiveFutility" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pmcid:PMC6472072", "pubmed:30999943" ; sc:description "Method for read extraction and realignment of high-throughput sequencing data." ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "Bazam" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ssadedin/bazam" ; biotools:primaryContact "Simon Sadedin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pubmed:31808510" ; sc: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""" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3195, edam:operation_3198, edam:operation_3472 ; sc:license "AGPL-3.0" ; sc:name "BCOOL" ; sc:url "http://github.com/Malfoy/BCOOL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0196, edam:topic_3068, edam:topic_3306, edam:topic_3385 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "BeamDelta" ; sc:url "https://github.com/MicronOxford/BeamDelta" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "A mine with common bean data from the Legume Info tripal.chado database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "BeanMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/beanmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6787812", "pubmed:31624564" ; sc: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""" ; sc:featureList edam:operation_0450, edam:operation_0524, edam:operation_2428, edam:operation_3258, edam:operation_3644 ; sc:name "Bellerophon" ; sc:url "https://github.com/JesseKerkvliet/Bellerophon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3517 ; sc:citation , "pmcid:PMC6556976", "pubmed:31056107" ; sc:description "Benchmarking gene and variant prioritization algorithms for GWAS data." ; sc:featureList edam:operation_0488 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Benchmarker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/RebeccaFine/benchmarker" ; biotools:primaryContact "Joel N. Hirschhorn", "Rebecca Fine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0611 ; sc:citation , "pubmed:29444233" ; sc:description "Program for reconstruction of amyloid structures containing adjacent β-arches." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "BetaSerpentine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://bioinfo.montp.cnrs.fr/b-serpentine" ; biotools:primaryContact "Andrey V. Kajava", "Stanislav A. Bondarev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation ; sc:description "Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure." ; sc:featureList edam:operation_0278, edam:operation_0491, edam:operation_0502 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BiAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/s-will/BiAlign" ; biotools:primaryContact "Ivo L. Hofacker", "Maria Waldl", "Michael T. Wolfinger", "Sebastian Will" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0091, edam:topic_0102, edam:topic_0623, edam:topic_3172, edam:topic_3697 ; sc:citation , "pmcid:PMC6917865", "pubmed:31768033" ; sc: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.""" ; sc:featureList edam:operation_0303, edam:operation_0496, edam:operation_3432 ; sc:name "BiG-SCAPE" ; sc:url "https://github.com/medema-group/BiG-SCAPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3293, edam:topic_3407 ; sc:citation , "pmcid:PMC7145653", "pubmed:31696234" ; sc: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.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3660 ; sc:name "BiGG Models" ; sc:softwareHelp , ; sc:url "http://bigg.ucsd.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6288881", "pubmed:30526492" ; sc:description "Spark-based highly scalable aligner for bisulfite sequencing data." ; sc:featureList edam:operation_3186, edam:operation_3198, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BiSpark" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/bhi-kimlab/BiSpark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0313, edam:operation_2454, edam:operation_3501 ; sc:name "BiTSC" ; sc:url "https://github.com/edensunyidan/BiTSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6876073", "pubmed:31760932" ; sc: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""" ; sc:featureList edam:operation_3435 ; sc:license "Other" ; sc:name "BiWalkLDA" ; sc:url "https://github.com/screamer/BiwalkLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_2258, edam:topic_3071, edam:topic_3336, edam:topic_3343 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_0482 ; sc:isAccessibleForFree true ; sc:name "BiasDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biasdb.drug-design.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:31384047" ; sc: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" ; sc:featureList edam:operation_0232, edam:operation_3552, edam:operation_3629 ; sc:license "GPL-2.0" ; sc:name "BigStitcher" ; sc:url "https://imagej.net/BigStitcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601 ; sc:citation , "pmcid:PMC6923822", "pubmed:31856704" ; sc: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""" ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3755 ; sc:name "Bigram-PGK" ; sc:url "https://github.com/abelavit/Bigram-PGK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3174 ; sc:citation , "pubmed:30052763" ; sc:description "Software for fast genome distance estimation on a typical personal laptop." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BinDash" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zhaoxiaofei/BinDash" ; biotools:primaryContact "XiaoFei Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC6717532", "pubmed:31406384" ; sc: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" ; sc:featureList edam:operation_0420, edam:operation_0445, edam:operation_3222 ; sc:name "BindSpace" ; sc:url "https://bitbucket.org/hy395/bindspace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_3172 ; sc:citation , "pmcid:PMC7828469", "pubmed:31642507" ; sc: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.""" ; sc:featureList edam:operation_3432 ; sc:name "Binner" ; sc:url "http://binner.med.umich.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2258, edam:topic_3372 ; sc:citation ; sc:description "A web-based tool for data and algorithms integration." ; sc:featureList edam:operation_2422 ; sc:name "Bio-DIA" ; sc:url "https://ucrania.imd.ufrn.br/biodia-app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_2258 ; sc:citation ; sc:description "Integration of Structured Biological Data Sources using Biological Expression Language." ; sc:featureList edam:operation_0533, edam:operation_1812, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Bio2BEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bio2bel" ; biotools:primaryContact "Charles Tapley Hoyt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3303 ; sc:citation , "pmcid:PMC7703786", "pubmed:31501885" ; sc: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" ; sc:featureList edam:operation_3280, edam:operation_3625 ; sc:name "BioBERT" ; sc:url "https://github.com/naver/biobert-pretrained" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , "pubmed:31119364" ; sc:description "Tool for converting cell lineage data from SIMI BioCell to MaMuT (Fiji)." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BioCell2XML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/guleom/BioCell2XML" ; biotools:primaryContact "Carsten Wolff", "Günther Loose", "Markus Pennerstorfer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0593, edam:topic_3474 ; sc:citation ; sc: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]""" ; sc:featureList edam:operation_0337, edam:operation_2425, edam:operation_2476, edam:operation_3799, edam:operation_3891 ; sc:name "BioEn" ; sc:url "http://github.com/bio-phys/BioEn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3382 ; sc:description "Visual designer for biofeedback. Provides environment and tools to create various types of processing tasks." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BioEra" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://bioera.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Program for real-time biophysical data acquisition, processing, and display." ; sc:isAccessibleForFree false ; sc:license "Other" ; sc:name "BioExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.7" ; sc:url "http://www.cyberevolution.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0602, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description "BioFabric is an open-source network visualization tool." ; sc:featureList edam:operation_0491, edam:operation_0496, edam:operation_3083 ; sc:name "BioFabric" ; sc:url "https://github.com/wjrl/BioFabric" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , "pmcid:PMC6324058", "pubmed:30476227" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_1777, edam:operation_1781, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:name "BioGRID Open Repository of CRISPR Screens (ORCS)" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://orcs.thebiogrid.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "SPARQL endpoint" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128 ; sc:citation , "pmcid:PMC7703768", "pubmed:31710663" ; sc:description "A triple store with RDF graphs obtained from various curated databases, queryable by SPARQL and through the Cytoscape plugin BioGateway App." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BioGateway" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "3.0" ; sc:url "https://www.biogateway.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3300, edam:topic_3314, edam:topic_3315, edam:topic_3407 ; sc:citation , "pmcid:PMC6813930", "pubmed:31681022" ; sc:description "BioGears® is a open source, comprehensive human physiology engine that will drive medical education, research, and training technologies." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3454 ; sc:license "Apache-2.0" ; sc:name "BioGears Engine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biogearsengine.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2258, edam:topic_3168, edam:topic_3336 ; sc:citation , "pubmed:31885044" ; sc: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""" ; sc:featureList edam:operation_0262, edam:operation_2929, edam:operation_3894 ; sc:license "GPL-2.0" ; sc:name "BioMedR" ; sc:url "https://CRAN.R-project.org/package=BioMedR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1288 ; sc:encodingFormat edam:format_1975 ; sc:name "Genome map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1860 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "QTL map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3055 ; sc:citation , "pubmed:15059820" ; sc: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." ; sc:featureList edam:operation_0282, edam:operation_2944 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BioMercator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.2.3" ; sc:url "https://sourcesup.renater.fr/projects/biomercator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6761945", "pubmed:30799505" ; sc:description "R package for Biological interpretation of DNA methylation data in the TCGA cancers context." ; sc:featureList edam:operation_0533, edam:operation_3207, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "BioMethyl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yuewangpanda/BioMethyl" ; biotools:primaryContact "Chao Cheng", "Yue Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0084, edam:topic_0154, edam:topic_0621 ; sc:citation ; sc: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 \"""" ; sc:name "BioMine-DB" ; sc:url "http://biomine.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0769, edam:topic_2259, edam:topic_3473 ; sc:citation , ; sc: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.""" ; sc:featureList edam:operation_0239, edam:operation_2422, edam:operation_3660 ; sc:name "BioNet-Mining" ; sc:url "https://github.com/FabienneL/BioNet-Mining" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769 ; sc:description "Bioinformatics workflows in the functional Nix language" ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "BioNix" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://github.com/PapenfussLab/bionix" ; biotools:primaryContact "Mailing list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0736, edam:topic_2830 ; sc:citation ; sc:description "Python tool for integration of protein structure and sequence-based features." ; sc:featureList edam:operation_0302, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BioStructMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://biostructmap.burnet.edu.au" ; biotools:primaryContact "Andrew Guy", "Dr. Paul Ramsland" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3070 ; sc:citation , "pubmed:31609384" ; sc: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)""" ; sc:featureList edam:operation_2497, edam:operation_3799 ; sc:name "BioSwitch" ; sc:url "https://sites.google.com/view/bioswitch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3489, edam:topic_3500 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2422 ; sc:license "BSD-3-Clause" ; sc:name "Biobtree" ; sc:url "https://www.github.com/tamerh/biobtree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0218, edam:topic_3473 ; sc:citation , "pmcid:PMC6584971", "pubmed:31249680" ; sc: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." ; sc:featureList edam:operation_0306, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BiocPkgTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioconductor.org/packages/BiocPkgTools" ; biotools:primaryContact "Sean Davis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3697, edam:topic_3810 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3552, edam:operation_3799 ; sc:name "BiofilmQ" ; sc:url "https://drescherlab.org/data/biofilmQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Suite", "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0121, edam:topic_0622, edam:topic_3293 ; sc:author , , ; sc:description "A collection of 40+ well-documented Docker images of commonly used bioinformatics applications and pipelines." ; sc:featureList edam:operation_0292, edam:operation_0324, edam:operation_2403, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "Bioinformatics Docker Images Project" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://pegi3s.github.io/dockerfiles/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0780, edam:topic_3174, edam:topic_3500 ; sc:citation , "pmcid:PMC7703761", "pubmed:31599923" ; sc: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)""" ; sc:featureList edam:operation_0277, edam:operation_0525, edam:operation_3439, edam:operation_3672 ; sc:name "BiomeNet" ; sc:url "http://kobic.re.kr/biomenet/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_3746 ; sc:name "Database search results" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "A Shiny R app for microbiome visualization, built around the \"microbiome\" package." ; sc:featureList edam:operation_0337 ; sc:name "Biome-Shiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9" ; sc:url "https://github.com/BioData-PT/Biome-Shiny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:author "Vid Podpečan" ; sc:citation , "pmcid:PMC6954666", "pubmed:31233141" ; sc:contributor "Hannu Toivonen", "Kristina Gruden", "Nada Lavrač", "Živa Ramšak" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3927 ; sc:name "Biomine Explorer" ; sc:provider "Jožef Stefan Institute, Department of Knowledge Technologies" ; sc:softwareHelp ; sc:url "https://biomine.ijs.si/" ; biotools:primaryContact "Vid Podpečan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102 ; sc:citation , "pmcid:PMC6755254", "pubmed:31544213" ; sc: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)" ; sc:featureList edam:operation_3435 ; sc:license "MIT" ; sc:name "Bionitio" ; sc:url "https://github.com/bionitio-team/bionitio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc: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)""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3196 ; sc:name "BitEpi" ; sc:url "https://github.com/aehrc/BitEpi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3855 ; sc:citation , "pmcid:PMC6509165", "pubmed:31073241" ; sc:description "Building machine learning models for predicting the bitter and sweet taste of small molecules." ; sc:featureList edam:operation_3216, edam:operation_3280, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "BitterSweet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cosylab.iiitd.edu.in/bittersweet/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3325 ; sc:citation , "pmcid:PMC8256816", "pubmed:34165986" ; sc: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)""" ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2495, edam:operation_3223, edam:operation_3436 ; sc:license "MIT" ; sc:name "BlackSheep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ruggleslab/blackSheep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0621, edam:topic_0769, edam:topic_3500 ; sc:citation , , "pmcid:PMC7144090", "pubmed:32071071" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_1812, edam:operation_3216, edam:operation_3431 ; sc:license "MIT" ; sc:name "BlobToolKit" ; sc:url "https://blobtoolkit.genomehubs.org/view" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31452088" ; sc:description "A cloud-based peptide search engine for MS/MS sequencing." ; sc:featureList edam:operation_2929, edam:operation_3645, edam:operation_3646 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Bolt" ; sc:url "http://www.optystech.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "An integrated data warehouse for the Bovine Genome Database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "BovineMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.4" ; sc:url "http://genomes.missouri.edu/bovinemine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "A random forest model for inferring higher-order trait interactions associated with complex biological phenotypes." ; sc:featureList edam:operation_2495, edam:operation_3659 ; sc:name "BowSaw" ; sc:url "https://github.com/ddimucci/BowSaw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BrainBay" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.4" ; sc:url "http://www.shifz.org/brainbay/" ; biotools:primaryContact "Chris Veigl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3334, edam:topic_3384 ; sc:citation , , "pmcid:PMC7058611", "pubmed:32139786" ; sc: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" ; sc:featureList edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "BrainSpace" ; sc:softwareHelp ; sc:url "http://github.com/MICA-MNI/BrainSpace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3304 ; sc:citation , "pmcid:PMC6838536", "pubmed:31677479" ; sc: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""" ; sc:featureList edam:operation_2429, edam:operation_3446 ; sc:name "Brain Interactome Explorer" ; sc:url "https://mpi-ie.shinyapps.io/braininteractomeexplorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3399, edam:topic_3408 ; sc:citation ; sc:description "Interactive, web-based tool for testing hypotheses and developing predictive models." ; sc:featureList edam:operation_3359, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Branch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/sulab/biobranch/src/default/" ; biotools:primaryContact "Andrew I. Su", "Benjamin M. Good" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3293, edam:topic_3474 ; sc:citation , , "pubmed:32602888" ; sc: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""" ; sc:featureList edam:operation_0327, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "Broccoli" ; sc:url "https://github.com/rderelle/Broccoli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_0749 ; sc:citation , "pmcid:PMC6851476", "pubmed:31365149" ; sc: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]" ; sc:featureList edam:operation_0272, edam:operation_0476, edam:operation_3350 ; sc:name "C-I-TASSER" ; sc:url "https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3292 ; sc:citation , "pubmed:31116383" ; sc: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." ; sc:featureList edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "C-InterSecture" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/NuriddinovMA/C-InterSecture" ; biotools:primaryContact "M. Nuriddinov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3517 ; sc:citation , "pubmed:31732979" ; sc: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)""" ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3791 ; sc:license "GPL-2.0" ; sc:name "C-JAMP" ; sc:url "https://cran.r-project.org/web/packages/CJAMP/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC6818389", "pubmed:31465854" ; sc: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" ; sc:name "Consensus Cancer driver gene Caller (C3)" ; sc:url "http://drivergene.rwebox.com/c3/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation , "pubmed:30816925" ; sc:description "Cross Cell-type Correlation in DNaseI hypersensitivity (C3D) - tool to predict 3D genomic interactions between cis-regulatory elements." ; sc:featureList edam:operation_0441 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "C3D" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/LupienLab/C3D" ; biotools:primaryContact "Tahmid Mehdi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3957 ; sc:citation , , "pmcid:PMC6933849", "pubmed:31682301", "pubmed:31733137" ; sc:description "A web application for flexible protein-peptide docking." ; sc:featureList edam:operation_0480, edam:operation_0482, edam:operation_2575, edam:operation_3631, edam:operation_3899 ; sc:name "CABS-dock" ; sc:url "http://biocomp.chem.uw.edu.pl/CABSdock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3474 ; sc:citation , "pubmed:31382223" ; sc: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" ; sc:name "CADOES" ; sc:url "http://osteomics.com/CADOES/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382 ; sc:citation , "pmcid:PMC6718774", "pubmed:31443860" ; sc: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" ; sc:featureList edam:operation_3450, edam:operation_3660 ; sc:name "CALIMA" ; sc:url "https://aethelraed.nl/calima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0637 ; sc:citation ; sc:description "Codon Aversion Motifs for Alignment-free Phylogenies." ; sc:featureList edam:operation_0284, edam:operation_2962, edam:operation_2964 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ridgelab/cam" ; biotools:primaryContact "Justin Miller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0610, edam:topic_0625, edam:topic_2269 ; sc:citation , "pmcid:PMC6912896", "pubmed:31871640" ; sc: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")""" ; sc:featureList edam:operation_0310, edam:operation_2426, edam:operation_3659, edam:operation_3695 ; sc:name "Community Assembly Model Inference (CAMI)" ; sc:url "https://github.com/ruffleymr/CAMI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6368784", "pubmed:30736849" ; sc:description "Software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets." ; sc:featureList edam:operation_0310, edam:operation_3460, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CAMISIM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/CAMI-challenge/CAMISIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:31838143" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3660 ; sc:name "CAMND" ; sc:url "http://eslahchilab.ir/softwares/dmn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC6499410", "pubmed:30304439" ; sc:description "R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis." ; sc:featureList edam:operation_0337, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CANDI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://candi.nextgenhealthcare.org/" ; biotools:primaryContact "M. A. Badgeley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2275, edam:topic_3336, edam:topic_3379 ; sc:citation , , "pmcid:PMC8098009", "pubmed:32515949" ; sc:description "CANDO is a open-source, unique computational drug discovery, design, and repurposing platform." ; sc:featureList edam:operation_0477, edam:operation_0478, edam:operation_2575 ; sc:license "BSD-3-Clause" ; sc:name "Computational Analysis of Novel Drug Opportunities (CANDO)" ; sc:url "https://github.com/ram-compbio/CANDO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063 ; sc:citation , "pubmed:31714219" ; sc: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""" ; sc:featureList edam:operation_3659 ; sc:name "CANet" ; sc:url "https://github.com/xmengli999/CANet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3320, edam:topic_3384, edam:topic_3474, edam:topic_3676 ; sc:citation , , "pmcid:PMC7446154", "pubmed:32831124" ; sc:description "A computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3461 ; sc:name "CAPICE" ; sc:url "https://molgenis43.gcc.rug.nl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2885, edam:topic_3174, edam:topic_3305, edam:topic_3673 ; sc:citation , "pmcid:PMC7145624", "pubmed:31665441" ; sc:description "Antibiotic resistome surveillance with the comprehensive antibiotic resistance database." ; sc:featureList edam:operation_0362, edam:operation_2421, edam:operation_3196, edam:operation_3461, edam:operation_3482 ; sc:name "The Comprehensive Antibiotic Resistance Database (CARD)" ; sc:softwareHelp ; sc:url "https://card.mcmaster.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0749, edam:topic_3308, edam:topic_3422 ; sc:citation , "pmcid:PMC6848167", "pubmed:31728204" ; sc: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""" ; sc:featureList edam:operation_0277, edam:operation_2436, edam:operation_3439 ; sc:name "CARNIVAL" ; sc:url "https://github.com/saezlab/CARNIVAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3292, edam:topic_3315, edam:topic_3452 ; sc:citation , "pmcid:PMC6716611", "pubmed:31474782" ; sc: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" ; sc:license "LGPL-2.1" ; sc:name "Colored Abstract Simplicial Complex (CASC)" ; sc:url "https://github.com/ctlee/casc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC7141873", "pubmed:31750900" ; sc: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.""" ; sc:featureList edam:operation_0326, edam:operation_0540, edam:operation_0557, edam:operation_3799 ; sc:name "CASet" ; sc:url "https://bitbucket.org/oesperlab/stereodist/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0209, edam:topic_0749 ; sc:citation , "pmcid:PMC6910964", "pubmed:31836830" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_2492, edam:operation_2575, edam:operation_3891 ; sc:license "LGPL-3.0" ; sc:name "Cosolvent Analysis Toolkit (CAT)" ; sc:url "https://github.com/ammvitor/CAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:author "Cheng-Kai Shiau" ; sc:citation ; sc:description "Tool for generating comprehensive annotations of alternative transcript events." ; sc:featureList edam:operation_0264, edam:operation_1812, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CATANA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/shiauck/CATANA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0102 ; sc:citation , "pubmed:31790141" ; sc: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""" ; sc:featureList edam:operation_0272, edam:operation_0302, edam:operation_0474 ; sc:name "CATHER" ; sc:url "http://yanglab.nankai.edu.cn/CATHER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2830, edam:topic_3170 ; sc:citation , , "pubmed:32399561" ; sc: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)" ; sc:featureList edam:operation_3192 ; sc:name "CATT" ; sc:url "http://bioinfo.life.hust.edu.cn/CATT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC7145620", "pubmed:31691819" ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3791 ; sc:name "CAUSALdb" ; sc:url "http://mulinlab.org/causaldb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC6534331", "pubmed:31060045" ; sc:description "Spiking Neural Network of cortico-basal ganglia-thalamus (CBGT) pathways." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CBGT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/CoAxLab/CBGT" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6907873", "pubmed:31790386" ; sc:description "Controllability based Biological Network Analysis (CBNA) is a tool to uncover coding and non-coding cancer drivers (i.e. miRNA cancer drivers)." ; sc:featureList edam:operation_0463, edam:operation_3202, edam:operation_3792 ; sc:name "CBNA" ; sc:url "https://github.com/pvvhoang/CancerDriver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3673 ; sc:citation , "pmcid:PMC6737777", "pubmed:31551994" ; sc: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" ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3644 ; sc:license "GPL-3.0" ; sc:name "CCBGpipe" ; sc:url "https://github.com/jade-nhri/CCBGpipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3315, edam:topic_3382 ; sc:citation , "pubmed:31870986" ; sc:description "CCC-Tool (Charting Continuous Colormaps) is a tool for creating, editing, and analyzing such application-specific colormaps." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3435 ; sc:name "CCC-Tool" ; sc:url "https://ccctool.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3518 ; sc:citation , , "pubmed:32510568" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_2495, edam:operation_3227 ; sc:name "Cancer Cell Line Authentication (CCLA)" ; sc:url "http://bioinfo.life.hust.edu.cn/web/CCLA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3697 ; sc:citation , "pmcid:PMC6719681", "pubmed:31482150" ; sc: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" ; sc:name "CCMP" ; sc:url "https://ccmp.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308, edam:topic_3697 ; sc:citation ; sc:description "Pipeline to classify organisms in metagenomes or metatranscriptomes accurately." ; sc:featureList edam:operation_3460, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CCMetagen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cge.cbs.dtu.dk/services/ccmetagen/" ; biotools:primaryContact "Vanessa R. Marcelino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0749, edam:topic_0780, edam:topic_3169 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0291, edam:operation_0362, edam:operation_3695 ; sc:name "CCSeq" ; sc:url "https://cran.r-project.org/web/packages/colocalized/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0637 ; sc:citation , "pmcid:PMC6726630", "pubmed:31485005" ; sc: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:" ; sc:featureList edam:operation_2492, edam:operation_3501 ; sc:name "CDAP" ; sc:url "http://www.eslahchilab.ir/softwares/cdap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3379, edam:topic_3401 ; sc:citation , , "pubmed:31077078", "pubmed:31087257" ; sc:description "Common Data Elements for Unruptured Intracranial Aneurysm and Subarachnoid Hemorrhage Clinical Research." ; sc:featureList edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cde.nlm.nih.gov/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3373, edam:topic_3379 ; sc:citation , "pmcid:PMC6693031", "pubmed:31411687" ; sc: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" ; sc:featureList edam:operation_0224, edam:operation_3431 ; sc:name "Clinical Drug Experience Knowledgebase (CDEK)" ; sc:softwareHelp ; sc:url "http://cdek.wustl.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_3053 ; sc:citation , "pubmed:31769930" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3659 ; sc:name "CDMetaPOP" ; sc:url "https://github.com/ComputationalEcologyLab/CDMetaPOP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6449719", "pubmed:30759968" ; sc:description "Web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CDRgator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cdrgator.ewha.ac.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2269, edam:topic_3170, edam:topic_3300 ; sc:citation , , "pmcid:PMC6907860", "pubmed:31790389" ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3629, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "CDSeq" ; sc:url "https://github.com/kkang7/CDSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3050, edam:topic_3174, edam:topic_3810 ; sc:citation , "pmcid:PMC6751219", "pubmed:31592221" ; sc:description "A portal for geographic reference data for the Amazon." ; sc:featureList edam:operation_2428 ; sc:name "CEBA geoportail" ; sc:url "http://vmcebagn-dev.ird.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3325, edam:topic_3376 ; sc:citation "pubmed:20841733" ; sc:description "Collection of continuous and complete records of patients with rare diseases, and their follow-up through a web-based Information System." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "CEMARA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cemara.org/presentation/show.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3382 ; sc:citation , "pmcid:PMC6792302", "pubmed:31649733" ; sc: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""" ; sc:featureList edam:operation_0531, edam:operation_3432, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "CEPICS" ; sc:url "https://github.com/GaoLabXDU/CEPICS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC6364436", "pubmed:30727967" ; sc: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)." ; sc:featureList edam:operation_0484, edam:operation_2495, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CERENKOV2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v0.1-alpha" ; sc:url "https://github.com/ramseylab/cerenkov" ; biotools:primaryContact "Stephen Ramsey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3444 ; sc:citation , ; sc: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" ; sc:featureList edam:operation_3096 ; sc:license "LGPL-2.1" ; sc:name "Computational Environment for Radiological Research (CERR)" ; sc:softwareHelp ; sc:url "https://www.github.com/cerr/CERR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0625, edam:topic_3308 ; sc:citation , "pmcid:PMC6821211", "pubmed:31552418" ; sc: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" ; sc:featureList edam:operation_3501, edam:operation_3642, edam:operation_3891 ; sc:name "CEVIChE" ; sc:url "https://saezlab.shinyapps.io/ceviche/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102, edam:topic_0130, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC6818797", "pubmed:31622328" ; sc: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.""" ; sc:featureList edam:operation_0272, edam:operation_0300, edam:operation_0303, edam:operation_0476, edam:operation_0477 ; sc:name "CEthreader" ; sc:url "https://zhanglab.ccmb.med.umich.edu/CEthreader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3407 ; sc:citation , "pubmed:31518497" ; sc: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" ; sc:featureList edam:operation_3799, edam:operation_3803 ; sc:name "CF-targeter" ; sc:url "http://www.rxnfinder.org/cf_targeter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2269, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3630 ; sc:name "Conserved Feature Discovery (CFD)" ; sc:url "https://github.com/Kingsford-Group/cfd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3173, edam:topic_3176 ; sc:citation , "pmcid:PMC6943076", "pubmed:31428785" ; sc: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" ; sc:featureList edam:operation_0432, edam:operation_2428, edam:operation_3192 ; sc:name "Cell-Free Epigenome Atlas (CFEA)" ; sc:url "http://www.bio-data.cn/CFEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6612823", "pubmed:31510662" ; sc: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" ; sc:featureList edam:operation_3443 ; sc:name "CFNet" ; sc:url "https://github.com/bchidest/CFNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3382 ; sc:citation , "pmcid:PMC6315083", "pubmed:30602526" ; sc: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" ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CFQuant-automatic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.energylabtau.com/cfquant" ; biotools:primaryContact "Eyal Dafni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0625, edam:topic_2640, edam:topic_3673, edam:topic_3676 ; sc:author "In-Hee Lee", "Jose A. Negron" ; sc:citation , "pmcid:PMC7180092", "pubmed:31691385" ; sc:contributor ; sc:description """An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. 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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. 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S. Burren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC4739640", "pubmed:25822800" ; sc: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" ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3792 ; sc:name "CIBERSORT" ; sc:url "https://cibersort.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0625, edam:topic_0749, edam:topic_3169, edam:topic_3170 ; sc:citation , "pmcid:PMC7145661", "pubmed:31701125" ; sc: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.""" ; sc:featureList edam:operation_1781, edam:operation_2436, edam:operation_3083, edam:operation_3439 ; sc:name "Causal Inference Enrichment (CIE)" ; sc:url "https://umbibio.math.umb.edu/cie/app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pubmed:30239607" ; sc:description "Central Informative Nodes in Network Analysis (CINNA) package gathers all required functions for centrality analysis in weighted/unweighted and directed/undirected networks." ; sc:featureList edam:operation_2497, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CINNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1.53" ; sc:url "https://cran.r-project.org/package=CINNA" ; biotools:primaryContact "Minoo Ashtiani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3320, edam:topic_3512 ; sc:author "Li Yang", "Xiao-Ou Zhang" ; sc:citation , "pubmed:30539552" ; sc:description "Genome-wide annotation of circRNAs and their alternative back-splicing/splicing." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CIRCexplorer2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://circexplorer2.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6339429", "pubmed:30660194" ; sc:description "CircRNA Identifier. A de novo circular RNA identification tool." ; sc:featureList edam:operation_0443, edam:operation_3644, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CIRI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/ciri" ; biotools:primaryContact "Fangqing Zhao", "Jinyang Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3379 ; sc:citation , "pubmed:31119495" ; sc:description "Tool for Predicting Cross-interaction or Self-interaction of Monoclonal Antibodies Using Sequences." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CISI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://i.uestc.edu.cn/eli/cgi-bin/cisi.pl" ; biotools:primaryContact "Jian Huang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1022 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence feature label" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_3033 ; sc:name "Nucleic acid report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3750 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3308 ; sc:description "Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment." ; sc:featureList edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CITE-seq-Count" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://hoohm.github.io/CITE-seq-Count/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0219, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , , "pmcid:PMC6891984", "pubmed:31796060" ; sc:description "CIViCmine is a literature-mined database of clinically relevant cancer biomarkers from data from PubMed and Pubmed Central Open Access subset." ; sc:featureList edam:operation_0306, edam:operation_1812, edam:operation_3778 ; sc:license "MIT" ; sc:name "CIViCmine" ; sc:url "http://bionlp.bcgsc.ca/civicmine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3379, edam:topic_3400 ; sc:citation , ; sc: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" ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3197 ; sc:license "MIT" ; sc:name "CIViCpy" ; sc:url "https://docs.civicpy.org/en/1.1/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_2229 ; sc:author ; sc: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." ; sc:featureList edam:operation_2233 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CLASTR" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "https://web.expasy.org/cellosaurus-str-search/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3372, edam:topic_3382 ; sc:citation , "pubmed:31740823" ; sc: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""" ; sc:featureList edam:operation_2409, edam:operation_3443 ; sc:name "CLIJ" ; sc:softwareHelp , ; sc:url "https://clij.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3168, edam:topic_3382 ; sc:citation , "pmcid:PMC6819642", "pubmed:31660851" ; sc: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." ; sc:featureList edam:operation_0570, edam:operation_2938, edam:operation_3432 ; sc:license "MIT" ; sc:name "CLINE" ; sc:softwareHelp , ; sc:url "http://mizuguchilab.org/cline/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3794 ; sc: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." ; sc:name "CLIP-Explorer" ; sc:url "https://clipseq.usegalaxy.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3063, edam:topic_3379, edam:topic_3794 ; sc:citation , , "pmcid:PMC7500653", "pubmed:32946464" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3891 ; sc:name "CLIPS" ; sc:url "https://corus.kaist.edu/clips" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3376, edam:topic_3474 ; sc:citation , "pubmed:31454273" ; sc: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" ; sc:license "BSD-2-Clause" ; sc:name "CLOBNET" ; sc:url "https://github.com/isoviita/CLOBNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3794 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CLiP Chlamydomonas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.chlamylibrary.org/" ; biotools:primaryContact "Jonikas lab", "Matt Laudon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3379, edam:topic_3400 ; sc:citation , "pmcid:PMC6701018", "pubmed:31429750" ; sc:description "A simple classification scheme for data elements of clinical data based on semantics" ; sc:featureList edam:operation_2422, edam:operation_3352, edam:operation_3559 ; sc:name "Clinical MetaData Ontology (CMDO)" ; sc:url "http://www.snubi.org/software/CMDO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0804, edam:topic_3324, edam:topic_3421, edam:topic_3489 ; sc:citation , "pubmed:31813095" ; sc: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""" ; sc:featureList edam:operation_0308, edam:operation_0477, edam:operation_2421 ; sc:name "CytoMegaloVirus DataBase (CMVdb)" ; sc:url "http://shaktisahislab.com/include/CMV/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3170, edam:topic_3474, edam:topic_3518 ; sc:citation , "pubmed:31581092" ; sc: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""" ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_3435 ; sc:name "CNAPE" ; sc:url "https://github.com/WangLabHKUST/CNAPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3673 ; sc:citation ; sc:description "Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CNAtra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AISKhalil/CNAtra" ; biotools:primaryContact "Ahmed Khalil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6874599", "pubmed:31758002" ; sc: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""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "CNN" ; sc:url "https://github.com/Jilab-biomechanics/CNN-brain-strains" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0601, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC6838336", "pubmed:31700141" ; sc:description """Problems with homepage (January 6th, 2021) | CNN-SuccSite is a web server for characterization and identification succinylation sites based on deep learning method.""" ; sc:featureList edam:operation_0417, edam:operation_3755 ; sc:name "CNN-SuccSite" ; sc:url "http://csb.cse.yzu.edu.tw/CNN-SuccSite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3172, edam:topic_3474, edam:topic_3542 ; sc:citation , "pubmed:31860715" ; sc: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.""" ; sc:featureList edam:operation_0267, edam:operation_2476, edam:operation_2488 ; sc:name "CNN-T4SE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://idrblab.org/cnnt4se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3673 ; sc:citation , , "pubmed:32219377" ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3435 ; sc:name "CNV-BAC" ; sc:url "https://github.com/LinjieWu/CNV-BAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pmcid:PMC9887538", "pubmed:31392308" ; sc: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" ; sc:featureList edam:operation_0484, edam:operation_3232, edam:operation_3800 ; sc:license "Artistic-2.0" ; sc:name "CNVRanger" ; sc:url "http://bioconductor.org/packages/CNVRanger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6887803", "pubmed:31832011" ; sc: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)""" ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3196, edam:operation_3659 ; sc:license "BSD-3-Clause" ; sc:name "CNVScope" ; sc:url "http://cnvscope.nci.nih.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation , "pmcid:PMC6954662", "pubmed:31141125" ; sc:description "Multi-omics Approach to Detecting Clinically Associated, Combinatory Genomic Signatures." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bsml320/CNet" ; biotools:primaryContact "Zhongming Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0602, edam:topic_3360 ; sc:citation , "pmcid:PMC6396937", "pubmed:30779739" ; sc:description "Component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications." ; sc:featureList edam:operation_1781, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "COAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ChengF-Lab/COAC" ; biotools:primaryContact "ChengF-Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2258, edam:topic_3172 ; sc:citation , "pmcid:PMC6635304", "pubmed:30787451" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "COBRA Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "3.0" ; sc:url "https://opencobra.github.io/cobratoolbox/" ; biotools:primaryContact "Ronan Fleming on behalf of the COBRA Toolbox Development Community" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3300, edam:topic_3407 ; sc:citation , "pmcid:PMC6538558", "pubmed:31138123" ; sc:description "Context-specific biological knowledge representation for systemic physiology analysis." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CODA-ML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MijinKwon/CODA-ML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3444 ; sc:citation , , "pubmed:31463859", "pubmed:32073269" ; sc: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;" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3803 ; sc:name "COLMARm" ; sc:url "http://spin.ccic.ohio-state.edu/index.php/colmarm/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3382, edam:topic_3855 ; sc:citation , "pubmed:31121098" ; sc:description "Data-Analysis Package for Combinatorial Materials Science." ; sc:featureList edam:operation_1812, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "COMBIgor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.COMBIgor.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6348648", "pubmed:30691411" ; sc:description "Web-based application used to download, collect and manage gene expression data from public databases." ; sc:featureList edam:operation_2495, edam:operation_3431, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "COMMAND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/marcomoretto/command" ; biotools:primaryContact "Marco Moretto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , , "pmcid:PMC7520036", "pubmed:32399572" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3802 ; sc:name "COMUNET" ; sc:url "https://github.com/ScialdoneLab/COMUNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6624895", "pubmed:31300005" ; sc:description "CCA (canonical correlation analysis) ON Features for INter-dataset Effect Detection." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:name "CONFINED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cozygene/CONFINED" ; biotools:primaryContact "Mike Thompson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3174, edam:topic_3810 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "COPO" ; sc:url "http://copo-project.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3382 ; sc:citation , "pubmed:31702166" ; sc: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)." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "CORDERLY" ; sc:url "https://github.com/adrena-lab/CORDERLY" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0654, edam:topic_2640 ; sc:citation , "pubmed:30378070" ; sc:description "Cores of Recurrent Events (CORE) is software tool for delineating regions of recurrent DNA copy number alteration in cancer." ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "CORE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "https://cran.r-project.org/package=CORE" ; biotools:primaryContact "Guoli Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3407 ; sc:citation , "pmcid:PMC6302372", "pubmed:30577744" ; sc:description "CORGi (COmplex Rearrangement detection with Graph-search), a method for the detection and visualization of complex local genomic rearrangements." ; sc:featureList edam:operation_0452, edam:operation_3185 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CORGi" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zstephens/CORGi" ; biotools:primaryContact "J. P. Kocher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "COSS (CompOmics Spectral Searching ) is a user-friendly spectral library search tool capable of processing large spectral libraries and supporting multiple file formats." ; sc:featureList edam:operation_3637, edam:operation_3649, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "COSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/compomics/COSS" ; biotools:primaryContact "Computational Omics and Systems Biology Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_0203, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC6934141", "pubmed:31800035" ; sc: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 !""" ; sc:featureList edam:operation_0284, edam:operation_0285, edam:operation_0335, edam:operation_2962, edam:operation_3435 ; sc:name "Codon Usage Similarity Index (COUSIN)" ; sc:url "http://cousin.ird.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , , "pmcid:PMC7198273", "pubmed:32132097" ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3891 ; sc:name "COXMEG" ; sc:url "https://CRAN.R-project.org/package=coxmeg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6602467", "pubmed:31066451" ; sc:description "Integrated plastome sequence annotator and analyzer." ; sc:featureList edam:operation_0464, edam:operation_0484, edam:operation_0526 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CPGAVAS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.herbalgenomics.org/cpgavas2" ; biotools:primaryContact "Chang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305 ; sc:citation , "pmcid:PMC6469151", "pubmed:30991962" ; sc:description "R package for p-value adjustment when looking for an optimal transformation of a single explanatory variable in generalized linear models." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CPMCGLM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "https://cran.r-project.org/package=CPMCGLM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3343, edam:topic_3892 ; sc:citation , "pubmed:31580670" ; sc: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""" ; sc:license "LGPL-3.0" ; sc:name "CPPE" ; sc:url "https://github.com/maxscheurer/CPPE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_2640, edam:topic_3168, edam:topic_3360, edam:topic_3577 ; sc:author , ; sc:citation , "pubmed:34310709" ; sc:contributor ; sc: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." ; sc:featureList edam:operation_0331, edam:operation_3225, edam:operation_3226, edam:operation_3661, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cancer Predisposition Sequencing Reporter (CPSR)" ; sc:softwareHelp , , , , ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/sigven/cpsr" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3300, edam:topic_3810, edam:topic_3855 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_2426, edam:operation_3454, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "CPlantBox" ; sc:url "https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3173 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0524, edam:operation_3198, edam:operation_3472 ; sc:name "CQF-deNoise" ; sc:url "https://github.com/Christina-hshi/CQF-deNoise" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0219 ; sc:citation , "pubmed:31725864" ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_3280, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "CRAFT" ; sc:url "https://github.com/UCDenver-ccp/CRAFT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640 ; sc:citation , "pmcid:PMC6617887", "pubmed:31288758" ; sc:description "Software package for conditional robustness analysis of cancer systems biology models in MATLAB." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "CRA toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gitlab.ict4life.com/SysBiOThe/CRA-Matlab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3500 ; sc:description "CRB-Anim is the online catalog of biological resources of the french national infrastructure supporting research on domestic animals." ; sc:name "CRB-Anim" ; sc:url "https://www.crb-anim.fr/crb-anim_eng/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2259, edam:topic_2269, edam:topic_2640 ; sc:citation ; sc:description "Conditional Robust Calibration (CRC) - Bayesian method for nonlinear model calibration and robustness analysis using omics data." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/fortunatobianconi/CRC" ; biotools:primaryContact "Fortunato Bianconi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3360 ; sc:citation ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRCRpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/crcrpred" ; biotools:primaryContact "Gajendra P. S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:31432077" ; sc: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" ; sc:featureList edam:operation_0478 ; sc:name "Consensus Reverse Docking System (CRDS)" ; sc:url "http://pbil.kaist.ac.kr/CRDS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6771399", "pubmed:31533978" ; sc: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" ; sc:featureList edam:operation_0441, edam:operation_3432, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "CREAM" ; sc:url "https://cran.r-project.org/web/packages/CREAM/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0736 ; sc:citation , "pmcid:PMC6513158", "pubmed:30295745" ; sc:description "cath-resolve-hits (CRH)- tool that resolves domain matches suspiciously quickly." ; sc:featureList edam:operation_0303, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CRH" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/UCLOrengoGroup/cath-tools" ; biotools:primaryContact "Ian Sillitoe", "Tony E Lewis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0749 ; sc:citation ; sc:description "Design tool for CRISPR-mediated gene editing, repression and activation." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRISPR-ERA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://crispr-era.stanford.edu/" ; biotools:primaryContact "Honglei Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description "Improved CRISPR/Cas9 tool for genome editing in plants" ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRISPR-P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://crispr.hzau.edu.cn/CRISPR2/" ; biotools:primaryContact "Kabin Xie", "Ling-Ling Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Suite of web applications for analysing Clustered Regularly Interspaced Short Palindromic Repeats." ; sc:name "CRISPRCas" ; sc:url "https://crisprcas.i2bc.paris-saclay.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0798 ; sc:citation , "pmcid:PMC6030898", "pubmed:29790974" ; sc: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." ; sc:featureList edam:operation_3211 ; sc:name "CRISPRCasFinder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.5 - I2BC" ; sc:url "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index" ; biotools:primaryContact "Christine Pourcel", "David Couvin", "Marie Touchon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3512, edam:topic_3912 ; sc:author "Kenian Chen" ; sc:citation , "pmcid:PMC6706119", "pubmed:31453219" ; sc: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" ; sc:featureList edam:operation_3096 ; sc:name "CRISPR Explorer" ; sc:url "http://crisprexplorer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation , "pmcid:PMC4382898", "pubmed:25414360" ; sc:description "Software for designing CRISPR/Cas guide RNA with reduced off-target sites." ; sc:featureList edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CRISPRdirect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://crispr.dbcls.jp/" ; biotools:primaryContact "Yuki Naito" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3512, edam:topic_3676, edam:topic_3912 ; sc:citation , "pubmed:31764961" ; sc: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.""" ; sc:featureList edam:operation_3096, edam:operation_3211, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "CRISPRitz" ; sc:url "https://github.com/pinellolab/CRISPRitz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC1892036", "pubmed:17521438" ; sc:description "Gateway to publicly accessible CRISPRs database." ; sc:name "CRISPRs Database" ; sc:url "http://crispr.i2bc.paris-saclay.fr/crispr/" ; biotools:primaryContact "Christine Pourcel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3383, edam:topic_3452 ; sc:citation , "pubmed:31617571" ; sc:description "A novel constrained reconstruction model towards high-resolution sub-tomogram averaging." ; sc:name "CRM-SIRT" ; sc:url "https://github.com/icthrm/CRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0659, edam:topic_3512 ; sc:citation ; sc:description "Web server for predicting the in vivo structure of RNA molecules." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CROSSalive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://service.tartaglialab.com/new_submission/crossalive" ; biotools:primaryContact "Gian Tartaglia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC6709893", "pubmed:31449539" ; sc: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" ; sc:featureList edam:operation_0335, edam:operation_3196 ; sc:name "CRUMBLER" ; sc:url "https://github.com/tamarcrum/CRUMBLER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0634, edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC6839171", "pubmed:31699133" ; sc: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.""" ; sc:featureList edam:operation_0438, edam:operation_3439, edam:operation_3463 ; sc:name "CRUP" ; sc:url "https://github.com/VerenaHeinrich/CRUP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3314 ; sc:citation , "pubmed:31077416" ; sc:description "Visualization environment for plotting properties of crystalline solids as computed by means of the CRYSTAL code." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRYSPLOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://crysplot.crystalsolutions.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0659 ; sc:citation , "pmcid:PMC6542128", "pubmed:31142266" ; sc:description "Pairwise visual comparison of small RNA secondary structures with base pair probabilities." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CS2BP2-Plot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nrcmonsrv01.nrc.ca/cs2bp2plot" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154, edam:topic_0593 ; sc:citation , "pubmed:31829591" ; sc:description "C2Structure: Extracting Structural Information Directly From NMR Chemical Shifts. Conditional Prediction of Ribonucleic Acid Secondary Structure Using Chemical Shifts." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0303, edam:operation_2441 ; sc:license "MIT" ; sc:name "CS2Structure" ; sc:url "https://github.com/atfrank/CS2Structure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0804, edam:topic_3673 ; sc:citation , "pmcid:PMC6486994", "pubmed:31029079" ; sc:description "R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR." ; sc:featureList edam:operation_0308, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CSESA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0" ; sc:url "https://cran.r-project.org/package=CSESA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3360, edam:topic_3520 ; sc:citation , "pubmed:31432427" ; sc: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" ; sc:featureList edam:operation_0306, edam:operation_3799 ; sc:name "CSF-PR" ; sc:url "https://proteomics.uib.no/csf-pr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6853676", "pubmed:31038684" ; sc:description "Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data." ; sc:featureList edam:operation_3501, edam:operation_3565, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CSHMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.andrew.cmu.edu/user/chiehl1/CSHMM/" ; biotools:primaryContact "Ziv Bar-Joseph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3063, edam:topic_3168, edam:topic_3263, edam:topic_3794 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3096, edam:operation_3222, edam:operation_3799 ; sc:name "CSI NGS Portal" ; sc:url "https://csibioinfo.nus.edu.sg/csingsportal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_0769, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31626280" ; sc: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""" ; sc:featureList edam:operation_3198, edam:operation_3454, edam:operation_3460 ; sc:name "Computation Subtraction-based Microbiome Discovery (CSMD)" ; sc:url "https://github.com/liuyu8721/csmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3318, edam:topic_3382, edam:topic_3474 ; sc:citation , , "pmcid:PMC7174840", "pubmed:32094267" ; sc: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""" ; sc:featureList edam:operation_3659, edam:operation_3799, edam:operation_3891 ; sc:license "MIT" ; sc:name "Cell Topography Regression Learner (CTRL)" ; sc:url "https://GitHub.com/sxslabjhu/CTRL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3360, edam:topic_3517 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:name "CVRMS" ; sc:url "https://github.com/gtayana/CVRMS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769 ; sc:author "Felix Xavier Amaladoss" ; sc:description "CWL VM environment is a repository which can be deployed on cloud to execute Biobb Mutations Workflow." ; sc:isAccessibleForFree true ; sc:name "Biobb Mutations Workflow" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/EMBL-EBI-TSI/cpa-bioexcel-cwl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3395 ; sc:citation , "pmcid:PMC6933651", "pubmed:31881827" ; sc: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""" ; sc:featureList edam:operation_2238, edam:operation_3432, edam:operation_3565 ; sc:name "CYBERTRACK" ; sc:url "https://github.com/kodaim1115/CYBERTRACK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3320, edam:topic_3382, edam:topic_3676 ; sc:citation , "pubmed:31674704" ; sc: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""" ; sc:featureList edam:operation_0331, edam:operation_3197, edam:operation_3461 ; sc:name "CYSMA" ; sc:url "https://cftr.iurc.montp.inserm.fr/cysma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0209, edam:topic_0804 ; sc:citation , "pubmed:27153651" ; sc:description "CaFE (Calculation of Free Energy) - a VMD plugin for binding affinity prediction using end-point free energy methods." ; sc:featureList edam:operation_0478, edam:operation_2476, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CaFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/huiliucode/cafe_plugin" ; biotools:primaryContact "Tingjun Hou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3298, edam:topic_3384, edam:topic_3421, edam:topic_3444 ; sc:citation , "pmcid:PMC6216519", "pmcid:PMC7113126", "pubmed:32191542" ; sc: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""" ; sc:featureList edam:operation_3443, edam:operation_3659, edam:operation_3799 ; sc:name "CaPTk" ; sc:url "http://www.cbica.upenn.edu/captk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068 ; sc:citation , "pmcid:PMC6129310", "pubmed:29668830" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CaSiAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://r3lab.uni.lu/web/casa" ; biotools:primaryContact "Alexander Skupin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3489 ; sc:citation , "pubmed:26224250" ; sc:description "General‐purpose software for making genotype–phenotype data discoverable in restricted or open access contexts." ; sc:featureList edam:operation_0224, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "Cafe Variome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cafevariome.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6548890", "pubmed:31103852" ; sc:description "Early Cancer Detection from Multianalyte Blood Test Results using Artificial Intelligence" ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CancerA1DE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://cancer.cs.cityu.edu.hk/" ; biotools:primaryContact "Ka-Chun Wong" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3242 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602 ; sc:author "Elisa Micarelli", "Prisca Lo SUrdo" ; sc:citation , "pmcid:PMC6943052", "pubmed:31598703" ; sc:contributor "Marta Iannuccelli" ; sc: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\"." ; sc:featureList edam:operation_2497 ; sc:isAccessibleForFree true ; sc:name "CancerGeneNet" ; sc:provider "Gianni Cesareni" ; sc:url "https://signor.uniroma2.it/CancerGeneNet/" ; biotools:primaryContact "Luana Licata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3173, edam:topic_3375 ; sc:citation , "pmcid:PMC6730898", "pubmed:31490960" ; sc: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" ; sc:featureList edam:operation_0417, edam:operation_3206, edam:operation_3207 ; sc:name "CancerLSP" ; sc:url "http://webs.iiitd.edu.in/raghava/cancerlsp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:31110280" ; sc:description "Literature-mined resource for drivers, oncogenes and tumor suppressors in cancer." ; sc:featureList edam:operation_0306, edam:operation_3431, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CancerMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bionlp.bcgsc.ca/cancermine/" ; biotools:primaryContact "Jake Lever" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6823463", "pubmed:31673075" ; sc: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""" ; sc:featureList edam:operation_0417, edam:operation_0463, edam:operation_3792, edam:operation_3800 ; sc:name "CancerSPP" ; sc:url "http://webs.iiitd.edu.in/raghava/cancerspp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0219, edam:topic_2640, edam:topic_3293, edam:topic_3360 ; sc:citation , "pubmed:31701131" ; sc: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""" ; sc:featureList edam:operation_0323, edam:operation_0531, edam:operation_2436 ; sc:name "CancerTracer" ; sc:url "http://cailab.labshare.cn/cancertracer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3307 ; sc: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." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CandiMeth" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bit.do/candimeth-github" ; biotools:primaryContact "Colum Walsh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0593, edam:topic_3292, edam:topic_3343 ; sc:citation ; sc:description "A Crowd-Sourced, Natural Product Screening Library for Exploring Biological Space." ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3802 ; sc:name "Canvass" ; sc:url "https://tripod.nih.gov/canvass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0634, edam:topic_0654 ; sc:citation , "pmcid:PMC6956725", "pubmed:31840950" ; sc: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""" ; sc:name "CaptureProbe" ; sc:url "https://sourceforge.net/projects/captureprobe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3300, edam:topic_3375, edam:topic_3377 ; sc:citation , "pubmed:31606584" ; sc: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’)""" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "CardiacPBPK" ; sc:url "https://github.com/jszlek/CardiacPBPK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3318, edam:topic_3335 ; sc:citation , "pmcid:PMC6381356", "pubmed:30666509" ; sc:description "R package for extraction and visualisation of heart rate profiles from wearable fitness trackers." ; sc:featureList edam:operation_0337, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CardiacProfileR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/VCCRI/CardiacProfileR" ; biotools:primaryContact "Victor Chang Cardiac Research Institute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3444 ; sc:citation , "pubmed:31076923" ; sc:description "Platform for noninvasive assessment of pulse transit time and pulsatile flow in hyperelastic vascular networks." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CardioFAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YasharVahedein/CardioFAN" ; biotools:primaryContact "Yashar Seyed Vahedein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3303 ; sc:citation ; sc:description "Online tool for assessing genome editing results using NGS data." ; sc:featureList edam:operation_0420, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Cas-analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rgenome.net/cas-analyzer/" ; biotools:primaryContact "Jin-Soo Kim", "Sangsu Bae" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0780, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0450, edam:operation_3192, edam:operation_3200, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "Cascabel" ; sc:url "https://github.com/AlejandroAb/CASCABEL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0749, edam:topic_2229 ; sc:citation , , "pmcid:PMC7155257", "pubmed:32290857" ; sc: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""" ; sc:featureList edam:operation_0326, edam:operation_3478, edam:operation_3745 ; sc:license "MIT" ; sc:name "Cassiopeia" ; sc:url "http://www.github.com/YosefLab/Cassiopeia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3332 ; sc:citation , "pmcid:PMC6538711", "pubmed:31138816" ; sc:description "Web-platform for sharing data and software for computational catalysis research." ; sc:featureList edam:operation_0384, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Catalysis Hub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.catalysis-hub.org" ; biotools:primaryContact "Kirsten Winther", "Thomas Bligaard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3407, edam:topic_3577 ; sc:citation , , "pmcid:PMC4359046", "pubmed:25780776" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:license "MIT" ; sc:name "CauseMap" ; sc:url "http://cyrusmaher.github.io/CauseMap.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3399 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2942, edam:operation_3463, edam:operation_3501 ; sc:name "CellAge" ; sc:url "https://genomics.senescence.info/cells/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2830, edam:topic_3170 ; sc:citation , "pubmed:31501550" ; sc: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" ; sc:featureList edam:operation_3431, edam:operation_3501, edam:operation_3891 ; sc:name "CellAssign" ; sc:url "https://github.com/irrationone/cellassign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3170 ; sc:citation , "pmcid:PMC7141847", "pubmed:31778143" ; sc: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""" ; sc:featureList edam:operation_0244, edam:operation_3557, edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "CellBench" ; sc:url "https://bioconductor.org/packages/CellBench" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "CellBender" ; sc:softwareHelp ; sc:url "https://github.com/broadinstitute/CellBender" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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." ; sc:name "CellBin" ; sc:url "https://github.com/STOmics/CellBin/tree/dev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3292, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3552 ; sc:license "MIT" ; sc:name "CellCountCV" ; sc:url "http://cellcounter.nprog.ru/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_3170, edam:topic_3360 ; sc:citation , , , "pmcid:PMC10330642", "pmcid:PMC6615556", "pmcid:PMC6889472", "pubmed:31113817", "pubmed:31733513", "pubmed:37140427" ; sc:description "Web application for exploration and analysis of cancer cell line pharmacogenomic data across different sources." ; sc:featureList edam:operation_0264, edam:operation_3501, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CellMinerCDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://discover.nci.nih.gov/cellminercdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3518 ; sc:citation , ; sc:description "Tool for quantifying data from biological images, particularly in high-throughput experiments." ; sc:featureList edam:operation_1812, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "CellProfiler" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cellprofiler.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3395 ; sc:citation , "pmcid:PMC6399906", "pubmed:30832570" ; sc:description "A software aims to calculate the similarity among different cells and predict their co-regulation networks." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CellSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "http://www.cellsim.nwsuaflmz.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2229, edam:topic_3474 ; sc:citation ; sc:description "Support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort." ; sc:featureList edam:operation_3501, edam:operation_3660, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CellSort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tyolab.northwestern.edu/tools/" ; biotools:primaryContact "Keith E. J. Tyo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6509836", "pubmed:31072405" ; sc:description "Genetic barcode-based sample multiplexing for single-cell genomics." ; sc:featureList edam:operation_1812, edam:operation_3200, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CellTag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/morris-lab/CellTag-Classifier" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229, edam:topic_3306 ; sc:citation , "pmcid:PMC6481718", "pubmed:31069304" ; sc:description "Platform for interactive, 3D graphical simulation of immunological processes." ; sc:featureList edam:operation_0337, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Cell Studio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cellstudio.info" ; biotools:primaryContact "Uri Nevo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC6558561", "pubmed:31104596" ; sc:description "Probabilistic census-travel model to predict introduction sites of exotic plant, animal and human pathogens." ; sc:featureList edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Census Travel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://epi-models.shinyapps.io/Census_Travel/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Software for interactive visualization of scRNA-seq data." ; sc:featureList edam:operation_1812, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cerebro" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/romanhaa/Cerebro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3444, edam:topic_3473 ; sc:citation , , "pubmed:32305449" ; sc: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." ; sc:featureList edam:operation_0303, edam:operation_3357 ; sc:license "GPL-3.0" ; sc:name "Cgrid" ; sc:url "https://github.com/mathijsraemaekers/Cgrid-toolbox" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_3006 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3173 ; sc:citation , , "pmcid:PMC5079470", "pubmed:27378294" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2451, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "ChAsE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1.2" ; sc:url "https://github.com/hyounesy/ChAsE/" ; biotools:primaryContact "Hamid Younesy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6602523", "pubmed:31114921" ; sc:description "Transcription factor enrichment analysis by orthogonal omics integration." ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ChEA3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://amp.pharm.mssm.edu/ChEA3" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3169, edam:topic_3179 ; sc:citation ; sc:description "Computational package to process the next-generation sequence data generated from ChIA-PET experiments." ; sc:featureList edam:operation_0443, edam:operation_3222, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ChIA-PET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3/" ; biotools:primaryContact "Guoliang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3534 ; sc:citation ; sc:description "ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them." ; sc:featureList edam:operation_0445, edam:operation_2464, edam:operation_3903 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ChIPSummitDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://summit.med.unideb.hu/summitdb/" ; biotools:primaryContact "Endre Barta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation ; sc: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:" ; sc:featureList edam:operation_3192, edam:operation_3222, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "ChIPdig" ; sc:url "https://github.com/rmesse/ChIPdig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC7523640", "pubmed:31566663" ; sc: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" ; sc:featureList edam:operation_3222, edam:operation_3501, edam:operation_3798 ; sc:license "Apache-2.0" ; sc:name "ChIPseqSpikeInFree" ; sc:url "https://pecan.stjude.cloud/permalink/spikefree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC6445533", "pubmed:30897079" ; sc:description "A Python3 framework to simulate read counts in a ChIP-seq experiment." ; sc:featureList edam:operation_0308, edam:operation_0445, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ChIPulate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/vishakad/chipulate" ; biotools:primaryContact "Vishaka Datta S" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pmcid:PMC6980795", "pubmed:31586868" ; sc: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.""" ; sc:featureList edam:operation_2426, edam:operation_3799 ; sc:name "ChaRTr" ; sc:url "https://github.com/mailchand/CHaRTr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749 ; sc:citation , "pubmed:31504177" ; sc: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" ; sc:featureList edam:operation_2492, edam:operation_3799 ; sc:name "ChaperISM" ; sc:url "https://github.com/BioinfLab/ChaperISM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:31430151" ; sc: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!" ; sc:featureList edam:operation_3216, edam:operation_3436 ; sc:name "ChemAGG" ; sc:url "http://admet.scbdd.com/ChemAGG/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_2258, edam:topic_3316, edam:topic_3489 ; sc:citation , "pmcid:PMC6895184", "pubmed:31804487" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0399 ; sc:license "MIT" ; sc:name "ChemDataExtractor" ; sc:softwareHelp ; sc:url "http://chemdataextractor.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC7412753", "pubmed:32831287" ; sc: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.""" ; sc:name "ChemEnv" ; sc:url "https://doi.org/10.26434/CHEMRXIV.11294480.V1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3314 ; sc:citation , "pubmed:31514773" ; sc: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." ; sc:license "MIT" ; sc:name "ChemPager" ; sc:url "https://www.ingentaconnect.com/content/scs/chimia/2019/00000073/00000009/art00007/supp-data/content-2019_73_9_724" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3474 ; sc:citation , "pubmed:30637953" ; sc:description "Package for chemoinformatics calculations and machine learning." ; sc:featureList edam:operation_2945, edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ChemSuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://14.139.57.41/chemsuiteweb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3173 ; sc:citation , "pmcid:PMC6532271", "pubmed:31118054" ; sc:description "Pipeline for analyzing and identificantion of chromation loops in CHi-C promoters data." ; sc:featureList edam:operation_0337, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ChiCMaxima" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yousra291987/ChiCMaxima" ; biotools:primaryContact "T. Sexton", "Y. Ben Zouari" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3070, edam:topic_3361 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3891 ; sc:name "Chi.Bio" ; sc:url "https://chi.bio" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "A mine with chickpea data (both desi and kabuli varieties) from the Legume Information Systems (LIS) tripal.chado database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "ChickpeaMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/chickpeamine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3500, edam:topic_3810 ; sc:citation , "pmcid:PMC6556980", "pubmed:31210271" ; sc:description "Chickspress Genome Browser." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Chickspress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://geneatlas.arl.arizona.edu/" ; biotools:primaryContact "Eric H Lyons", "Fiona M McCarthy", "Shane C Burgess" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3489, edam:topic_3500 ; sc:citation , ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3891 ; sc:name "Chipper" ; sc:url "https://github.com/asearfos/chipper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0797, edam:topic_3293, edam:topic_3489 ; sc:citation , "pmcid:PMC7145651", "pubmed:31665454" ; sc: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""" ; sc:featureList edam:operation_0303, edam:operation_2421, edam:operation_2422 ; sc:name "ChlamDB" ; sc:softwareHelp ; sc:url "https://chlamdb.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_3697 ; sc:citation , "pubmed:31539022" ; sc: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!" ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:license "MIT" ; sc:name "Chordomics" ; sc:url "https://kmcd.shinyapps.io/chordomics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6612838", "pubmed:31510655" ; sc: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" ; sc:featureList edam:operation_0441, edam:operation_3192, edam:operation_3439 ; sc:license "MIT" ; sc:name "ChromDragoNN" ; sc:url "https://github.com/kundajelab/ChromDragoNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_2815, edam:topic_3293 ; sc:citation , "pmcid:PMC6792252", "pubmed:31615393" ; sc: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""" ; sc:featureList edam:operation_0558, edam:operation_0564, edam:operation_0567 ; sc:license "Apache-2.0" ; sc:name "ChromaClade" ; sc:url "http://github.com/chrismonit/chroma_clade" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0798, edam:topic_3382 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0496, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "Chromatiblock" ; sc:url "https://github.com/mjsull/chromatiblock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3336 ; sc:citation , "pmcid:PMC4341901", "pubmed:25349306" ; sc: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." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CiDD" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://cidd.scheetlabsoftware.org/" ; biotools:primaryContact "Paul Scheet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3308 ; sc:citation , "pmcid:PMC6726224", "pubmed:31483836" ; sc: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" ; sc:featureList edam:operation_0420, edam:operation_0445, edam:operation_2464 ; sc:name "CiiiDER" ; sc:url "http://www.ciiider.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_3676 ; sc:citation , "pmcid:PMC6522010", "pubmed:31095607" ; sc:description "An integrated and validated compendium of ciliary genes." ; sc:featureList edam:operation_3501, edam:operation_3629, edam:operation_3638 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CiliaCarta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/" ; biotools:primaryContact , "Martijn A. Huynen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3505 ; sc:encodingFormat edam:format_2330 ; sc:name "Bibliography" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1087 ; sc:encodingFormat edam:format_2196 ; sc:name "Ontology concept ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_3064 ; sc:citation , ; sc:description "The first ontology describing the anatomy and the development of Ciona robusta, based on the Hotta developmental table." ; sc:featureList edam:operation_0226, edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Ciona robusta Anatomy and Development Ontology" ; sc:url "https://www.aniseed.fr/aniseed/anatomy/find_devstage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0092, edam:topic_0203 ; sc:citation , "pmcid:PMC6380029", "pubmed:30777018" ; sc:description "Visualises non-redundant two-level hierarchically structured ontology terms from gene expression data in a 2D space." ; sc:featureList edam:operation_0570, edam:operation_2942, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Circular Gene Ontology (CirGO)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/IrinaVKuznetsova/CirGO.git" ; biotools:primaryContact "Artur Lugmayr", "Irina Kuznetsova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_0749, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC6795751", "pubmed:31649739" ; sc: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""" ; sc:featureList edam:operation_0436, edam:operation_0570, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "CircCode" ; sc:url "https://github.com/PSSUN/CircCode" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3512 ; sc:author "Dahui Hu", "Ming Chen", "Xianwen Meng" ; sc:citation , "pmcid:PMC6360206", "pubmed:30715276" ; sc:description "Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions." ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "CircFunBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bis.zju.edu.cn/CircFunBase/" ; biotools:primaryContact "Ming Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:29028266" ; sc:description "Integrated tool for the identification of circRNAs with protein-coding potential." ; sc:featureList edam:operation_0436, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CircPro" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bis.zju.edu.cn/CircPro/" ; biotools:primaryContact "Ming Chen", "Xianwen Meng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC6709551", "pubmed:31446897" ; sc: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" ; sc:featureList edam:operation_0441, edam:operation_0443, edam:operation_2495 ; sc:name "CircRiC" ; sc:url "https://hanlab.uth.edu/cRic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3070 ; sc:citation , "pubmed:31588519" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3659 ; sc:name "CircaCompare" ; sc:url "https://github.com/RWParsons/circacompare/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC6909605", "pubmed:31830908" ; sc: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.""" ; sc:featureList edam:operation_3198, edam:operation_3227, edam:operation_3435 ; sc:license "MIT" ; sc:name "Circle-Map" ; sc:url "https://github.com/iprada/Circle-Map" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6602521", "pubmed:31053864" ; sc:description "Web server for functional enrichment analysis of transcription factor ChIP-seq peaks." ; sc:featureList edam:operation_3222, edam:operation_3223, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Cistrome-GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://go.cistrome.org/" ; biotools:primaryContact "Clifford A Meyer", "X Shirley Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , , "pubmed:32353146" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3799 ; sc:name "CiteFuse" ; sc:url "http://SydneyBioX.github.io/CiteFuse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3293 ; sc:citation , "pmcid:PMC6396423", "pubmed:30718334" ; sc: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." ; sc:featureList edam:operation_0533, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "CladePP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dolevrahat/CladePP" ; biotools:primaryContact "D. Rahat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3047, edam:topic_3295, edam:topic_3474 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0525, edam:operation_3196, edam:operation_3227 ; sc:license "BSD-3-Clause" ; sc:name "Clair" ; sc:url "https://github.com/HKU-BAL/Clair" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description "Field-scouting software for the identification of wildlife in camera trap images." ; sc:featureList edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ClassifyMe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://classifymeapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0637, edam:topic_2258, edam:topic_3314 ; sc:citation , "pubmed:31576380" ; sc: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." ; sc:featureList edam:operation_2422, edam:operation_2996, edam:operation_3359 ; sc:name "ClassyFire" ; sc:url "http://classyfire.wishartlab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3517 ; sc:citation , "pmcid:PMC6595587", "pubmed:31391866" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:name "ClickGene" ; sc:softwareHelp ; sc:url "http://www.clickgenome.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3518, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0452, edam:operation_3227, edam:operation_3435 ; sc:license "MIT" ; sc:name "ClinCNV" ; sc:url "https://github.com/imgag/ClinCNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3305, edam:topic_3324, edam:topic_3382 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3431 ; sc:license "GPL-2.0" ; sc:name "ClinEpiDB" ; sc:url "https://clinepidb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3400 ; sc:description "Visual analytics tool for breast cancer treatment stratification." ; sc:featureList edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ClinOmicsTrail" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://clinomicstrail.bioinf.uni-sb.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3400 ; sc:citation , "pmcid:PMC6954665", "pubmed:31038669" ; sc:description "Visual analytics tool for breast cancer treatment stratification." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ClinOmicsTrailbc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://clinomicstrail.bioinf.uni-sb.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC6174354", "pubmed:30220433" ; sc:description "Efficient tool for identifying disease-relevant nonsynonymous single nucleotide variants." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3461 ; sc:name "ClinPred" ; sc:url "https://sites.google.com/site/clinpred/" ; biotools:primaryContact "Jacek Majewski", "Najmeh Alirezaie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0749 ; sc:citation , "pubmed:30765865" ; sc:description "Quick evaluation of the clinical relevance of copy number variants (CNVs) in the context of topologically associated domains (TADs)." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "ClinTAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.clintad.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0769, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC7141851", "pubmed:31830259" ; sc: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." ; sc:featureList edam:operation_0310, edam:operation_0331, edam:operation_0337, edam:operation_3226, edam:operation_3227 ; sc:license "MIT" ; sc:name "ClinVAP" ; sc:url "https://github.com/PersonalizedOncology/ClinVAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC6792096", "pubmed:30903689" ; sc:description "Computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network." ; sc:featureList edam:operation_3798, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CliqueMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.3.2" ; sc:url "https://github.com/osenan/cliqueMS" ; biotools:primaryContact "Oriol Senan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3794 ; sc:citation , , "pmcid:PMC7016857", "pubmed:31947823" ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3198 ; sc:name "Clirc" ; sc:url "https://github.com/Minzhe/Clirc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_3168 ; sc:citation , , "pmcid:PMC6936074", "pubmed:31888455" ; sc:description """Clonal reconstruction from time course genomic sequencing data. ClonalTREE (Clonal reconstruction in Time couRse long-term Evolution Experiment). Usage: python3 ClonalTREE.py """ ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3226 ; sc:license "GPL-3.0" ; sc:name "ClonalTREE" ; sc:url "https://github.com/COL-IU/ClonalTREE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:30649189" ; sc:description "R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics." ; sc:featureList edam:operation_0337, edam:operation_3627, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CluMSID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tdepke/CluMSID/" ; biotools:primaryContact "Tobias Depke" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293 ; sc:citation , "pubmed:17846036" ; sc:description "Create Neighbor-joining or UPGMA phylogentic trees from a multiple sequence alignment using ClustalW." ; sc:featureList edam:operation_0323 ; sc:name "ClustalW2 Phylogeny API EBI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/seqdb/confluence/pages/viewpage.action?pageId=54651945" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC7148287", "pubmed:31089956" ; sc:description "R package for the analysis of hierarchical data using generalized linear models with the cluster bootstrap." ; sc:featureList edam:operation_0552, edam:operation_3432, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ClusterBootstrap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://cran.r-project.org/package=ClusterBootstrap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3305, edam:topic_3512, edam:topic_3676 ; sc:citation , , "pmcid:PMC8327322", "pubmed:32732227" ; sc: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""" ; sc:featureList edam:operation_2454, edam:operation_3225, edam:operation_3461, edam:operation_3791 ; sc:name "ClusterBurden" ; sc:url "https://github.com/adamwaring/ClusterBurden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:citation , "pubmed:29912285" ; sc: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)." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ClusterScan" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , ; sc:url "https://github.com/pyrevo/ClusterScan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pubmed:28187414" ; sc: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." ; sc:name "CmPIweb" ; sc:url "http://CmPIweb.CELLmicrocosmos.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Script" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_2259, edam:topic_3070 ; sc:citation , "pubmed:31359031" ; sc: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." ; sc:featureList edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoBAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.1.4" ; sc:url "https://github.com/BioSystemsUM/cobamp" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6901076", "pubmed:31141144" ; sc:description "Count Corrector for nested genes and multi-mapped reads." ; sc:featureList edam:operation_3563, edam:operation_3798, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3336, edam:topic_3379 ; sc:citation , "pmcid:PMC6637175", "pubmed:31360332" ; sc: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" ; sc:name "CoDReS" ; sc:url "http://bioinformatics.cing.ac.cy/codres" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_1963 ; sc:name "Gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1963 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_0128, edam:topic_2269, edam:topic_3520 ; sc:citation , "pmcid:PMC6327379", "pubmed:30626316" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0276, edam:operation_0531, edam:operation_0571, edam:operation_2238, edam:operation_2495, edam:operation_2935, edam:operation_3083, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CoExpresso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://computproteomics.bmb.sdu.dk/Apps/CoExpresso/" ; biotools:primaryContact "Veit Schwämmle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3517 ; sc:citation ; sc:description "Collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information." ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoMM-S" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gordonliu810822/CoMM" ; biotools:primaryContact "Jin Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0524, edam:operation_2495, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoMW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/anwarMZ/CoMW" ; biotools:primaryContact "Carsten Suhr Jacobsen", "Muhammad Zohaib Anwar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407 ; sc:author "Alexandra Zaharia" ; sc:citation , "pmcid:PMC6327494", "pubmed:30630411" ; sc:description "CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods) - exploration tool for conserved organizational motifs at both the metabolic and genomic level." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CoMetGeNe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cometgene.lri.fr" ; biotools:primaryContact "Alexandra Zaharia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0780 ; sc:citation , , "pubmed:31988262" ; sc: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" ; sc:featureList edam:operation_0313, edam:operation_3463, edam:operation_3766 ; sc:name "CoNekT-Plants" ; sc:url "http://conekt.plant.tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3520 ; sc:author "Marzieh Ayati", "Mehmet Koyuturk" ; sc:citation , "pmcid:PMC6411229", "pubmed:30811403" ; sc:description "Method for Co-phosphorylation-based Kinase-substrate interaction prediction (CophosK)." ; sc:featureList edam:operation_0417, edam:operation_3501, edam:operation_3639 ; sc:isAccessibleForFree true ; sc:name "CoPhosK" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://compbio.case.edu/omics/software/cophosk/index.html" ; biotools:primaryContact "Mark R. Chance", "Marzieh Ayati" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3957 ; sc:citation , , "pmcid:PMC7356028", "pubmed:32580303" ; sc: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" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_2492 ; sc:name "CoRNeA" ; sc:url "https://github.com/krits04/cornea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3520 ; sc:citation , "pmcid:PMC6958516", "pubmed:31042389" ; sc:description "Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry." ; sc:featureList edam:operation_0244 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoSIMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/ChristopherAMyers/CoSIMS" ; biotools:primaryContact "Alan A. Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3308, edam:topic_3810 ; sc:citation , , "pmcid:PMC5603072", "pubmed:21186351", "pubmed:28915793" ; sc:contributor ; sc:description "The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources." ; sc:featureList edam:operation_0292, edam:operation_3184, edam:operation_3559 ; sc:funder "ANR" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Cocoa Genome Hub" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://cocoa-genome-hub.southgreen.fr/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0780, edam:topic_3168, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0278, edam:operation_0436, edam:operation_0524, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "CodAn" ; sc:url "https://github.com/pedronachtigall/CodAn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2885 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0282, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CodataGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/CodataGS/index.html" ; biotools:primaryContact "E. F. Mouresan", "Lars Ronnegard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0780 ; sc:description "Coding Sequence optimization for Chlamydomonas reinhardtii" ; sc:isAccessibleForFree true ; sc:name "Coding Sequence Optimization for Chlamydomonas reinhardtii" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/65416-iddoweiner-coding-sequence-optimization-for-chlamydomonas-reinhardtii" ; biotools:primaryContact "Iddo Weiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_3512 ; sc:citation , "pubmed:23466472" ; sc: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." ; sc:name "Codonome" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://apollo11.isto.unibo.it/software/Codonome/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0780 ; sc:author "Alexis Dereeper", "Gaetan Droc" ; sc:citation , , "pmcid:PMC4383925", "pubmed:25190796", "pubmed:25392413" ; sc: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." ; sc:featureList edam:operation_0361, edam:operation_0564 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Coffee Genome Hub" ; sc:softwareHelp ; sc:url "https://coffee-genome-hub.southgreen.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0623 ; sc:citation , , "pmcid:PMC7200068", "pubmed:32100706" ; sc: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""" ; sc:featureList edam:operation_2238, edam:operation_2422, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "Coinfinder" ; sc:url "https://github.com/fwhelan/coinfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316, edam:topic_3382 ; sc:citation , "pubmed:31216308" ; sc:description "Python package for the analysis of bacterial fluorescence microscopy data." ; sc:featureList edam:operation_3431, edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ColiCoords" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Jhsmit/ColiCoords" ; biotools:primaryContact "J. H. Smit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3474 ; sc:citation , "pmcid:PMC6538547", "pubmed:31138109" ; sc:description "Collaboration of deep neural networks for biomedical named entity recognition." ; sc:featureList edam:operation_3280, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CollaboNet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/wonjininfo/CollaboNet" ; biotools:primaryContact "Jaewoo Kang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0202, edam:topic_0209 ; sc:citation , "pubmed:28968713" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Collector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://phi.upf.edu/collector/" ; biotools:primaryContact "Manuel Pastor", "Oriol L. Massaguer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3520 ; sc:citation , , "pmcid:PMC7214035", "pubmed:32049317" ; sc: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" ; sc:featureList edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "ColocML" ; sc:url "https://github.com/metaspace2020/coloc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3382 ; sc:citation , "pmcid:PMC6307751", "pubmed:30589908" ; sc:description "Software tool for the quantification of metastatic colony growth dynamics and size distributions in vitro and in vivo." ; sc:featureList edam:operation_3443, edam:operation_3795, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ColonySizeDistributions" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/sbhoyar1/ColonySizeDistributions" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_1781, edam:operation_2454, edam:operation_3439 ; sc:name "ComHub" ; sc:url "https://gitlab.com/Gustafsson-lab/comhub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0780 ; sc:citation , "pmcid:PMC6266932", "pubmed:30497367" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ComParaLogS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "http://biosrv.cab.unina.it/comparalogs/gene/search" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3068, edam:topic_3399 ; sc:citation , "pubmed:30689768" ; sc:description "Tool for interactive analysis of disease comorbidities over large patient datasets." ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Comorbidity4j" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://comorbidity.eu/comorbidity4web/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3372 ; sc:citation , , "pmcid:PMC4845442", "pmcid:PMC6869179", "pubmed:27112575", "pubmed:31747901" ; sc: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""" ; sc:featureList edam:operation_0277, edam:operation_3083 ; sc:name "CompNet" ; sc:url "https://web.rniapps.net/compnet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:31449403" ; sc: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.""" ; sc:featureList edam:operation_0482, edam:operation_3501 ; sc:name "CompScore" ; sc:url "http://bioquimio.udla.edu.ec/compscore/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_2330 ; sc:name "ID list" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_2330 ; sc:name "ID list" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:author ; sc: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." ; sc:featureList edam:operation_2424 ; sc:isAccessibleForFree true ; sc:name "Compare Two Lists" ; sc:url "https://compare.tartaglialab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_3308 ; sc:citation , "pmcid:PMC6547514", "pubmed:31159772" ; sc:description "Differential analysis of combinatorial protein complexes." ; sc:featureList edam:operation_3258, edam:operation_3630, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CompleXChange" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/complexchange/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein interaction data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3508 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508, edam:format_3603 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_0128, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0276, edam:operation_0531, edam:operation_0571, edam:operation_2238, edam:operation_2428, edam:operation_2495, edam:operation_2938, edam:operation_2939, edam:operation_2940, edam:operation_3083, edam:operation_3282, edam:operation_3435, edam:operation_3463, edam:operation_3659, edam:operation_3799 ; sc:name "ComplexBrowser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://computproteomics.bmb.sdu.dk/Apps/ComplexBrowser/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3158 ; sc:name "Protein interaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3464 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation , , "pmcid:PMC4384031", "pmcid:PMC6323931", "pubmed:25313161", "pubmed:30357405" ; sc: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." ; sc:featureList edam:operation_2422, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Complex Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ebi.ac.uk/complexportal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_2885 ; sc:citation , "pmcid:PMC6029450", "pubmed:29625053" ; sc:description "CompositeDriver combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers" ; sc:featureList edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CompositeDriver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "https://github.com/khuranalab/CompositeDriver" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_0798 ; sc:citation , "pmcid:PMC6301336", "pubmed:30576494" ; sc:description "Comprehensive database of transposable elements in conifers." ; sc:featureList edam:operation_0524, edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ConTEdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genedenovoweb.ticp.net:81/conTEdb/index.php" ; biotools:primaryContact "Fangqun Ouyang", "Fei Yi", "Junhui Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC6444814", "pubmed:30935387" ; sc:description "Software for unsupervised discovery of clonal somatic mutations in single cells through read phasing." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Conbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/conbase/conbase" ; biotools:primaryContact "Ezeddin Al Hakim", "Marie Kindblom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc: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" ; sc:license "Apache-2.0" ; sc:name "ConnectedReads" ; sc:url "https://github.com/atgenomix/connectedreads" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0610, edam:topic_3489 ; sc:citation , "pmcid:PMC6863500", "pubmed:31679497" ; sc:description "A database portal containing esources that can be used to infer baseline species conditions." ; sc:name "Conservation Archive" ; sc:url "https://conservationarchive.shinyapps.io/ConservationArchive/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:encodingFormat edam:format_3475 ; sc:name "NCBI taxonomy ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:encodingFormat edam:format_3475 ; sc:name "NCBI taxonomy ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3475 ; sc:name "Evidence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3475 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author ; sc:citation , , "pmcid:PMC7218494", "pubmed:32398145" ; sc: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." ; sc:featureList edam:operation_2478, edam:operation_2479 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Conterminator" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1-c74b5" ; sc:url "https://conterminator.mmseqs.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229 ; sc:citation , "pmcid:PMC6331134", "pubmed:30601802" ; sc:description "Analysis of spatially organized protein expression in high-throughput screens." ; sc:featureList edam:operation_3443, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Context-explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://contextexplorer.readthedocs.io/en/latest/" ; biotools:primaryContact "Joel Ostblom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0176, edam:topic_0611 ; sc:citation , , "pmcid:PMC6933837", "pubmed:31693263", "pubmed:36244611" ; sc: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.""" ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3457, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "ContinuousFlex" ; sc:url "https://pypi.org/project/scipion-em-continuousflex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3047, edam:topic_3474 ; sc:citation , "pmcid:PMC6831742", "pubmed:31737032" ; sc: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.""" ; sc:featureList edam:operation_2476, edam:operation_3435, edam:operation_3893 ; sc:name "ContraDRG" ; sc:url "https://cdrg.mathematik.uni-marburg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6921240", "pubmed:31767541" ; sc: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.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3659 ; sc:name "ConvPath" ; sc:softwareHelp ; sc:url "https://qbrc.swmed.edu/projects/cnn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_3678 ; sc:citation , "pmcid:PMC6853199", "pubmed:31763041" ; sc: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""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "CorDiff" ; sc:url "https://cran.r-project.org/web/packages/CorDiff/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:31657800" ; sc: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.""" ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_3223 ; sc:name "CorEx" ; sc:url "http://corex.isi.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3855 ; sc:citation , "pmcid:PMC6525400", "pubmed:31101011" ; sc:description "Transcriptomic database for 14 species of scleractinian corals." ; sc:featureList edam:operation_3258, edam:operation_3431, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CoralTBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.comp.hkbu.edu.hk/~db/CoralTBase" ; biotools:primaryContact , "Jianliang Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC6371488", "pubmed:30744586" ; sc:description "Enables extraction of morphomic markers from CT images by non-technically skilled clinicians." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CoreSlicer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://coreslicer.com/" ; biotools:primaryContact "Louis Mullie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_3168 ; sc:citation , , "pmcid:PMC3964939", "pmcid:PMC5727400", "pubmed:24203703", "pubmed:31725859" ; sc:description "A genomics, genetics and breeding web portal for cotton research." ; sc:featureList edam:operation_0282, edam:operation_2421, edam:operation_3196, edam:operation_3208 ; sc:name "CottonGen" ; sc:url "http://cottongen.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3382 ; sc:citation , "pmcid:PMC6683572", "pubmed:31404403" ; sc: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" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "CoverageTool" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/lianneovnat/CoverageTool" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "A mine containing both cowpea genetic and genomic data, courtesy UC-Riverside" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "CowpeaMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/cowpeamine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3360, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC6927105", "pubmed:31865908" ; sc: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""" ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_2497 ; sc:name "Cox-PASNet" ; sc:url "https://github.com/DataX-JieHao/Cox-PASNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC8275978", "pubmed:31808791" ; sc:description """A Python Package for DNA Methylation Analysis. Python package to analyze DNA methylation data. $ pip3 install git+https://github.com/liguowang/cpgtools.git""" ; sc:featureList edam:operation_3204, edam:operation_3659, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "CpGtools" ; sc:url "https://github.com/liguowang/cpgtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2885, edam:topic_3293 ; sc:citation , "pubmed:31453748" ; sc: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" ; sc:featureList edam:operation_3192, edam:operation_3460, edam:operation_3891 ; sc:name "CpnClassiPhyR" ; sc:url "http://cpnclassiphyr.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6821367", "pubmed:31099383" ; sc:description "Reference-Based Decompression in Node and the Browser." ; sc:featureList edam:operation_0337, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cram-JS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GMOD/cram-js" ; biotools:primaryContact "Robert Buels" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation , "pmcid:PMC6735888", "pubmed:30649181" ; sc:description "Software to generate CRISPR guide RNAs against genomes annotated with individual variation." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Crisflash" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/crisflash/crisflash" ; biotools:primaryContact "Margus Lukk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6501434", "pubmed:31058278" ; sc:description "Comprehensive circular RNA resource for crops in response to abiotic stress." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CropCircDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://deepbiology.cn/crop/" ; biotools:primaryContact , "Hongwei Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC6330393", "pubmed:30634901" ; sc: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." ; sc:featureList edam:operation_3222, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Cropper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.geenivaramu.ee/en/tools/cropper" ; biotools:primaryContact "T. Haller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3174, edam:topic_3308 ; sc:author "Ahmed Hafez", "Hrant Hovhannisyan" ; sc:citation , "pmcid:PMC7049214", "pubmed:31392323" ; sc: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" ; sc:license "GPL-3.0" ; sc:name "Crossmapper" ; sc:softwareHelp ; sc:softwareVersion "v1.1.1" ; sc:url "https://github.com/Gabaldonlab/crossmapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0610 ; sc:citation ; sc: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" ; sc:license "GPL-3.0" ; sc:name "CrowdGO" ; sc:url "https://gitlab.com/mreijnders/CrowdGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3305, edam:topic_3474 ; sc:citation , "pmcid:PMC6476276", "pubmed:31037238" ; sc:description "Tracking Health Trends Using Public Social Media Data and Crowdsourcing." ; sc:featureList edam:operation_0560, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Crowdbreaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.crowdbreaks.org/" ; biotools:primaryContact "Marcel Salathé", "Martin Müller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3263 ; sc:citation , "pmcid:PMC6298042", "pubmed:30020420" ; sc: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." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Cryfa" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cobilab/cryfa" ; biotools:primaryContact "Morteza Hosseini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3077, edam:topic_3382 ; sc:citation , , "pubmed:32233514" ; sc: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""" ; sc:featureList edam:operation_2422, edam:operation_2940, edam:operation_3457 ; sc:name "CryoFLARE" ; sc:softwareHelp , ; sc:url "http://www.cryoflare.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2828, edam:topic_3452 ; sc:citation , , "pmcid:PMC6400257", "pubmed:30821710" ; sc:description "Software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CrystFEL" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , ; sc:url "http://www.desy.de/~twhite/crystfel/" ; biotools:primaryContact "Thomas White" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3314, edam:topic_3474 ; sc:citation , "pubmed:31615262" ; sc: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""" ; sc:featureList edam:operation_3432 ; sc:license "LGPL-3.0" ; sc:name "CrystaLattE" ; sc:url "https://github.com/carlosborca/CrystaLattE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3416 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2939, edam:operation_3096, edam:operation_3680 ; sc:license "BSD-3-Clause" ; sc:name "Cumulus" ; sc:softwareHelp ; sc:url "https://github.com/klarman-cell-observatory/cumulus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3379, edam:topic_3400 ; sc:citation , "pubmed:31416842" ; sc: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" ; sc:featureList edam:operation_0416 ; sc:name "Curatopes Melanoma" ; sc:softwareHelp ; sc:url "https://www.curatopes.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3315 ; sc:citation , "pmcid:PMC6507062", "pubmed:31072334" ; sc:description "Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model." ; sc:featureList edam:operation_0490, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CutpointsOEHR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=CutpointsOEHR" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3751 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2984 ; sc:encodingFormat edam:format_3751 ; sc:name "Pathway or network report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0204 ; sc:author ; sc:citation , "pmcid:PMC5899412", "pubmed:29653518" ; sc: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." ; sc:featureList edam:operation_1781 ; sc:funder "Ministry of Education, Youth and Sports of the Czech Republic" ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "CyGenexpi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0", "1.4.2" ; sc:url "https://github.com/cas-bioinf/genexpi/wiki/CyGenexpi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3360 ; sc:citation , "pmcid:PMC5473464", "pubmed:28663787" ; sc:description "Differential discovery in high-throughput high-dimensional cytometry datasets." ; sc:featureList edam:operation_2938, edam:operation_2939, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CyTOF workflow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3474 ; sc:citation , , "pmcid:PMC3855388", "pmcid:PMC6707396", "pubmed:24340000", "pubmed:31489175" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "CyTargetLinker" ; sc:softwareHelp , ; sc:url "https://cytargetlinker.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520, edam:topic_3697 ; sc:citation , "pubmed:31864964" ; sc: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""" ; sc:featureList edam:operation_0524, edam:operation_3644, edam:operation_3860 ; sc:name "CycloNovo" ; sc:url "https://github.com/bbehsaz/cyclonovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3170 ; sc:citation ; sc:description "Package to tackle cell cycle. It provides methods to recover cell cycle information and remove cell cycle factor from the scRNA-seq data." ; sc:featureList edam:operation_2436, edam:operation_3629, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cyclum" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KChen-lab/cyclum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3518 ; sc:citation , "pmcid:PMC6739950", "pubmed:31510921" ; sc: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" ; sc:featureList edam:operation_1812, edam:operation_3196 ; sc:name "CytoConverter" ; sc:url "https://jxw773.shinyapps.io/Cytogenetic__software/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3303, edam:topic_3518 ; sc:citation , ; sc:description "CytoGenetic Pattern Sleuth (CytoGPS) - web-enabled karyotype analysis tool for cytogenetics." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CytoGPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.8" ; sc:url "http://cytogps.org/" ; biotools:primaryContact "Institute for Informatics, Washington University School of Medicine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3934 ; sc:citation , "pmcid:PMC7078957", "pubmed:31633883" ; sc:description "A Normalization Algorithm for Cytometry Data. A R library to normalize cytometry data." ; sc:featureList edam:operation_3200, edam:operation_3432, edam:operation_3435, edam:operation_3436 ; sc:license "GPL-2.0" ; sc:name "CytoNorm" ; sc:softwareHelp ; sc:softwareVersion "0.0.5" ; sc:url "http://www.github.com/saeyslab/CytoNorm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC6821329", "pubmed:31114843" ; sc:description "Web-interface for simulating multi-dimensional cell imaging." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CytoPacq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cbia.fi.muni.cz/simulator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3395 ; sc:citation ; sc:description "Single-cell transcriptional diversity is a hallmark of developmental potential" ; sc:featureList edam:operation_2436, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CytoTRACE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cytotrace.stanford.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3360, edam:topic_3382 ; sc:citation , "pmcid:PMC6720861", "pubmed:31477013" ; sc: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. 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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." ; sc:featureList edam:operation_0476 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "DENOPTIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/denoptim-project/DENOPTIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Densitometry software written for Mathlab." ; sc:featureList edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "DENSIFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/46205-densife" ; biotools:primaryContact "Lorena" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:author "Daniele Raimondi", "Ibrahim Tanyalcin" ; sc:citation , "pmcid:PMC5570203", "pubmed:28498993" ; sc:description "Sequence-based predictor of deleteriousness of amino acid variants in human proteins" ; sc:featureList edam:operation_0331 ; sc:name "DEOGEN2" ; sc:url "http://deogen2.mutaframe.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3751 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:encodingFormat edam:format_3508, edam:format_3603 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3308 ; sc:author , , "Eric Charpentier", "Erwan Delage" ; sc:citation , , "pmcid:PMC6850038", "pmcid:PMC6944699", "pubmed:30977188", "pubmed:31907355" ; sc:contributor "Damien Vintache" ; sc:description "Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes." ; sc:featureList edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "DEPIB" ; sc:provider "BiRD bioinformatics facility" ; sc:softwareVersion "1.0" ; sc:url "https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipeline" ; biotools:primaryContact "Eric Charpentier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3334, edam:topic_3538 ; sc:citation , "pubmed:31870849" ; sc: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""" ; sc:featureList edam:operation_0470, edam:operation_1777, edam:operation_1812, edam:operation_3904 ; sc:name "DEPICTER" ; sc:url "http://biomine.cs.vcu.edu/servers/DEPICTER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0160, edam:topic_0219, edam:topic_3489 ; sc:citation , "pmcid:PMC6911163", "pubmed:31836896" ; sc: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." ; sc:featureList edam:operation_0417, edam:operation_3083, edam:operation_3208 ; sc:name "Human Dephosphorylation Database (DEPOD)" ; sc:url "http://depod.bioss.uni-freiburg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3322, edam:topic_3384, edam:topic_3452 ; sc:citation , "pmcid:PMC6532897", "pubmed:31120982" ; sc:description "Multi-domain tuberculosis data analysis resource." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DEPOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://depot.tbportals.niaid.nih.gov" ; biotools:primaryContact "Andrei Gabrielian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3510 ; sc:citation , "pmcid:PMC6735894", "pubmed:31372637" ; sc: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." ; sc:featureList edam:operation_0238, edam:operation_0441, edam:operation_0445 ; sc:name "Deep Sequence and Shape Motif (DESSO)" ; sc:url "https://bmbl.bmi.osumc.edu/DESSO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_3170 ; sc:author "Maximilian Hastreiter", "Tim Jeske" ; sc:citation , "pmcid:PMC6853685", "pubmed:31228198" ; sc:description "R package for accurate small RNA profiling based on differential expression of unique sequences." ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DEUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://ibis.helmholtz-muenchen.de/deus/" ; biotools:primaryContact "Tim Jeske" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:30849608" ; sc: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).""" ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DEWE: Differential Expression Workflow Executor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "https://www.sing-group.org/dewe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6399874", "pubmed:30832568" ; sc:description "R package for aggregation and visualization of differential expression data." ; sc:featureList edam:operation_2495, edam:operation_3436, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.0" ; sc:name "DEvis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=DEVis" ; biotools:primaryContact "Adam Price" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3407 ; sc:citation , , "pmcid:PMC6571761", "pubmed:31137754", "pubmed:32692571" ; sc: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." ; sc:featureList edam:operation_0394, edam:operation_0482, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "DIA-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bio-hpc.ucam.edu/dia-db/" ; biotools:primaryContact , "Zeno Apostolides" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC6949130", "pubmed:31768060" ; sc: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)""" ; sc:featureList edam:operation_3767, edam:operation_3799, edam:operation_3801 ; sc:name "DIA-NN" ; sc:softwareHelp ; sc:url "https://github.com/vdemichev/diann" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3654 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3655, edam:format_3747 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3475 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pmcid:PMC4399776", "pubmed:25599550" ; sc: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." ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3630, edam:operation_3631, edam:operation_3633, edam:operation_3649, edam:operation_3801, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "DIA-Umpire" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://sourceforge.net/projects/diaumpire/" ; biotools:primaryContact "Chih-Chiang Tsou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , , "pmcid:PMC7335186", "pubmed:32620816" ; sc: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" ; sc:featureList edam:operation_0313, edam:operation_2238, edam:operation_3192 ; sc:name "Debris Identification using Expectation Maximization (DIEM)" ; sc:url "https://github.com/marcalva/diem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6612874", "pubmed:31510699" ; sc: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." ; sc:featureList edam:operation_0264, edam:operation_3766, edam:operation_3798 ; sc:license "MIT" ; sc:name "DIFFUSE" ; sc:url "https://github.com/haochenucr/DIFFUSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0634, edam:topic_0804, edam:topic_3308 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2495 ; sc:name "Disease-gene Immune cell Expression (DIME)" ; sc:url "https://bitbucket.org/systemsimmunology/dime" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0202, edam:topic_0820, edam:topic_3300, edam:topic_3892 ; sc:citation , , "pubmed:32096817" ; sc:description "Exploring and visualizing possible GPCR dimer." ; sc:featureList edam:operation_0269, edam:operation_0337, edam:operation_2995 ; sc:name "DIMERBOW" ; sc:softwareHelp ; sc:url "http://lmc.uab.es/dimerbow/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC3931231", "pubmed:24600385" ; sc:description "DIPY is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments" ; sc:featureList edam:operation_2939, edam:operation_3446, edam:operation_3891 ; sc:name "Diffusion Imaging in Python (DIPY)" ; sc:url "http://dipy.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pmcid:PMC6794908", "pubmed:31615418" ; sc: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.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0278, edam:operation_0474, edam:operation_2441 ; sc:name "Direct Information Reweighted by Contact Templates (DIRECT)" ; sc:url "https://zhaolab.com.cn/DIRECT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3192, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "Design of an Identifiable Synthetic Community of Microbes (DISCo-microbe)" ; sc:url "https://github.com/dlcarper/DISCo-microbe" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3242 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3242 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3325 ; sc:author "Alberto Calderone", "Prisca Lo Surdo" ; sc:citation "pubmed:29036667" ; sc:contributor "Gianni Cesareni", "Luana Licata", "Marta Iannuccelli" ; sc: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." ; sc:featureList edam:operation_3083, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "DISNOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" ; sc:softwareHelp ; sc:url "https://disnor.uniroma2.it/" ; biotools:primaryContact "Livia Perfetto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0123, edam:topic_3538 ; sc:citation , "pmcid:PMC6933862", "pubmed:31642118" ; sc: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" ; sc:featureList edam:operation_0468, edam:operation_0470, edam:operation_3904 ; sc:name "DISOselect" ; sc:url "http://biomine.cs.vcu.edu/servers/DISOselect/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3569 ; sc:citation , "pmcid:PMC6680062", "pubmed:31392032" ; sc: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.)" ; sc:featureList edam:operation_0487, edam:operation_2939, edam:operation_3196 ; sc:license "MIT" ; sc:name "Distribution-based modeling of Sequence space time dynamics (DISSEQT)" ; sc:url "https://github.com/rasmushenningsson/DISSEQT.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6716629", "pubmed:31469855" ; sc: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" ; sc:featureList edam:operation_0239, edam:operation_0445, edam:operation_0476 ; sc:license "GPL-3.0" ; sc:name "DIpartite" ; sc:url "https://github.com/Mohammad-Vahed/DIpartite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3050, edam:topic_3474 ; sc:citation ; sc: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" ; sc:license "MIT" ; sc:name "DL-SDM" ; sc:url "https://github.com/naturalis/trait-geo-diverse-dl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:citation , "pmcid:PMC6686496", "pubmed:31392430" ; sc: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" ; sc:featureList edam:operation_0482, edam:operation_3501, edam:operation_3899 ; sc:license "MIT" ; sc:name "DLIGAND2" ; sc:url "https://github.com/sysu-yanglab/DLIGAND2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pmcid:PMC6838938", "pubmed:31648791" ; sc: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.""" ; sc:name "DLITE" ; sc:softwareHelp ; sc:url "https://github.com/AllenCellModeling/DLITE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0654 ; sc:citation , , "pmcid:PMC7140825", "pubmed:32164155" ; sc: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" ; sc:featureList edam:operation_3211, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "DLO Hi-C" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/GuoliangLi-HZAU/DLO-Hi-C-Tool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC6726615", "pubmed:31484923" ; sc: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" ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_0476 ; sc:license "GPL-3.0" ; sc:name "DMPfold" ; sc:url "https://github.com/psipred/DMPfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0196, edam:topic_0749, edam:topic_3318, edam:topic_3895 ; sc:citation , , "pmcid:PMC7476404", "pubmed:32995552" ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_3435 ; sc:license "MIT" ; sc:name "DNA-BOT" ; sc:softwareHelp ; sc:url "https://github.com/BASIC-DNA-ASSEMBLY/dnabot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3314 ; sc:citation , "pmcid:PMC6662285", "pubmed:30576403" ; sc:description "R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments." ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DNABarcodeCompatibility" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/comoto-pasteur-fr" ; biotools:primaryContact "Céline Trébeau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0632, edam:topic_0654, edam:topic_3500 ; sc:citation , , "pubmed:32647895" ; sc: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!""" ; sc:featureList edam:operation_3095, edam:operation_3096 ; sc:license "MIT" ; sc:name "DNA Chisel" ; sc:url "https://edinburgh-genome-foundry.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3169, edam:topic_3173 ; sc:citation , "pmcid:PMC7867998", "pubmed:31373608" ; sc: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" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "DNA Rchitect" ; sc:url "http://shiny.immgen.org/DNARchitect/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3399 ; sc:citation , "pmcid:PMC6708158", "pubmed:31443728" ; sc:description "A chronological age predictor based on DNA methylation. Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3891 ; sc:name "DNA-methyaltion-based age predictor" ; sc:url "https://github.com/qzhang314/DNAm-based-age-predictor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0154, edam:topic_0166, edam:topic_0654, edam:topic_3542 ; sc:citation , "pmcid:PMC7145614", "pubmed:31612957" ; sc: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""" ; sc:featureList edam:operation_0570, edam:operation_2421, edam:operation_2422, edam:operation_2488, edam:operation_2939 ; sc:name "DNAproDB" ; sc:softwareHelp ; sc:url "https://dnaprodb.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3316, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6487045", "pubmed:31029080" ; sc:contributor "Dr Alfredo Iacoangeli", "Dr Stephen J Newhouse" ; sc:description "Personal computer compatible NGS analysis, annotation and visualisation." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DNAscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KHP-Informatics/DNAscan" ; biotools:primaryContact "KCL IoPPN: NIHR BRC-MH Bioinformatics Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC7703788", "pubmed:31504181" ; sc: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" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0476 ; sc:license "GPL-3.0" ; sc:name "DNCON2" ; sc:url "http://sysbio.rnet.missouri.edu/dncon2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_0634 ; sc:citation , "pmcid:PMC6929334", "pubmed:31874600" ; sc:description """differential network local consistency analysis. Using Local Moran's I for detection of differential network local consistency""" ; sc:featureList edam:operation_2497, edam:operation_3463 ; sc:license "GPL-2.0" ; sc:name "DNLC" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/DNLC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC6943050", "pubmed:31598709" ; sc: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""" ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:name "DNA Methylation Interactive Visualization Database (DNMIVD)" ; sc:url "http://www.unimd.org/dnmivd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0160, edam:topic_3542 ; sc:citation ; sc:description "Improved ab initio protein secondary structure prediction using advanced deep learning architectures." ; sc:featureList edam:operation_0468, edam:operation_0469, edam:operation_0470 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DNSS2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/multicom-toolbox/DNSS2" ; biotools:primaryContact "Jianlin Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6737531", "pubmed:31081635" ; sc:description "Data-Driven Optimization of Mass Spectrometry Methods." ; sc:featureList edam:operation_2428, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DO-MS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://do-ms.slavovlab.net" ; biotools:primaryContact "Nikolai Slavov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0736, edam:topic_3308 ; sc:citation , , "pmcid:PMC6602495", "pubmed:27153665", "pubmed:31076763" ; sc:description "Domain-based transcriptome and proteome quality assessment." ; sc:featureList edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DOGMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://domainworld-services.uni-muenster.de/dogma/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3068, edam:topic_3407 ; sc:citation , "pubmed:31581093" ; sc: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!""" ; sc:featureList edam:operation_0224, edam:operation_3083, edam:operation_3660 ; sc:name "DORMAN" ; sc:url "http://ciceklab.cs.bilkent.edu.tr/dorman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3423, edam:topic_3512, edam:topic_3577 ; sc:citation , "pmcid:PMC6382494", "pubmed:30450799" ; sc:description "DMD Open-access Variant Explorer (DOVE) - web-based aid for DMD variant interpretation which additionally reports variant-specific predicted molecular eligibility for therapy." ; sc:featureList edam:operation_0446, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DOVE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.dmd.nl/DOVE" ; biotools:primaryContact "Mitch Bailey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31621827" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3629 ; sc:license "MIT" ; sc:name "DPre" ; sc:url "https://github.com/LoaloaF/DPre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3063, edam:topic_3379 ; sc:citation , "pmcid:PMC6798577", "pubmed:31390010" ; sc:description "DQueST is a web applciation for reducing information overload for trial seekers using dynamic questionnaires." ; sc:featureList edam:operation_3280 ; sc:name "DQueST" ; sc:url "https://github.com/stormliucong/dquest-flask" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3318, edam:topic_3489 ; sc:citation , "pubmed:31584610" ; sc: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.""" ; sc:featureList edam:operation_3557, edam:operation_3659, edam:operation_3799 ; sc:license "MIT" ; sc:name "DR-thermo" ; sc:url "https://github.com/samansalike/DR-thermo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3301, edam:topic_3379 ; sc:citation , "pmcid:PMC6692298", "pubmed:31409791" ; sc: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" ; sc:featureList edam:operation_3431, edam:operation_3482, edam:operation_3646 ; sc:name "DRAMP" ; sc:softwareHelp ; sc:url "http://dramp.cpu-bioinfor.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3673 ; sc:citation , , "pmcid:PMC7179940", "pubmed:32282793" ; sc: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." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3431, edam:operation_3659, edam:operation_3802 ; sc:name "DRAMS" ; sc:url "https://github.com/Yi-Jiang/DRAMS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3855 ; sc:citation , "pubmed:31515012" ; sc: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" ; sc:name "DREAP" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31515012" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6685255", "pubmed:31387525" ; sc: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" ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3501 ; sc:license "MIT" ; sc:name "DROPA" ; sc:url "https://github.com/marcrusso/DROPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3047, edam:topic_3336 ; sc:citation , "pubmed:31605102" ; sc:description "DRUDIT, Web-Based DRUgs DIscovery Tools to Design Small Molecules as Modulators of Biological Targets." ; sc:featureList edam:operation_3761 ; sc:name "DRUDIT" ; sc:softwareHelp ; sc:url "http://www.drudit.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0166 ; sc:citation , "pmcid:PMC7141859", "pubmed:31793988" ; sc:description "DNA Readout Viewer is a free on-line service providing novel and intuitive visualisation modes for displaying sequence specific DNA-protein interactions." ; sc:featureList edam:operation_0239, edam:operation_0337, edam:operation_3894 ; sc:name "DNA Readout Viewer" ; sc:softwareHelp , ; sc:url "https://drv.brc.hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3336, edam:topic_3855 ; sc:citation , "pmcid:PMC6528253", "pubmed:31113359" ; sc:description "Tool for the analysis of discrete data from multi-well plate assays." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DRfit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.structuralchemistry.org/pcsb/drfit.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602 ; sc:citation , "pmcid:PMC4795590", "pubmed:26415724" ; sc: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." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "DSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dsea.tigem.it/" ; biotools:primaryContact "Diego Carrella", "Diego di Bernardo", "Francesco Napolitano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_1317 ; sc:description "A collection of databases, tools and web servers for structural biology." ; sc:name "DSIMB tools" ; sc:url "http://www.dsimb.inserm.fr/tools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6929406", "pubmed:31874618" ; sc: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""" ; sc:featureList edam:operation_0524, edam:operation_3258, edam:operation_3472 ; sc:name "DTA-SiST" ; sc:url "https://github.com/Jane110111107/DTA-SiST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258 ; sc:citation , , "pmcid:PMC6645132", "pmcid:PMC6645227", "pubmed:31458051", "pubmed:31459245" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3799, edam:operation_3891 ; sc:name "DTCLab" ; sc:url "http://teqip.jdvu.ac.in/QSAR_Tools/DTCLab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:31885041" ; sc: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" ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_3435 ; sc:name "DTI-CDF" ; sc:url "https://github.com//a96123155/DTI-CDF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_0749 ; sc:citation , "pmcid:PMC6954663", "pubmed:31389563" ; sc: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" ; sc:featureList edam:operation_0244, edam:operation_0303, edam:operation_3799 ; sc:name "DUETT" ; sc:url "https://github.com/BagheriLab/DUETT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pmcid:PMC6582333", "pubmed:31106330" ; sc:description "Algorithm based on the distance variation allowed by secondary structure (DVASS), which ranks restraints according to their importance to RNA tertiary structure prediction." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DVASS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/dokhlab/dvass" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3542 ; sc:citation , , "pmcid:PMC6135855", "pmcid:PMC6602439", "pubmed:30209260", "pubmed:31114872" ; sc: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." ; sc:featureList edam:operation_0481 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "DaReUS-Loop" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::DaReUS-Loop" ; biotools:primaryContact "Pierre Tufféry", "Sjoerd de Vries" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174, edam:topic_3361 ; sc:citation , "pmcid:PMC6892282", "pubmed:31801633" ; sc:description "Fast and accurate genomic distances using HyperLogLog. dashing sketches and computes distances between fasta and fastq data." ; sc:featureList edam:operation_3211, edam:operation_3472, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "Dashing" ; sc:url "https://github.com/dnbaker/dashing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2828, edam:topic_3794 ; sc:author "Natasha Stander" ; sc:citation , "pmcid:PMC6878877", "pubmed:31798364" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3436, edam:operation_3695, edam:operation_3802 ; sc:name "DatView" ; sc:softwareHelp , ; sc:url "https://github.com/nstander/DatView" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0610, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:citation , , ; sc: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.""" ; sc:featureList edam:operation_0227, edam:operation_2421, edam:operation_3625, edam:operation_3908 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "DataDiscovery" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , ; sc:url "https://urgi.versailles.inrae.fr/data-discovery/" ; biotools:primaryContact "urgi-support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3394, edam:topic_3571 ; sc:author , "Jacek Lebioda", "Kavita Rege", "Yohan Jarosz" ; sc:citation , "pmcid:PMC6892452", "pubmed:31800037" ; sc:contributor , , "Christophe Trefois", "Sandrine Munoz", "Vilem Ded" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Data Information System (DAISY)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0" ; sc:url "https://github.com/elixir-luxembourg/daisy" ; biotools:primaryContact , "Regina Becker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0605 ; sc:author , , "Jan Slifka" ; sc:citation , , ; sc:contributor , "Rob Hooft" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Data Stewardship Wizard" ; sc:softwareHelp , , ; sc:url "https://ds-wizard.org" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0108, edam:topic_0203 ; sc:citation , , "pmcid:PMC7110638", "pubmed:32238171" ; sc: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" ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3282 ; sc:name "Datab.io" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://datab.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3068 ; sc:citation , "pmcid:PMC6506717", "pubmed:31042286" ; sc:description "Workflow and package for delivering successive versions of 'evolving data' directly into R." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Datastorr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/ropenscilabs/datastorr" ; biotools:primaryContact , "Rich FitzJohn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3421, edam:topic_3474 ; sc:author ; sc:citation , "pubmed:31751268" ; sc: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." ; sc:featureList edam:operation_3443, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "De-smokeGCN" ; sc:url "https://github.com/melights/cnn_desmoke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2275, edam:topic_3047, edam:topic_3303, edam:topic_3474 ; sc:citation , , "pmcid:PMC7189367", "pubmed:32195587" ; sc: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""" ; sc:featureList edam:operation_3216, edam:operation_3435, edam:operation_3891 ; sc:name "DeLinker" ; sc:url "https://github.com/oxpig/DeLinker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:31095815" ; sc:description "Software for automatic detection of neuronal dendritic branch terminals via an artificial neural network." ; sc:featureList edam:operation_3450 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeTerm" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/skibbe/DeTerm/wiki/Home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3370, edam:topic_3520 ; sc:citation , "pubmed:31436405" ; sc: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." ; sc:featureList edam:operation_3629, edam:operation_3637, edam:operation_3803 ; sc:name "DecoMetDIA" ; sc:url "https://github.com/ZhuMSLab/DecoMetDIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC6472186", "pubmed:30999839" ; sc:description "Tool for detecting contaminating organisms in human unmapped sequences." ; sc:featureList edam:operation_3187, edam:operation_3219, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DecontaMiner" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www-labgtp.na.icar.cnr.it/decontaminer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6768553", "pubmed:31129958" ; sc:description "On-demand decoy glycopeptide generator that can produce a high volume of decoys with low mass differences." ; sc:featureList edam:operation_0417, edam:operation_2929, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DecoyDeveloper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://glycopro.chem.ku.edu/JHome.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6848155", "pubmed:31712594" ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3792 ; sc:name "DeePathology" ; sc:url "https://github.com/SharifBioinf/DeePathology" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31686039" ; sc: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)""" ; sc:featureList edam:operation_3450, edam:operation_3457, edam:operation_3552 ; sc:name "Deep-Z" ; sc:softwareHelp , ; sc:url "https://github.com/puppy101puppy/Deep-Z" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2830, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0252, edam:operation_2492, edam:operation_3439 ; sc:name "DeepAttentionPan" ; sc:url "https://github.com/jjin49/DeepAttentionPan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1936 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3474 ; sc:citation , "pmcid:PMC6765103", "pubmed:31400112" ; sc: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" ; sc:featureList edam:operation_0306, edam:operation_3803 ; sc:license "MIT" ; sc:name "DeepBGC" ; sc:url "https://github.com/Merck/deepbgc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3474 ; sc:citation , "pmcid:PMC6661145", "pubmed:31380152" ; sc:description "A deep learning based method for estimating effective protein-ligand affinity." ; sc:featureList edam:operation_0482 ; sc:license "MIT" ; sc:name "DeepBindRG" ; sc:url "https://github.com/haiping1010/DeepBindRG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3518 ; sc:citation , "pmcid:PMC6697729", "pubmed:31420533" ; sc: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)" ; sc:featureList edam:operation_2436 ; sc:license "MIT" ; sc:name "DeepCC" ; sc:url "https://cityuhk-compbio.github.io/DeepCC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , , "pmcid:PMC7438055", "pubmed:32699072" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3450 ; sc:license "MIT" ; sc:name "DeepCINAC" ; sc:softwareHelp , , ; sc:url "https://gitlab.com/cossartlab/deepcinac" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3585 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_4002 ; sc:name "Mathematical model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_3464 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3474, edam:topic_3794 ; sc:author , , "Alexander Gulliver Bjørnholt Grønning" ; sc:citation , , "pmcid:PMC7367176", "pubmed:32558887" ; sc: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" ; sc:featureList edam:operation_0441, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DeepCLIP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://deepclip.compbio.sdu.dk" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0204, edam:topic_2640 ; sc:citation , "pubmed:31504186" ; sc: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)" ; sc:featureList edam:operation_3501 ; sc:license "MIT" ; sc:name "Deep gene compound profiler (DeepCOP)" ; sc:url "https://github.com/godwinwoo/DeepCOP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2640, edam:topic_3534 ; sc:citation , "pmcid:PMC6694742", "pubmed:31440276" ; sc: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" ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_0422 ; sc:name "DeepCalpain" ; sc:url "http://deepcalpain.cancerbio.info/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:31077303" ; sc:description "R package for deep learning of the back-splicing code for circular RNA formation." ; sc:featureList edam:operation_0264, edam:operation_1812, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DeepCirCode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BioDataLearning/DeepCirCode" ; biotools:primaryContact "Jun Wang", "Liangjiang Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3534 ; sc:citation , "pmcid:PMC8215920", "pubmed:31566664" ; sc: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" ; sc:featureList edam:operation_0366, edam:operation_0422 ; sc:name "DeepCleave" ; sc:url "http://deepcleave.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0654, edam:topic_3169, edam:topic_3474 ; sc:citation , ; sc:description "Deep Neural Networks for Identification of DNA-binding Proteins." ; sc:featureList edam:operation_3767, edam:operation_3900, edam:operation_3901 ; sc:name "DeepDBP" ; sc:url "https://github.com/antorkhan/DNABinding" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_2815, edam:topic_3474, edam:topic_3796 ; sc:citation , "pmcid:PMC6805717", "pubmed:31639043" ; sc: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." ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3695 ; sc:license "MIT" ; sc:name "DeepDNA" ; sc:url "https://github.com/rongjiewang/DeepDNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0121, edam:topic_0203, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:31722485" ; sc: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""" ; sc:featureList edam:operation_3900, edam:operation_3901 ; sc:name "DeepDRBP-2L" ; sc:url "http://bliulab.net/DeepDRBP-2L" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC6886168", "pubmed:31787076" ; sc: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." ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_3439 ; sc:license "MIT" ; sc:name "DeepEP" ; sc:url "https://github.com/CSUBioGroup/DeepEP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6753114", "pubmed:31537810" ; sc: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)" ; sc:featureList edam:operation_0308, edam:operation_3096, edam:operation_3216 ; sc:name "DeepHF" ; sc:url "http://www.DeepHF.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC6838785", "pubmed:31736974" ; sc: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""" ; sc:featureList edam:operation_0252, edam:operation_0331, edam:operation_0416 ; sc:license "GPL-2.0" ; sc:name "DeepHLApan" ; sc:url "http://biopharm.zju.edu.cn/deephlapan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0605, edam:topic_3382, edam:topic_3398, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3096, edam:operation_3435, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "DeepImageJ" ; sc:url "https://deepimagej.github.io/deepimagej/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6798445", "pubmed:31627739" ; sc: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." ; sc:featureList edam:operation_2940, edam:operation_3557 ; sc:license "MIT" ; sc:name "DeepImpute" ; sc:url "https://github.com/lanagarmire/DeepImpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382, edam:topic_3421, edam:topic_3474 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:license "MIT" ; sc:name "DeepInsight" ; sc:url "https://github.com/CYHSM/DeepInsight" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830 ; sc:citation , "pmcid:PMC6612839", "pubmed:31510651" ; sc: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" ; sc:featureList edam:operation_0252 ; sc:license "MIT" ; sc:name "DeepLigand" ; sc:url "https://github.com/gifford-lab/DeepLigand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "Evaluating the quality of metagenomic assemblies" ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3180 ; sc:license "MIT" ; sc:name "Deep learning for Metagenome Assembly Error Detection (DeepMAsED)" ; sc:url "https://github.com/leylabmpi/DeepMAsED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3308 ; sc:citation , , "pmcid:PMC6933662", "pubmed:31881818" ; sc: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" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:name "DeepMF" ; sc:url "https://github.com/paprikachan/DeepMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0160, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC7141871", "pubmed:31738385" ; sc: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""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0292, edam:operation_0303, edam:operation_3192 ; sc:name "DeepMSA" ; sc:url "https://zhanglab.ccmb.med.umich.edu/DeepMSA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31529040" ; sc: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" ; sc:featureList edam:operation_0252, edam:operation_0418, edam:operation_2929 ; sc:license "MIT" ; sc:name "DeepMSPeptide" ; sc:url "https://github.com/vsegurar/DeepMSPeptide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3400, edam:topic_3474, edam:topic_3697 ; sc:citation , , "pmcid:PMC7138789", "pubmed:32265477" ; sc: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.""" ; sc:featureList edam:operation_3200, edam:operation_3359, edam:operation_3891 ; sc:license "MIT" ; sc:name "DeepMicro" ; sc:url "https://github.com/minoh0201/DeepMicro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6933638", "pubmed:31881831" ; sc:description "Fast and accurate microRNA search using CNN." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:name "DeepMir" ; sc:url "https://github.com/HubertTang/DeepMir" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0140 ; sc:citation , , "pmcid:PMC6956790", "pmcid:PMC7493403", "pubmed:31218353", "pubmed:32938368" ; sc:description "Predictor of protein sub-mitochondrial localization based on deep learning" ; sc:featureList edam:operation_2489, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DeepMito" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://busca.biocomp.unibo.it/deepmito" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6853695", "pubmed:31081512" ; sc:description "Deep neural network based polyadenylation site analysis." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0428 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeepPASTA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/arefeen/DeepPASTA" ; biotools:primaryContact "Ashraful Arefeen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3474, edam:topic_3510, edam:topic_3542 ; sc:citation , "pubmed:31593229" ; sc: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.""" ; sc:featureList edam:operation_2492, edam:operation_3092, edam:operation_3439, edam:operation_3899 ; sc:license "MIT" ; sc:name "DeepPPISP" ; sc:url "http://bioinformatics.csu.edu.cn/PPISP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3676 ; sc:citation , "pmcid:PMC6364462", "pubmed:30727941" ; sc: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." ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-4-Clause" ; sc:name "DeepPVP" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/bio-ontology-research-group/phenomenet-vp" ; biotools:primaryContact "Bio-Ontology Research Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_3474, edam:topic_3577 ; sc:citation , , "pmcid:PMC7710064", "pubmed:33206638" ; sc:description "DeepPheno is a method for predicting gene-phenotype (HPO classes) associations from gene functional annotations (GO classes). Predicting single gene knockout phenotypes." ; sc:featureList edam:operation_2454, edam:operation_3196, edam:operation_3672 ; sc:license "BSD-3-Clause" ; sc:name "DeepPheno" ; sc:url "https://github.com/bio-ontology-research-group/deeppheno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3304, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC6897514", "pubmed:31570119" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3215, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "DeepPoseKit" ; sc:url "https://github.com/jgraving/deepposekit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3511, edam:topic_3512 ; sc:citation , "pubmed:31714956" ; sc: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""" ; sc:featureList edam:operation_0278, edam:operation_0417, edam:operation_0443 ; sc:name "DeepPromise" ; sc:softwareHelp ; sc:url "http://DeepPromise.erc.monash.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0888 ; sc:encodingFormat edam:format_3590 ; sc:name "Structure similarity score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2996 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "DeepRank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.0" ; sc:url "https://github.com/DeepRank/deeprank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_3172, edam:topic_3314, edam:topic_3474 ; sc:citation , "pmcid:PMC6955231", "pubmed:31871149" ; sc: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.""" ; sc:featureList edam:operation_0436, edam:operation_3629 ; sc:name "DeepRiPP" ; sc:url "http://deepripp.magarveylab.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168, edam:topic_3175, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6909530", "pubmed:31830921" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_3199, edam:operation_3227 ; sc:name "DeepSV" ; sc:url "https://github.com/CSuperlei/DeepSV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC6790966", "pubmed:31608949" ; sc: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.""" ; sc:featureList edam:operation_3644, edam:operation_3659 ; sc:name "DeepScreening" ; sc:url "http://deepscreening.xielab.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3474 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3439 ; sc:name "DeepSeqPanII" ; sc:url "https://github.com/pcpLiu/DeepSeqPanII" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6923924", "pubmed:31861979" ; sc: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.""" ; sc:featureList edam:operation_0492, edam:operation_2495, edam:operation_3800 ; sc:name "DeepShape" ; sc:url "https://github.com/cuihf06/DeepShape" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_0209, edam:topic_2840, edam:topic_3379 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2495 ; sc:license "MIT" ; sc:name "DeepSide" ; sc:url "http://github.com/OnurUner/DeepSide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0749, edam:topic_3168 ; sc:citation , , "pmcid:PMC6834390", "pubmed:31723604" ; sc: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" ; sc:name "DeepSpCas9" ; sc:softwareHelp ; sc:url "http://deepcrispr.info/DeepSpCas9" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6307148", "pubmed:30591034" ; sc:description "Deep learning based splice junction sequence classifier." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeepSplice" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zhangyimc/DeepSplice" ; biotools:primaryContact "Yi Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3360, edam:topic_3384, edam:topic_3444, edam:topic_3577 ; sc:citation , "pmcid:PMC6788344", "pubmed:31636533" ; sc: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.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "DeepSymNet" ; sc:url "https://gitlab.com/lgianca/longitudinal-deepsymnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3068, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc: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." ; sc:featureList edam:operation_2454, edam:operation_3501, edam:operation_3672 ; sc:name "Deep Functional Synthesis (DeepSyn)" ; sc:url "http://github.com/wangshenguiuc/DeepSyn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2640, edam:topic_3361 ; sc:citation ; sc:description "Deep Learning Approach to Identifying Breast Cancer Subtypes Using High-Dimensional Genomic Data." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeepType" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.acsu.buffalo.edu/~yijunsun/lab/DeepType.html" ; biotools:primaryContact "Yijun Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0602 ; sc:citation , "pmcid:PMC6379983", "pubmed:30777029" ; sc:description "Deep Learning Framework for Prediction of Ubiquitination Sites in Proteins." ; sc:featureList edam:operation_0417, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeepUbi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Sunmile/DeepUbi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2840, edam:topic_3047, edam:topic_3336 ; sc:citation , , "pmcid:PMC7318080", "pubmed:32607441" ; sc: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.""" ; sc:featureList edam:operation_0478 ; sc:license "MIT" ; sc:name "Deep Docking" ; sc:url "https://github.com/vibudh2209/D2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6722613", "pubmed:31374967" ; sc: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" ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:name "Deep Splicing Code (DSC)" ; sc:url "https://home.jbnu.ac.kr/NSCL/dsc.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_1781, edam:operation_2495, edam:operation_3439, edam:operation_3766 ; sc:license "GPL-3.0" ; sc:name "DeltaNeTS+" ; sc:url "http://www.github.com/cabsel/deltanetsplus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3399, edam:topic_3405 ; sc:citation , "pubmed:31521901" ; sc: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" ; sc:name "Dentareport" ; sc:url "http://dentareport.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3518 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3557, edam:operation_3629, edam:operation_3891 ; sc:name "DepMap" ; sc:url "https://depmap.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3321, edam:topic_3518 ; sc:description "Tool to determine the optimal read depth for reduced-representation sequencing." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3230 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DepthFinder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bitbucket.org/jerlar73/depthfinder/src/master/" ; biotools:primaryContact "Jerome Laroche" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_3168 ; sc:citation , "pubmed:26803162" ; sc:description "Tool for designing primers that yields amplicons with distinct signatures." ; sc:featureList edam:operation_0308 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DesignSignatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www2.decipher.codes/DesignSignatures.html" ; biotools:primaryContact "Kalin H. Vetsigian" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_2330 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585, edam:format_3464 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3895 ; sc:citation , "pmcid:PMC11223873", "pubmed:38634809" ; sc:description "A web server for engineering detectable pathways for bio-based chemical production." ; sc:featureList edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DetSpace" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://detspace.carbonelllab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154 ; sc:citation , "pmcid:PMC6736138", "pubmed:30649183" ; sc:description "Software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry." ; sc:featureList edam:operation_0252, edam:operation_2929, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Deuteros" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/andymlau/Deuteros" ; biotools:primaryContact "Argyris Politis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0798, edam:topic_2885 ; sc:citation , "pmcid:PMC6791034", "pubmed:31056858" ; sc:description "Assembly-free analysis and visualization of mobile genetic element composition." ; sc:featureList edam:operation_0427, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DeviaTE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/W-L/deviaTE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3332 ; sc:citation , "pubmed:31702762" ; sc: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.""" ; sc:featureList edam:operation_3431, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "DiNGO" ; sc:softwareHelp ; sc:url "https://www.vin.bg.ac.rs/180/tools/DiNGO.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC6509638", "pubmed:31130993" ; sc:description "Interactive and Integrated Web-Based Visualization Tool for Comparing Gene Lists." ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DiVenn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://divenn.noble.org/" ; biotools:primaryContact "Liang Sun", "Yinbing Ge", "Zach Robinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:28186229" ; sc:description "Tool for discovery of new molecules by mass spectrometry." ; sc:featureList edam:operation_3627, edam:operation_3645, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DiagnoProt" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://patternlabforproteomics.org/diagnoprot/" ; biotools:primaryContact "André R.F Silva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593 ; sc: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." ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "DiffAtOnce" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.diffatonce.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6527599", "pubmed:31139204" ; sc:description "Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DiffExpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://simplicity.nsilico.com/dea" ; biotools:primaryContact "Cintia C. Palu", "Paul Walsh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6519793", "pubmed:31091224" ; sc:description "Identification of disease-gene-chemical relationships from Medline abstracts." ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DigChem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gcancer.org/digchem" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation ; sc:description "Web-based database system for flow cell management." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DigestiFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bihealth/digestiflow-server" ; biotools:primaryContact "Manuel Holtgrewe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6824295", "pubmed:31708961" ; sc: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""" ; sc:featureList edam:operation_0560, edam:operation_3629, edam:operation_3800 ; sc:name "Digitaldlsorter" ; sc:url "https://github.com/cartof/digitalDLSorter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3305, edam:topic_3519 ; sc:citation , "pmcid:PMC6735924", "pubmed:31528358" ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3472 ; sc:name "DisCVR" ; sc:url "https://bioinformatics.cvr.ac.uk/software/discvr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6904532", "pubmed:31187352" ; sc:description "Software Package for Assessing Reproducibility of Brain Networks and their Discriminability across Disorders." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DisConICA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.01.1", "1.01.2" ; sc:url "https://bitbucket.org/masauburn/disconica/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6542142", "pubmed:31142265" ; sc:description "Software for HPV detection in RNA sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DisV-HPV16" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/ybq1204/DisV-HPV16" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0769, edam:topic_3063 ; sc:citation , "pmcid:PMC7703757", "pubmed:31702788" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "DiscoRhythm" ; sc:url "https://disco.camh.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation , "pmcid:PMC6378931", "pubmed:30059974" ; sc:description "R package for multi-omic data driven prediction of synthetic lethality in cancers." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DiscoverSL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/shaoli86/DiscoverSL/releases/tag/V1.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3336 ; sc:citation , "pmcid:PMC6688218", "pubmed:31399045" ; sc: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" ; sc:featureList edam:operation_0452, edam:operation_0484, edam:operation_0525 ; sc:license "MIT" ; sc:name "DiscoverY" ; sc:url "https://github.com/makovalab-psu/DiscoverY" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7038986", "pubmed:31879784" ; sc:description "Scripts for disentangling small RNA-sequencing (sRNA-Seq) data for libraries containing information from two interacting organisms to study RNA communication between species." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_3258, edam:operation_3792 ; sc:name "Disentangling sRNA-Seq" ; sc:url "https://github.com/ObedRamirez/Disentangling-sRNA-Seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0736 ; sc:citation , "pubmed:31593887" ; sc: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.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_2488 ; sc:name "DistAA" ; sc:url "http://andromeda.matf.bg.ac.rs/aadis_dynamic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3174, edam:topic_3518 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "Divergence" ; sc:url "http://www.bioconductor.org/packages/release/bioc/html/divergence.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2333 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071 ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_3349 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityAgents" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , ; sc:url "https://diversityworkbench.net/Portal/DiversityAgents" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3706 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330 ; sc:name "Ecological data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_2332, edam:format_3706 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_2332, edam:format_3706 ; sc:name "Ecological data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780, edam:topic_3050, edam:topic_3071, edam:topic_3299, edam:topic_3301, edam:topic_3382, edam:topic_3500, edam:topic_3678, edam:topic_3679 ; sc: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." ; sc:featureList edam:operation_0226, edam:operation_0337, edam:operation_2409, edam:operation_2945, edam:operation_3429, edam:operation_3434 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityCollection" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , , ; sc:url "https://diversityworkbench.net/Portal/DiversityCollection" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2332, edam:format_2350 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2350 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2350 ; sc:name "Ecological data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2332, edam:format_2350 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_2350 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2332, edam:format_2350 ; sc:name "Ecological data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3050, edam:topic_3070, edam:topic_3071, edam:topic_3391, edam:topic_3678, edam:topic_3855 ; sc:citation ; sc:contributor "Universität Bayreuth, Department of Mycology" ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_2429, edam:operation_2945, edam:operation_3434, edam:operation_3438 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityDescriptions" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityDescriptions" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3070, edam:topic_3071 ; sc:contributor "SNSB, Botanische Staatssammlung München" ; sc: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." ; sc:featureList edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityExsiccatae" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , , ; sc:url "https://diversityworkbench.net/Portal/DiversityExsiccatae" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2333 ; sc:name "Map" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2333 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3855 ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityGazetteers" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityGazetteers" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2333, edam:format_2350 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_2330 ; sc:name "Text" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071 ; sc:contributor "Universität Bayreuth, Department of Mycology" ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_3438, edam:operation_3443 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityImageInspector" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:url "https://diversityworkbench.net/Portal/DiversityImageInspector" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_3706 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_3706 ; sc:name "Biodiversity data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_3706 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_3706 ; sc:name "Ecological data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web service" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3070, edam:topic_3071 ; sc:author "University of Bayreuth, Chair of Databases and Information Systems" ; sc:contributor "Universität Bayreuth, Department of Mycology" ; sc: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." ; sc:featureList edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityMobile" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:url "https://diversityworkbench.net/Portal/DiversityMobile" ; biotools:primaryContact "SNSB IT Center" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071, edam:topic_3678 ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_2428 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityProjects" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , ; sc:url "https://diversityworkbench.net/Portal/DiversityProjects" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3070, edam:topic_3071 ; sc: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." ; sc:featureList edam:operation_0226, edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityReferences" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityReferences" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Ecological data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Ecological data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3855 ; sc: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." ; sc:featureList edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversitySamplingPlots" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversitySamplingPlots" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Ontology data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070, edam:topic_3071, edam:topic_3303, edam:topic_3314, edam:topic_3855 ; sc: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." ; sc:featureList edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityScientificTerms" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityScientificTerms" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Taxonomy" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2376 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070, edam:topic_3071 ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_2945, edam:operation_2990, edam:operation_3434 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityTaxonNames" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityTaxonNames" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2330, edam:format_2333, edam:format_2350 ; sc:name "Map" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2330, edam:format_2333, edam:format_2350 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071, edam:topic_3855 ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_2430 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Diversity GIS Editor" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , ; sc:url "https://diversityworkbench.net/Portal/DiversityGisEditor" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3068, edam:topic_3070, edam:topic_3071, edam:topic_3391, edam:topic_3678, edam:topic_3855 ; sc:contributor "Universität Bayreuth, Department of Mycology" ; sc: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." ; sc:featureList edam:operation_0226, edam:operation_2409, edam:operation_2425, edam:operation_2945, edam:operation_3429, edam:operation_3434 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Diversity Workbench" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , , ; sc:url "https://diversityworkbench.net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3068 ; sc:citation , "pmcid:PMC4443683", "pubmed:25637558" ; sc:description "Bayesian evidence analysis tool for systems biology." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Dizzy-Beats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/p/bayesevidence/home/Home/" ; biotools:primaryContact "Stuart Aitken" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3306, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6803556", "pubmed:31680924" ; sc: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:""" ; sc:featureList edam:operation_2425, edam:operation_2426, edam:operation_3629 ; sc:license "MIT" ; sc:name "Dmipy" ; sc:url "https://github.com/AthenaEPI/dmipy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3385, edam:topic_3474 ; sc:citation , "pmcid:PMC6533009", "pubmed:31083649" ; sc:description "Deep architecture for synapse detection in multiplexed fluorescence images." ; sc:featureList edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DoGNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kulikovv/dognet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625 ; sc:citation , "pmcid:PMC6602487", "pubmed:31106327" ; sc:description "Web application for efficient and accurate Human Phenotype Ontology (HPO) concept curation." ; sc:featureList edam:operation_1812, edam:operation_3280, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Doc2Hpo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://impact2.dbmi.columbia.edu/doc2hpo/" ; biotools:primaryContact , "Kai Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:31578656" ; sc: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""" ; sc:featureList edam:operation_0482, edam:operation_3659, edam:operation_3899 ; sc:name "DockBox" ; sc:url "https://pypi.org/project/dockbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:citation ; sc: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!" ; sc:featureList edam:operation_0249, edam:operation_0482, edam:operation_3899 ; sc:name "DockThor" ; sc:url "https://dockthor.lncc.br/v2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , "pmcid:PMC6982331", "pubmed:31906249" ; sc: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/).""" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Docker4Circ" ; sc:operatingSystem "Linux" ; sc:softwareVersion "version 1" ; sc:url "https://github.com/kendomaniac/docker4seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0130, edam:topic_0736 ; sc:citation , "pmcid:PMC6816169", "pubmed:31660857" ; sc: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""" ; sc:featureList edam:operation_0303, edam:operation_0327, edam:operation_3435, edam:operation_3767 ; sc:name "Domainoid" ; sc:url "https://bitbucket.org/sonnhammergroup/domainoid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3500, edam:topic_3679 ; sc:citation , "pubmed:31816295" ; sc: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""" ; sc:featureList edam:operation_2426 ; sc:name "Dominance Sharing Assessment" ; sc:url "https://bitbucket.org/CameronLHall/dominancesharingassessmentmatlab/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3572 ; sc:description "Detection of doublets (technical errors) in single-cell RNA-seq count matrices." ; sc:featureList edam:operation_0337, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DoubletDetection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/JonathanShor/DoubletDetection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3318, edam:topic_3892 ; sc:citation , "pubmed:31542001" ; sc: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" ; sc:featureList edam:operation_0244 ; sc:license "GPL-3.0" ; sc:name "DrDiff" ; sc:url "https://github.com/ronaldolab/DrDiff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0621, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC7145660", "pubmed:31691822" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_3216, edam:operation_3454 ; sc:name "DrLLPS" ; sc:softwareHelp ; sc:url "http://llps.biocuckoo.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC10251767", "pubmed:31710658" ; sc: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 )""" ; sc:featureList edam:operation_0337, edam:operation_3646, edam:operation_3755 ; sc:license "GPL-3.0" ; sc:name "DrawGlycan-SNFG" ; sc:softwareHelp ; sc:url "https://virtualglycome.org/drawglycan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_0659, edam:topic_2640, edam:topic_3173 ; sc:citation , "pmcid:PMC10767848", "pubmed:37956338" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:name "DriverDBv4" ; sc:url "http://driverdb.bioinfomics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_2640, edam:topic_3518, edam:topic_3577 ; sc:citation , "pubmed:31626284" ; sc: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""" ; sc:featureList edam:operation_2454, edam:operation_3435, edam:operation_3439 ; sc:name "DriverSub" ; sc:url "https://github.com/JianingXi/DriverSub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC6602441", "pubmed:31066443" ; sc:description "> COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/predrbr (DENGLAB.ORG), bio.tools/deepsacon (DENGLAB.ORG), bio.tools/predhs (DENGLAB.ORG) | an integrative cancer drug combination data portal | DrugComb is an open-access, community-driven data portal where the results of drug combination screening studies for a large variety of cancer cell lines are accumulated, standardized and harmonized. An actively expanding array of data visualization and computational tools is provided for the analysis of drug combination data | Please pay attention that the template header format is changed. Analysis function is also updated | response column should be renamed to inhibition as in the template file | Sharing data leads to novel knowledge | Start analyzing your own drug combination data by uploading | File should be a comma separated value(csv)" ; sc:featureList edam:operation_2929, edam:operation_3431, edam:operation_3894 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DrugComb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://drugcomb.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2640, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC7145671", "pubmed:31665429" ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_3659, edam:operation_3799 ; sc:name "DrugCombDB" ; sc:softwareHelp ; sc:url "http://drugcombdb.denglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:31096089" ; sc:description "Database for drug repurposing, combination therapy, and replacement therapy." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DrugR+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.drugr.ir" ; biotools:primaryContact "Ali Masoudi-Nejad", "Massoud Amanlou", "Yadollah Omidi", "Yosef Masoudi-Sobhanzadeh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3379 ; sc:citation , "pmcid:PMC6602481", "pubmed:31106379" ; sc:description "Web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning." ; sc:featureList edam:operation_0420, edam:operation_0478, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Drug ReposER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mfrlab.org/drugreposer/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3374 ; sc:citation , "pubmed:31368482" ; sc:description "A database protal for drug target predictions based knowledge graph embeddings." ; sc:featureList edam:operation_0463, edam:operation_2489 ; sc:license "CC-BY-NC-SA-3.0" ; sc:name "Drug Targets" ; sc:url "http://drugtargets.insight-centre.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304 ; sc:citation , "pmcid:PMC7148288", "pubmed:31062193" ; sc: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" ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DstarM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=DstarM" ; biotools:primaryContact "Don van den Bergh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_2885 ; sc:citation ; sc:description "Fast calculation of the ABBA-BABA statistics across many populations/species." ; sc:featureList edam:operation_3196, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Dsuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/millanek/Dsuite" ; biotools:primaryContact "Milan Malinsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6383267", "pubmed:30791939" ; sc:description "Tool for identification of different modes of duplicated gene pairs." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "DupGen_finder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/qiao-xin/DupGen_finder" ; biotools:primaryContact "Xin Qiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3337 ; sc:author ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Dwarna" ; sc:softwareHelp ; sc:url "https://github.com/NicholasMamo/dwarna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6663215", "pubmed:31410378" ; sc: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" ; sc:featureList edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "DyNeuSR" ; sc:url "https://braindynamicslab.github.io/dyneusr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3173 ; sc:citation , "pmcid:PMC6693283", "pubmed:31409281" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_3439 ; sc:name "DynOVis" ; sc:url "https://tjmkuijpers.shinyapps.io/dynovistool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3172, edam:topic_3343 ; sc:citation , "pmcid:PMC6572260", "pubmed:31052310" ; sc:description "Dynamic Retention Time Database for Steroidomics." ; sc:featureList edam:operation_3454, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DynaStI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dynasti.vital-it.ch" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3518 ; sc:citation , "pubmed:31609429" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3695, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "Dynalogo" ; sc:url "https://dynalogo.cam.uchc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation , "pubmed:31793979" ; sc: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.""" ; sc:featureList edam:operation_3731 ; sc:license "GPL-3.0" ; sc:name "Dynamic Meta-Storms" ; sc:url "https://github.com/qibebt-bioinfo/dynamic-meta-storms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC6701490", "pubmed:31430368" ; sc:description "Scripts used during the genome assembly of Dysdera silvatica." ; sc:featureList edam:operation_3192, edam:operation_3216, edam:operation_3501 ; sc:license "MIT" ; sc:name "Dysdera silvatica genome" ; sc:url "https://github.com/molevol-ub/Dysdera_silvatica_genome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0121, edam:topic_0749, edam:topic_2229, edam:topic_3308 ; sc:citation , , "pmcid:PMC7549788", "pubmed:33045012" ; sc: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.""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3799 ; sc:name "E-Flow" ; sc:url "https://github.com/vanNimwegenLab/E-Flow" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3475 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3120 ; sc:author , "Matteo Manfredi" ; sc:citation , "pmcid:PMC9710551", "pubmed:36227117" ; sc:description "E-SNPs&GO is a machine-learning method the pathogenicity of human variations. E-SNPs&GO classify input variations into pathogenic or benign." ; sc:featureList edam:operation_0331 ; sc:isAccessibleForFree true ; sc:name "E-SNPs and GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:url "https://esnpsandgo.biocomp.unibo.it/" ; biotools:primaryContact , , "Matteo Manfredi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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." ; sc:name "Efficient and Adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics" ; sc:url "https://github.com/STOmics/EAGS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6505892", "pubmed:31067213" ; sc:description "Predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches." ; sc:featureList edam:operation_0441, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EAT-Rice" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://predictor.nchu.edu.tw/EAT-Rice" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC6736067", "pubmed:30649199" ; sc:description "Evolutionary-based BIClustering (EBIC), a next-generation biclustering algorithm for mining genetic data." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "EBIC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/EpistasisLab/ebic" ; biotools:primaryContact "Jason H. Moore", "Patryk Orzechowski" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3508 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:encodingFormat edam:format_3033 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation , "pmcid:PMC5001598", "pubmed:27207878" ; sc:description "A computational method for the statistical inference of cell lineage relationships from single-cell gene expression data." ; sc:featureList edam:operation_0313, edam:operation_0571 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ECLAIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GGiecold/ECLAIR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , , "pmcid:PMC8150141", "pubmed:33305308" ; sc: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.""" ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3439 ; sc:name "ECMarker" ; sc:url "https://github.com/daifengwanglab/ECMarker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068 ; sc:citation , "pmcid:PMC6822939", "pubmed:31671102" ; sc:description "A new toolbox for time series analysis and forecasting. Some Features found in a few packages or none at all." ; sc:featureList edam:operation_0337, edam:operation_3565, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "ECOTOOL" ; sc:url "https://github.com/djpt999/ECOTOOL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0194, edam:topic_2269, edam:topic_3293 ; sc:citation , , "pmcid:PMC7743758", "pubmed:32877529" ; sc:description "EDCluster is a method for obtaining stationary distributions that can be used to construct empirical stationary distribution mixture models." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "EDCluster" ; sc:url "https://github.com/dschrempf/edcluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_0769, edam:topic_0780, edam:topic_0798 ; sc:citation , "pmcid:PMC6913007", "pubmed:31843001" ; sc: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." ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3629 ; sc:name "The Extensive de novo TE Annotator (EDTA)" ; sc:url "https://github.com/oushujun/EDTA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304 ; sc:citation , "pmcid:PMC6413114", "pubmed:30781869" ; sc:description "Platform to enable EEG measurements and general purposes Brain Computer Interface experimentations." ; sc:name "Open-Electroencephalography (EEG)" ; sc:url "http://openeeg.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Prototype neurofeedback application." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EEGMIR" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://uazu.net/eegmir/" ; biotools:primaryContact "Jim Peters" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3334 ; sc:citation , "pmcid:PMC6815881", "pubmed:31381946" ; sc: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""" ; sc:name "EEGSourceSim" ; sc:url "https://github.com/svndl/EEGSourceSim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3174 ; sc:citation , "pmcid:PMC7057060", "pubmed:31553576" ; sc: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" ; sc:featureList edam:operation_0362 ; sc:name "EFI" ; sc:url "https://efi.igb.illinois.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3379 ; sc:citation , "pubmed:31433187" ; sc: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" ; sc:featureList edam:operation_0224, edam:operation_3454 ; sc:name "EK-DRD" ; sc:url "http://www.idruglab.com/drd/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Ensemble Learning Approach for Stability Prediction of Interface and Core mutations." ; sc:featureList edam:operation_0250, edam:operation_0331, edam:operation_2480 ; sc:name "ELASPIC" ; sc:softwareHelp ; sc:url "http://elaspic.kimlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3324, edam:topic_3489, edam:topic_3519, edam:topic_3577 ; sc:citation , "pubmed:31588775" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:license "MIT" ; sc:name "ELIMU-MDx" ; sc:url "https://sparclex.github.io/elimu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_3305, edam:topic_3489, edam:topic_3810 ; sc:citation ; sc: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).""" ; sc:featureList edam:operation_3557 ; sc:name "EM-DAT" ; sc:url "https://www.emdat.be/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3174, edam:topic_3512 ; sc:citation , "pmcid:PMC6328100", "pubmed:30629718" ; sc: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." ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "EMBL2checklists" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/michaelgruenstaeudl/EMBL2checklists" ; biotools:primaryContact "Michael Gruenstaeudl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3324, edam:topic_3474 ; sc:citation , "pmcid:PMC6760811", "pubmed:31518349" ; sc: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" ; sc:license "Apache-2.0" ; sc:name "EMULSION" ; sc:softwareHelp ; sc:url "https://sourcesup.renater.fr/www/emulsion-public" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0749, edam:topic_2885, edam:topic_3512 ; sc:citation , "pmcid:PMC7145688", "pubmed:31665430" ; sc: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" ; sc:featureList edam:operation_0224, edam:operation_0440, edam:operation_2495 ; sc:name "ENdb" ; sc:url "http://www.licpathway.net/ENdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation , "pmcid:PMC6368480", "pubmed:30165689" ; sc: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." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "EPA-ng" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/Pbdas/epa-ng" ; biotools:primaryContact "Pierre Barbera" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3170 ; sc:citation , "pubmed:31099391" ; sc:description "Effector and Perturbation Estimation Engine (EPEE) conducts differential analysis of transcription factor activity from gene expression data." ; sc:featureList edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "EPEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Cobanoglu-Lab/EPEE" ; biotools:primaryContact "Murat Can Çobanoğlu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3375 ; sc:citation ; sc:description "Tool for designing peptide ligand libraries based on epitope–paratope interactions." ; sc:featureList edam:operation_0252, edam:operation_0272, edam:operation_0416 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EPI-peptide designer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biocomp.icb.ufmg.br/biocomp/software-and-databases/epi-peptide-designer/" ; biotools:primaryContact "Viart Benjamin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC6602470", "pubmed:31106358" ; sc:description "Analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies." ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EPIC-TABSAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tabsat.ait.ac.at/" ; biotools:primaryContact , "Stephan Pabinger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2269 ; sc:citation , , "pmcid:PMC7583457", "pubmed:31975601" ; sc:description "EPIFANY is a protein inference engine based on a Bayesian network." ; sc:featureList edam:operation_3649, edam:operation_3767 ; sc:name "Efficient Bayesian protein inference (EPIFANY)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://OpenMS.de/epifany" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3173, edam:topic_3512 ; sc:citation ; sc: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)""" ; sc:featureList edam:operation_0417, edam:operation_0463, edam:operation_3800 ; sc:license "MIT" ; sc:name "EPIGENE" ; sc:url "https://github.com/imbbLab/EPIGENE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3168 ; sc:citation , "pmcid:PMC7963088", "pubmed:31410461" ; sc:description "A novel approach for condition-specific enhancer-promoter interaction prediction." ; sc:featureList edam:operation_0272, edam:operation_2492, edam:operation_3901 ; sc:name "EPIP" ; sc:url "http://www.cs.ucf.edu/~xiaoman/EPIP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:31588505" ; sc: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""" ; sc:featureList edam:operation_0440, edam:operation_3435 ; sc:name "EPIVAN" ; sc:url "https://github.com/hzy95/EPIVAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3168 ; sc:citation , "pubmed:31751246" ; sc: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.""" ; sc:featureList edam:operation_3196, edam:operation_3199, edam:operation_3435 ; sc:name "ERINS" ; sc:url "https://github.com/BDanalysis/ERINS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3318 ; sc:citation , "pubmed:31125060" ; sc:description "Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search." ; sc:featureList edam:operation_0482, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "EROS-DOCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://erosdock.loria.fr" ; biotools:primaryContact "Isaure Chauvot de Beauchêne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3399 ; sc:citation , , "pmcid:PMC5638550", "pmcid:PMC6735795", "pubmed:28968389" ; sc:description "A unique tool to help understand HIV prevention among high-risk young women in Ukraine | Estimate time since infection from NGS diversity" ; sc:name "ETI" ; sc:url "https://hiv.biozentrum.unibas.ch/ETI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3403, edam:topic_3407, edam:topic_3423 ; sc:citation , "pmcid:PMC6692943", "pubmed:31412866" ; sc: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" ; sc:featureList edam:operation_3280, edam:operation_3803 ; sc:name "ETM-DB" ; sc:url "http://biosoft.kaist.ac.kr/etm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3855 ; sc:citation ; sc:description "A Low-Cost, Open Source, Self-Contained Bacterial EVolutionary biorEactor (EVE)" ; sc:featureList edam:operation_3798 ; sc:license "MIT" ; sc:name "EVE" ; sc:url "https://github.com/vishhvaan/eve-pi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0654, edam:topic_3810 ; sc:citation , "pmcid:PMC6794827", "pubmed:31615397" ; sc: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." ; sc:featureList edam:operation_0335, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "EVR" ; sc:url "https://github.com/mbglab/EVR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0820, edam:topic_2275 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0272, edam:operation_0477, edam:operation_0478, edam:operation_2492 ; sc:license "MIT" ; sc:name "EVcouplings" ; sc:url "https://evcouplings.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3512 ; sc:citation ; sc:description "Predicting functional long non-coding RNAs validated by low throughput experiments." ; sc:featureList edam:operation_0525, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EVlncRNA-pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biophy.dzu.edu.cn/lncrnapred/index.html" ; biotools:primaryContact "Jihua Wang", "Yaoqi Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3295, edam:topic_3517 ; sc:citation , "pmcid:PMC6061808", "pubmed:29566144" ; sc:description "Epigenome-wide association study software." ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioapp.org/ewas/" ; biotools:primaryContact "Fanwu Kong", "Liangde Xu", "Yongshuai Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6943079", "pubmed:31584095" ; sc:description "A resource of DNA methylation array data and metadata." ; sc:featureList edam:operation_2422, edam:operation_3186, edam:operation_3207 ; sc:name "EWAS Data Hub" ; sc:softwareHelp ; sc:url "https://bigd.big.ac.cn/ewas/datahub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_3957 ; sc:citation , "pmcid:PMC6744658", "pubmed:31521132" ; sc:description "A Python script for identifying protein complexes based on an edge weight algorithm and core-attachment structure." ; sc:featureList edam:operation_0277, edam:operation_2492, edam:operation_3439 ; sc:name "EWCA" ; sc:url "https://github.com/RongquanWang/EWCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31100387" ; sc:description "EXPANDER (EXPression ANalyzer and DisplayER) is a comprehensive software package for analysis of expression data." ; sc:featureList edam:operation_3223, edam:operation_3501, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "EXPANDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://acgt.cs.tau.ac.il/expander/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_2830, edam:topic_3421 ; sc:citation , "pmcid:PMC8248894", "pubmed:31750874" ; sc: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.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:name "Easy-HLA" ; sc:url "https://hla.univ-nantes.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:31743827" ; sc: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""" ; sc:license "GPL-3.0" ; sc:name "EasyMEG" ; sc:url "https://tonywu2018.github.io/EasyMEG/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3315 ; sc:citation , "pubmed:31504183" ; sc:description "A user-friendly tool for building and analysis of simple mathematical models in systems biology" ; sc:featureList edam:operation_2426, edam:operation_3096, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "EasyModel" ; sc:url "https://easymodel.udl.cat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2275, edam:topic_3277 ; sc:citation , "pmcid:PMC6530084", "pubmed:31117939" ; sc: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)." ; sc:featureList edam:operation_3431, edam:operation_3501, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EcRBPome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://caps.ncbs.res.in/ecrbpome" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3172, edam:topic_3375 ; sc:citation , "pmcid:PMC6591011", "pubmed:31047795" ; sc:description "Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies." ; sc:featureList edam:operation_3482, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "EcoPrestMet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zampierigroup.shinyapps.io/EcoPrestMet" ; biotools:primaryContact "Mattia Zampieri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3382 ; sc:citation , "pmcid:PMC6684082", "pubmed:31386677" ; sc: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" ; sc:featureList edam:operation_0313, edam:operation_3463, edam:operation_3766 ; sc:license "MIT" ; sc:name "EdgeScaping" ; sc:url "https://github.com/bhusain/EdgeScaping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31119671" ; sc:description "> HOMEPAGE MISSING! | A Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics | Analysis of large metabolomic datasets is becoming commonplace with the increased realization of the role that metabolites play in biology and pathophysiology. While there are many open-source analysis tools to extract peaks from liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and tandem mass spectrometry (LC-MS MS) data, these tools are not very interactive and are suboptimal when a large number of samples are to be analyzed. El-MAVEN is an open-source analysis platform that extends MAVEN and provides fast, powerful, and interactive analysis capabilities especially for datasets containing over 100 samples. The El-MAVEN workflow is easy to use with just four steps from loading data to exporting of the results" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "El-MAVEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31119671" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Program for neurofeedback that supports modularEEG. Uses fast Fourier transform to extract frequency bands from the raw signal." ; sc:isAccessibleForFree true ; sc:name "Electric Guru" ; sc:operatingSystem "Windows" ; sc:url "https://realization.org/old/page/topics/electric_guru.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC6381631", "pubmed:30782135" ; sc:description "Software tool to correct LC-MS data in isotope labeling experiments." ; sc:featureList edam:operation_3629, edam:operation_3632, edam:operation_3638 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ElemCor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/4dsoftware/elemcor" ; biotools:primaryContact "Di Du", "Xiaoyang Su" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3382, edam:topic_3542 ; sc:citation , "pmcid:PMC6717539", "pubmed:31358979" ; sc: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" ; sc:featureList edam:operation_0468, edam:operation_0470, edam:operation_2488 ; sc:license "GPL-3.0" ; sc:name "Emap2sec" ; sc:url "http://www.kiharalab.org/emap2sec/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , , "pmcid:PMC7496207", "pubmed:32938367" ; sc: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" ; sc:featureList edam:operation_3891 ; sc:name "EnClaSC" ; sc:url "https://github.com/xy-chen16/EnClaSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3474 ; sc:citation , "pubmed:31125056" ; sc:description "R package for imputing dropout events in single cell RNA sequencing data via ensemble learning." ; sc:featureList edam:operation_3192, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EnImpute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Zhangxf-ccnu/EnImpute" ; biotools:primaryContact "Xiao-Fei Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31628884" ; sc:description "Bringing faster and smarter functional annotation to non-model eukaryotic transcriptomes." ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3192, edam:operation_3258, edam:operation_3501 ; sc:name "EnTAP" ; sc:softwareHelp ; sc:url "https://gitlab.com/EnTAP/EnTAP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3246 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3621 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3621 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3245 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:30510204" ; sc: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." ; sc:featureList edam:operation_0335, edam:operation_3215, edam:operation_3631, edam:operation_3646, edam:operation_3649, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "EncyclopeDIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.8.1" ; sc:url "https://bitbucket.org/searleb/encyclopedia/" ; biotools:primaryContact "Brian Searle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC6344666", "pubmed:30689845" ; sc:description "Database to discover the regulate relationships in the context of enhancers." ; sc:featureList edam:operation_0441, edam:operation_3232, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "EnhancerDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lcbb.swjtu.edu.cn/EnhancerDB/" ; biotools:primaryContact "Z. Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0194, edam:topic_0797, edam:topic_3293 ; sc:citation , "pmcid:PMC2652215", "pubmed:19029536" ; sc:description "Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level." ; sc:featureList edam:operation_0323, edam:operation_0324, edam:operation_0491, edam:operation_0492, edam:operation_0558, edam:operation_2403, edam:operation_3182, edam:operation_3460, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Ensembl Compara" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "e56", "e81" ; sc:url "http://www.ensembl.org/info/genome/compara/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3318 ; sc:citation , "pmcid:PMC6910589", "pubmed:30709308" ; sc: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." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Enspara" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://enspara.readthedocs.io/en/latest/" ; biotools:primaryContact "Bowman Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3305, edam:topic_3796 ; sc:citation , , "pmcid:PMC7641423", "pubmed:32726198" ; sc:description "Global genomic population structure of Clostridioides difficile" ; sc:featureList edam:operation_0524, edam:operation_3216, edam:operation_3840 ; sc:name "EnteroBase" ; sc:url "http://enterobase.warwick.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602, edam:topic_3068 ; sc:citation , "pmcid:PMC6821292", "pubmed:31077305" ; sc:description "Python library to dynamically interact with the NCBI Entrez databases." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "Entrezpy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/entrezpy/" ; biotools:primaryContact "Jan buchmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3316 ; sc: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." ; sc:featureList edam:operation_3223 ; sc:name "Eoulsan" ; sc:url "http://outils.genomique.biologie.ens.fr/eoulsan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6868350", "pubmed:31511888" ; sc: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" ; sc:featureList edam:operation_2428, edam:operation_2929, edam:operation_3227 ; sc:name "EphaGen" ; sc:url "https://github.com/m4merg/EphaGen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation , "pmcid:PMC6712799", "pubmed:31455207" ; sc:description "An approach of epistasis mining based on genetic Tabu algorithm and Bayesian network" ; sc:featureList edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "Epi-GTBN" ; sc:url "http://122.205.95.139/Epi-GTBN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3173 ; sc:citation , "pmcid:PMC6648345", "pubmed:31045217" ; sc:description "Alignment-based bioinformatic tool for comparing chromatin state sequences." ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "EpiAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zzz3639/EpiAlign" ; biotools:primaryContact , "Haowen Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169, edam:topic_3173 ; sc:citation , "pmcid:PMC6602515", "pubmed:31114924" ; sc:description "Alignment of genomic regions with both sequence and epigenomic information." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "EpiAlignment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://epialign.ucsd.edu/" ; biotools:primaryContact "Sheng Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3173 ; sc:citation , "pmcid:PMC5860030", "pubmed:28605501" ; sc:description "Tool to define and explore genomic regions with tissue or cell type-specific epigenomic features." ; sc:featureList edam:operation_0438, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EpiCompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://epigenome.wustl.edu/EpiCompare/" ; biotools:primaryContact "Yu He" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3315, edam:topic_3324, edam:topic_3375 ; sc:citation , "pmcid:PMC7105007", "pubmed:31624039" ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_2426, edam:operation_3799 ; sc:name "EpiEstim" ; sc:softwareHelp ; sc:url "https://shiny.dide.imperial.ac.uk/epiestim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC7394332", "pubmed:30717649" ; sc:description "R package for large-scale integrated analysis in methylation hotspots linked to genetic regulation." ; sc:featureList edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "EpiMethEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/giupardeb/EpiMethEx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6868874", "pubmed:31752933" ; sc: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""" ; sc:featureList edam:operation_3186, edam:operation_3207, edam:operation_3222 ; sc:name "EpiMethylTag" ; sc:url "https://github.com/skoklab/EpiMethylTag" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3295, edam:topic_3520 ; sc:citation , "pmcid:PMC6581051", "pubmed:31123082" ; sc:description """Analysis of histone post-translational modifications by direct infusion mass spectrometry .""" ; sc:featureList edam:operation_0417, edam:operation_2929, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EpiProfileLite" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/zfyuan/EpiProfileLite" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC7703766", "pubmed:31501853" ; sc: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:" ; sc:featureList edam:operation_0441, edam:operation_3222, edam:operation_3501 ; sc:name "EpiSAFARI" ; sc:url "https://github.com/harmancilab/EpiSAFARI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:31466478" ; sc: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" ; sc:featureList edam:operation_0417 ; sc:name "EpiSmokEr" ; sc:url "https://github.com/sailalithabollepalli/EpiSmokEr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1931 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3173, edam:topic_3512 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3563, edam:operation_3677 ; sc:funder "Agencia Estatal de Investigación" ; sc:license "MIT" ; sc:name "Epigenomics Workflow on Galaxy and Jupyter" ; sc:softwareHelp ; sc:url "https://github.com/wilkinsonlab/epigenomics_pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170, edam:topic_3674, edam:topic_3794 ; sc:citation , "pmcid:PMC7141862", "pubmed:31794005" ; sc: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""" ; sc:featureList edam:operation_0308, edam:operation_2495, edam:operation_3186, edam:operation_3799 ; sc:license "BSD-2-Clause" ; sc:name "Episo" ; sc:url "https://github.com/liujunfengtop/Episo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3398 ; sc:citation ; sc:description "Tool for Model Discovery and Assembly with the Physiome Model Repository." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Epithelial Modelling Platform" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://epithelial-modelling-platform.nectar.auckland.ac.nz/" ; biotools:primaryContact "Dewan M. Sarwar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3407 ; sc:citation , "pmcid:PMC7703767", "pubmed:31598631" ; sc: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." ; sc:featureList edam:operation_0481, edam:operation_3660 ; sc:name "ErrorTracer" ; sc:url "https://github.com/TheAngryFox/ModelExplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0121, edam:topic_0128, edam:topic_0621, edam:topic_2640 ; sc:citation , "pmcid:PMC6943034", "pubmed:31598693" ; sc: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" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3902 ; sc:name "EuRBPDB" ; sc:url "http://EuRBPDB.syshospital.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation , "pubmed:26720812" ; sc:description "Open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EuroForMix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1.0" ; sc:url "http://www.euroformix.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3301, edam:topic_3305 ; sc:citation , , "pmcid:PMC7717563", "pubmed:33216746" ; sc: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." ; sc:featureList edam:operation_3280 ; sc:name "EventEpi" ; sc:url "https://github.com/aauss/EventEpi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6763948", "pubmed:31616466" ; sc: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" ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0337 ; sc:name "Evidence Based Microbial Associations Miner (EviMass)" ; sc:softwareHelp ; sc:url "https://web.rniapps.net/evimass/evimass/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3517 ; sc:citation , "pmcid:PMC6612835", "pubmed:31510680" ; sc: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" ; sc:featureList edam:operation_3436, edam:operation_3501, edam:operation_3766 ; sc:license "Apache-2.0" ; sc:name "EvidenceAggregatedDriverRanking" ; sc:url "https://github.com/Sage-Bionetworks/EvidenceAggregatedDriverRanking" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:name "Evidence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_1209 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0203 ; sc: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." ; sc:featureList edam:operation_2454 ; sc:name "EvidenceModeler" ; sc:url "https://github.com/EVidenceModeler/EVidenceModeler.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_2814, edam:topic_3170 ; sc:citation , "pmcid:PMC6806525", "pubmed:31640563" ; sc:description "RNA 3D structure prediction guided by independent folding of homologous sequences and multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io." ; sc:featureList edam:operation_0278, edam:operation_0295, edam:operation_0303, edam:operation_0476, edam:operation_2441 ; sc:license "GPL-3.0" ; sc:name "EvoClustRNA" ; sc:softwareHelp ; sc:url "https://github.com/mmagnus/EvoClustRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0736, edam:topic_3318 ; sc:citation , "pmcid:PMC7144094", "pubmed:31588495" ; sc: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.""" ; sc:featureList edam:operation_0303, edam:operation_0480, edam:operation_2492, edam:operation_3644 ; sc:license "MIT" ; sc:name "EvoEF2" ; sc:url "https://zhanglab.ccmb.med.umich.edu/EvoEF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3293 ; sc:citation , , "pmcid:PMC6916070", "pubmed:31842729" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "EvoFreq" ; sc:url "https://github.com/MathOnco/EvoFreq" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128 ; sc:author , , "Noé Vázquez" ; sc:citation , , "pubmed:30707359" ; sc:contributor , ; sc:description "EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for the same and distinct species." ; sc:featureList edam:operation_2422 ; sc:name "EvoPPI" ; sc:url "http://evoppi.i3s.up.pt/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3407 ; sc:citation , , "pmcid:PMC7703780", "pubmed:31560365", "pubmed:36806474" ; sc: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." ; sc:featureList edam:operation_2422, edam:operation_3432 ; sc:name "EvolClust" ; sc:softwareVersion "1.0" ; sc:url "http://evolclustdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0659 ; sc: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)." ; sc:name "EvryRNA" ; sc:url "https://evryrna.ibisc.univ-evry.fr/evryrna/evryrna/evryrna_home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31082210" ; sc:description "Integrated Solution for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis." ; sc:featureList edam:operation_2929, edam:operation_3627, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ExMS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hx2.med.upenn.edu/EXms/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3068 ; sc:citation , "pmcid:PMC4514929", "pubmed:25819675" ; sc:description "Tool for phylogenomic analyses on supercomputers." ; sc:featureList edam:operation_0547 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ExaML" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "https://github.com/stamatak/ExaML" ; biotools:primaryContact "Alexandros Stamatakis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3068, edam:topic_3292 ; sc:citation , , "pmcid:PMC7291460", "pubmed:32527218" ; sc: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.""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3659 ; sc:license "LGPL-3.0" ; sc:name "ExaStoLog" ; sc:url "https://github.com/sysbio-curie/exact-stoch-log-mod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3676 ; sc:citation ; sc:description "User-friendly tool for region-based rare variant association analysis (RVAA)." ; sc:featureList edam:operation_3196, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Exautomate" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/exautomate/Exautomate-Core" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7145592", "pubmed:31642488" ; sc: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""" ; sc:featureList edam:operation_0436, edam:operation_0446, edam:operation_2436 ; sc:name "ExonSkipDB" ; sc:url "https://ccsm.uth.edu/ExonSkipDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC6853681", "pubmed:31134279" ; sc:description "Sequence-graph-based tool to analyze variation in short tandem repeat regions." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ExpansionHunter" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Illumina/ExpansionHunter/" ; biotools:primaryContact "Illumina Open Source Software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0157, edam:topic_0196, edam:topic_2885 ; sc:citation , , "pmcid:PMC7187524", "pubmed:32345345" ; sc: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.""" ; sc:featureList edam:operation_0379, edam:operation_3196, edam:operation_3198 ; sc:license "Apache-2.0" ; sc:name "ExpansionHunter Denovo" ; sc:softwareHelp ; sc:url "https://github.com/Illumina/ExpansionHunterDenovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3320 ; sc:citation , "pmcid:PMC5540791", "pubmed:28673540" ; sc:description "Suite for single-cell alternative splicing analysis. Consists of outrigger, anchor and bonvoyage." ; sc:featureList edam:operation_2499 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Expedition" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YeoLab/Expedition" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3379, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , , "pubmed:32526385" ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:name "ExploreASL" ; sc:softwareHelp ; sc:url "http://www.ExploreASL.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3172, edam:topic_3305, edam:topic_3360, edam:topic_3390 ; sc:citation , "pmcid:PMC7145555", "pubmed:31724701" ; sc: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.""" ; sc:featureList edam:operation_2421 ; sc:name "Exposome Explorer" ; sc:softwareVersion "2.0" ; sc:url "http://exposome-explorer.iarc.fr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_3475 ; sc:name "Text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "Easy interface for determining the Clermont 2013 phylotype of an E. coli isolate" ; sc:featureList edam:operation_3478 ; sc:name "EzClermont" ; sc:url "http://ezclermont.hutton.ac.uk/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0632, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC6896590", "pubmed:31810454" ; sc: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""" ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "FACEPAI" ; sc:url "https://github.com/emmawahl/facepai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3382 ; sc:citation , "pmcid:PMC6851223", "pubmed:31401715" ; sc: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" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "FAConstructor" ; sc:url "https://github.com/3d-pli/FAConstructor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070, edam:topic_3518 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3501 ; sc:license "MIT" ; sc:name "FAIR" ; sc:url "https://github.com/FAIRMetrics/Metrics" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3256 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3956 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3256 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0605 ; sc:author , "Kees burger" ; sc:citation ; sc:contributor , "Kees burger", "Mark Thompson" ; sc: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." ; sc:featureList edam:operation_0226 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FAIRDataPoint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/FAIRDataTeam/FAIRDataPoint" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3071 ; sc: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." ; sc:name "FAIR Data tools" ; sc:url "https://www.dtls.nl/fair-data/find-fair-data-tools/#seventh" ; biotools:primaryContact "Rob Hooft" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3077 ; sc:description "FAIR search engine, designed as a prototype for finding FAIR resources." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FAIR Search Engine" ; sc:url "https://fairtraining.fair-dtls.surf-hosted.nl/search/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3345 ; sc: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." ; sc:isAccessibleForFree true ; sc:name "FAIRifier" ; sc:url "https://github.com/FAIRDataTeam/FAIRifier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3375, edam:topic_3407 ; sc:citation , "pubmed:31361490" ; sc: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" ; sc:featureList edam:operation_2939, edam:operation_3454, edam:operation_3891 ; sc:name "FAME 3" ; sc:url "https://nerdd.zbh.uni-hamburg.de/fame3/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_2269 ; sc:citation , "pmcid:PMC6697322", "pubmed:31419221" ; sc: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" ; sc:featureList edam:operation_2426, edam:operation_3891 ; sc:license "MIT" ; sc:name "FAMoS" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/FAMoS/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6522071", "pubmed:31059559" ; sc:description "Fast And Robust DEconvolution of Expression Profiles (FARDEEP) - machine learning tool for enumerating immune cell subsets from whole tumor tissue samples." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FARDEEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YuningHao/FARDEEP.git" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3512 ; sc:citation , , "pmcid:PMC7415647", "pubmed:32531203" ; sc: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" ; sc:featureList edam:operation_0278, edam:operation_0476, edam:operation_0483 ; sc:name "FARFAR2" ; sc:softwareHelp ; sc:url "https://rosie.rosettacommons.org/farfar2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC280013", "pubmed:3162770" ; sc:description "FASTA stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison." ; sc:featureList edam:operation_0346, edam:operation_2451 ; sc:name "FASTA API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/sss/fasta_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Bill Pearson" ; sc:citation , , , "pmcid:PMC11223882", "pmcid:PMC9252731", "pubmed:35412617", "pubmed:38597606" ; sc: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)." ; sc:featureList edam:operation_0346, edam:operation_2451 ; sc:name "FASTA (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University of Virginia" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/sss/fasta" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3400, edam:topic_3421 ; sc:citation , "pmcid:PMC6511155", "pubmed:31077222" ; sc: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." ; sc:featureList edam:operation_3352, edam:operation_3501, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FASTO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioportal.bioontology.org/ontologies/FASTO" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "a Perl module to parse FASTA/FASTQ files" ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "FASTX::Reader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.6" ; sc:url "https://metacpan.org/pod/FASTX::Reader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0820, edam:topic_3068 ; sc:citation ; sc:description "Software to analyze Molecular Dynamics simulations of membranes." ; sc:featureList edam:operation_2476, edam:operation_3279 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FATSLiM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fatslim.github.io/" ; biotools:primaryContact "Sébastien Buchoux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2830, edam:topic_3170, edam:topic_3308 ; sc:citation , , "pmcid:PMC7062913", "pubmed:32194545" ; sc: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:""" ; sc:featureList edam:operation_3200, edam:operation_3680, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "FB5P-seq" ; sc:url "https://github.com/MilpiedLab/FB5P-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3794 ; sc:citation , "pubmed:27663496" ; sc:description "Fast Bayesian-bound tool to calibrate RNA-seq aligners." ; sc:featureList edam:operation_3198, edam:operation_3627 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FBB" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/irenerodriguez/fbb/src/master/" ; biotools:primaryContact "Ramón Huerta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_3382 ; sc:author ; sc:citation , "pubmed:31878664" ; sc: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.""" ; sc:featureList edam:operation_3432 ; sc:name "FCM-m" ; sc:url "https://github.com/bishun945/FCMm" ; biotools:primaryContact "Yunmei Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3063, edam:topic_3474 ; sc:citation , "pmcid:PMC6818468", "pubmed:31695723" ; sc: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""" ; sc:featureList edam:operation_3439, edam:operation_3463, edam:operation_3660 ; sc:name "FCNN" ; sc:softwareHelp ; sc:url "https://bmbl.bmi.osumc.edu/FCNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "A calculator of conservation and allele frequency for variant pathogenic prediction." ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3461 ; sc:name "Frequency Conservation Score (FCS)" ; sc:url "http://bioinfo.cnic.es/FCS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3016 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3796 ; sc:description "File format converter for FImpute" ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FConverter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://github.com/herrsalmi/FConverter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC6471690", "pubmed:30999847" ; sc:description "Software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing." ; sc:featureList edam:operation_0436, edam:operation_3096, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "FEDRO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://math.unipa.it/rombo/FEDRO" ; biotools:primaryContact "Simona E. Rombo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3399, edam:topic_3577 ; sc:citation , "pubmed:31542453" ; sc:description "An Individualized Prediction Model for Long-term Lung Function Trajectory and Risk of COPD in the General Population" ; sc:name "FEV1" ; sc:softwareHelp ; sc:url "http://resp.core.ubc.ca/ipress/FraminghamFEV1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3316 ; sc:citation , , "pubmed:31574354" ; sc: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.""" ; sc:name "FEniCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fenicsproject.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_0749 ; sc:citation , "pubmed:31830251" ; sc: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""" ; sc:featureList edam:operation_0463, edam:operation_1781, edam:operation_3792 ; sc:name "FFLtool" ; sc:url "http://bioinfo.life.hust.edu.cn/FFLtool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC6836741", "pubmed:31649055" ; sc:description "Analysis pipeline for FFPEcap-seq. A method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3211, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "FFPEcap-seq" ; sc:url "https://github.com/jeffpkamp/FFPEcap-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_0625, edam:topic_3314, edam:topic_3382 ; sc:citation , "pmcid:PMC6822706", "pubmed:31671091" ; sc: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.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "Fungal Feature Tracker (FFT)" ; sc:url "https://github.com/hsueh-lab/FFT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_2885, edam:topic_3293 ; sc:citation ; sc:description "Method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "WTFPL" ; sc:name "FGTpartitioner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/tkchafin/FGTpartitioner" ; biotools:primaryContact "Tyler K. Chafin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3063, edam:topic_3324, edam:topic_3400, edam:topic_3489 ; sc:citation , , "pmcid:PMC6784845", "pmcid:PMC6913576", "pubmed:31598581", "pubmed:31621639" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422, edam:operation_3192, edam:operation_3891 ; sc:name "FHIR" ; sc:softwareHelp , ; sc:softwareVersion "4.0.1" ; sc:url "https://www.hl7.org/fhir/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3301 ; sc:citation , , "pmcid:PMC7653809", "pubmed:33172489" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "FINET" ; sc:url "https://github.com/anyouwang/finet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6916105", "pubmed:31847917" ; sc: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""" ; sc:featureList edam:operation_3227, edam:operation_3629, edam:operation_3675, edam:operation_3695 ; sc:license "MIT" ; sc:name "FIREVAT" ; sc:url "https://github.com/cgab-ncc/FIREVAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382, edam:topic_3855 ; sc:citation , "pubmed:31443908" ; sc: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" ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "FISIK" ; sc:url "https://github.com/kjaqaman/FISIK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3518, edam:topic_3855 ; sc:citation ; sc:description "Statistical modeling tool for transcriptome dynamics under fluctuating field conditions." ; sc:featureList edam:operation_1812, edam:operation_3659, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "FIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.0.6" ; sc:url "https://cran.r-project.org/package=FIT" ; biotools:primaryContact "Koji Iwayama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780 ; sc:description "Integrative database around plant genomes." ; sc:name "FLAGdb" ; sc:url "http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31384046" ; sc: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" ; sc:featureList edam:operation_0308, edam:operation_0428, edam:operation_3192 ; sc:name "FLAM-seq analysis pipeline" ; sc:url "https://github.com/rajewsky-lab/FLAMAnalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC6314628", "pubmed:30543621" ; sc:description "Full-Length Envelope Analyzer (FLEA) - tool for longitudinal analysis of viral amplicons." ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FLEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/veg/flea-pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3372 ; sc:citation , "pubmed:31473443" ; sc: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" ; sc:license "GPL-3.0" ; sc:name "FLEXOR" ; sc:url "https://github.com/FlexorSoftware/flexor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0736, edam:topic_3318 ; sc:citation , "pmcid:PMC7032052", "pubmed:31490691" ; sc: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-Hückel potential)" ; sc:featureList edam:operation_0409, edam:operation_2929, edam:operation_3454 ; sc:name "FMAPB2" ; sc:url "http://pipe.rcc.fsu.edu/fmapb2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , , "pmcid:PMC7748281", "pubmed:33290385" ; sc: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" ; sc:license "GPL-3.0" ; sc:name "FOCAL3D" ; sc:url "https://github.com/MilsteinLab/FOCAL3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3361, edam:topic_3474 ; sc:author ; sc:citation , "pmcid:PMC6895225", "pubmed:31804528" ; sc:description "Computing the statistical significance of optimized communities in networks." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3562 ; sc:license "Apache-2.0" ; sc:name "Fast Optimized Community Significance (FOCS)" ; sc:url "https://github.com/google/fast-optimized-community-significance" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3321, edam:topic_3474 ; sc:citation , "pmcid:PMC6949135", "pubmed:30480667" ; sc:description "Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks." ; sc:featureList edam:operation_2238, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "FORECasT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://partslab.sanger.ac.uk/FORECasT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0202, edam:topic_0769 ; sc:citation ; sc:contributor "Ali Esfahani" ; sc:description "Tool for the systematic comparison of translational drug response modeling pipelines." ; sc:featureList edam:operation_1812, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FORESEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://osf.io/rf6qk/" ; biotools:primaryContact "L. Turnhoff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3676 ; sc:citation , "pmcid:PMC6296055", "pubmed:30558649" ; sc:description "Tool for ranking variants and building an optimal graph genome." ; sc:featureList edam:operation_3211, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FORGe" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/langmead-lab/FORGe/tree/v1.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2229, edam:topic_3067, edam:topic_3170 ; sc:citation ; sc:description "A Python package automatic computed fusion of ontologies." ; sc:license "GPL-3.0" ; sc:name "FOntCell" ; sc:url "https://gitlab.com/JavierCabau/fontcell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0607, edam:topic_3077, edam:topic_3572 ; sc: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.""" ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "FP-LIMS" ; sc:operatingSystem "Windows" ; sc:provider "Philip Moerke" ; sc:softwareHelp ; sc:url "https://www.fp-lims.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:31070725" ; sc:description "Molecular featurizer for learning molecular properties." ; sc:featureList edam:operation_3216, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FP2VEC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wsjeon92/FP2VEC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:30886412" ; sc:description "Community-editable fluorescent protein database, cataloging an expanded range of proteins and parameters, including a new spectra viewer." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FPbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "https://www.fpbase.org/" ; biotools:primaryContact "Talley Lambert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3174 ; sc:citation , "pmcid:PMC6694608", "pubmed:31416440" ; sc: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" ; sc:featureList edam:operation_3180, edam:operation_3218, edam:operation_3359 ; sc:name "FQStat" ; sc:softwareHelp ; sc:url "http://otulab.unl.edu/FQStat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3325, edam:topic_3512 ; sc:author ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0433, edam:operation_2499, edam:operation_3196 ; sc:license "MIT" ; sc:name "FRASER" ; sc:url "http://bioconductor.org/packages/release/bioc/html/FRASER.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3474 ; sc:author ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3196 ; sc:license "LGPL-2.0" ; sc:name "FRESA" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=FRESA.CAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3315, edam:topic_3855 ; sc:citation , "pubmed:30580414" ; sc:description "Food Spoilage and Safety Predictor (FSSP)" ; sc:featureList edam:operation_2426, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "FSSP" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fssp.food.dtu.dk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation , "pubmed:31384919" ; sc: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" ; sc:featureList edam:operation_0503, edam:operation_0509, edam:operation_0510 ; sc:name "FTAlign" ; sc:url "http://huanglab.phys.hust.edu.cn/ftalign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2229, edam:topic_2640, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC7141866", "pubmed:31750879" ; sc: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""" ; sc:featureList edam:operation_2426, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "FUMOSO" ; sc:url "https://github.com/aresio/FUMOSO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2828 ; sc:citation , "pmcid:PMC6878879", "pubmed:31798363" ; sc: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.""" ; sc:featureList edam:operation_2409, edam:operation_3435, edam:operation_3453 ; sc:name "FXD-CSD-GUI" ; sc:url "https://owncloud.gwdg.de/index.php/s/JGluHlEp0pEUcAH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3399, edam:topic_3500 ; sc:citation , "pubmed:31532469" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3891 ; sc:isAccessibleForFree false ; sc:name "FaceGen" ; sc:url "https://facegen.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3794 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FaceSync" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cosanlab/facesync" ; biotools:primaryContact "Jin Hyun Cheong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_3047 ; sc:citation ; sc:description "PubChem and ChEMBL Beyond Lipinski." ; sc:featureList edam:operation_0337 ; sc:name "Faerun" ; sc:url "http://faerun.gdb.tools/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3474 ; sc:author ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_0253 ; sc:name "FastFeatGen" ; sc:url "https://github.com/khaled-rahman/FastFeatGen" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC6580563", "pubmed:31208325" ; sc:description "Fast preprocessing of next-generation sequencing reads." ; sc:featureList edam:operation_3192, edam:operation_3219, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FastProNGS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/Megagenomics/FastProNGS" ; biotools:primaryContact "G. Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Tools to deal with fastq sequences and paired-end reads." ; sc:name "FastqProcessing" ; sc:url "https://bioweb.pasteur.fr/packages/pack@FastqProcessing@0.38.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6500068", "pubmed:31053060" ; sc:contributor "Claudio Lottaz", "Julia Engelmann", "Paula Pérez Rubio" ; sc:description "High-performance preprocessing tool for RNA-seq data." ; sc:featureList edam:operation_3180, edam:operation_3219, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FastqPuri" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/jengelmann/FastqPuri" ; biotools:primaryContact "Julia Engelmann" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "An integrated Omics data warehouse for FAW, Spodoptera frugiperda" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "FawMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "http://insectmine.org:8080/fawmine" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2350 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3780 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0099 ; sc:description "A Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs" ; sc:featureList edam:operation_0292, edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Fcirc" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://github.com/WangHYLab/fcirc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_3174 ; sc:citation , , "pmcid:PMC7005843", "pubmed:32082281" ; sc: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)" ; sc:featureList edam:operation_0310, edam:operation_3798 ; sc:name "FeGenie" ; sc:url "https://github.com/Arkadiy-Garber/FeGenie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pmcid:PMC6446290", "pubmed:30943889" ; sc:description "Software for feature selection based on machine learning approaches." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "FeatureSelect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LBBSoft/FeatureSelect" ; biotools:primaryContact "LBBSoft" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3292 ; sc:citation , "pmcid:PMC6656964", "pubmed:31372542" ; sc:description "A web application for new bioactive peptides from food protein" ; sc:featureList edam:operation_0366, edam:operation_0482, edam:operation_3646 ; sc:name "FeptideDB" ; sc:url "http://www4g.biotec.or.th/FeptideDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3676 ; sc:citation , "pmcid:PMC4937191", "pubmed:27153588" ; sc:description "Tool to extract data from the 1000 Genomes Project." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Ferret" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://limousophie35.github.io/Ferret/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:31362508" ; sc: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" ; sc:featureList edam:operation_3639 ; sc:name "Fertility-GRU" ; sc:url "https://github.com/khanhlee/fertility-gru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3067, edam:topic_3444 ; sc:citation , "pmcid:PMC6532268", "pubmed:31118056" ; sc:description "Numerical phantom for fetal cardiovascular magnetic resonance imaging." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Fetal XCMR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cwroy/Fetal-XCMR/" ; biotools:primaryContact "Chris Roy", "Christopher K. Macgowan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2885 ; sc:citation , "pmcid:PMC6602425", "pubmed:31114899" ; sc:description "Webserver for scoring the impact of single nucleotide variants in the dog genome." ; sc:featureList edam:operation_0331, edam:operation_0484, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Fido-SNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fidosnp.bca.unipd.it/" ; biotools:primaryContact , "Piero Fariselli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0632, edam:topic_3855 ; sc:citation , "pubmed:31425088" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3501 ; sc:name "FieldView" ; sc:url "https://cmci.colorado.edu/visualab/fieldview" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3467, edam:format_3548, edam:format_3579, edam:format_3591, edam:format_3592, edam:format_3603, edam:format_3990 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3467, edam:format_3548, edam:format_3579, edam:format_3591, edam:format_3592, edam:format_3603, edam:format_3990 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , , "pmcid:PMC3855844", "pmcid:PMC6861648", "pubmed:22743772", "pubmed:31763187" ; sc:description """A quantitative method to analyse F-actin distribution in cells. 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Fiji bundles together many popular and useful ImageJ plugins for image analysis into one installation, and automatically manages their dependencies and updating.""" ; sc:featureList edam:operation_3434, edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Fiji" ; sc:url "https://fiji.sc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0196, edam:topic_3474, edam:topic_3542 ; sc:citation , , "pmcid:PMC7577475", "pubmed:33035205" ; sc:description "interpretable supervised contact prediction using inter-domain coevolution." ; sc:featureList edam:operation_0272, edam:operation_0476, edam:operation_2950, edam:operation_3350 ; sc:name "FilterDCA" ; sc:url "http://gitlab.lcqb.upmc.fr/muscat/FilterDCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3175, edam:topic_3673 ; sc:citation , "pmcid:PMC6836550", "pubmed:31694722" ; sc:description """whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. 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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""" ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3227, edam:operation_3695, edam:operation_3802 ; sc:name "FixVAF" ; sc:url "https://github.com/danchubb/FixVAF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3304, edam:topic_3474 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0551, edam:operation_2422 ; sc:license "MIT" ; sc:name "Flagser" ; sc:url "https://github.com/luetge/flagser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31542415" ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "FlashWeave" ; sc:url "https://github.com/meringlab/FlashWeave.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3172, edam:topic_3336, edam:topic_3390 ; sc:citation , "pmcid:PMC6823394", "pubmed:31696036" ; sc: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.""" ; sc:featureList edam:operation_0305, edam:operation_3216, edam:operation_3799, edam:operation_3891 ; sc:name "FlavoDb" ; sc:url "http://bioinfo.net.in/flavodb/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6612844", "pubmed:31510682" ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3211 ; sc:license "MIT" ; sc:name "Flint" ; sc:softwareHelp , , ; sc:url "https://camilo-v.github.io/flint/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3398, edam:topic_3452 ; sc:citation , "pubmed:31482902" ; sc: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." ; sc:license "MIT" ; sc:name "FlowSculpt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.flowsculpt.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_0781, edam:topic_3305 ; sc:citation , "pubmed:31687905" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2429 ; sc:name "FluNet" ; sc:softwareHelp ; sc:url "https://www.who.int/influenza/gisrs_laboratory/flunet/en/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3293, edam:topic_3324 ; sc:citation , "pubmed:31774482" ; sc:description "A database for the study of genomic reassortments among influenza viruses." ; sc:featureList edam:operation_0323, edam:operation_0552, edam:operation_3431 ; sc:name "FluReassort" ; sc:url "https://www.jianglab.tech/FluReassort" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3305 ; sc:citation , "pubmed:31687905" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2429 ; sc:name "FluView" ; sc:url "https://www.cdc.gov/flu/weekly/fluviewinteractive.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3372, edam:topic_3382 ; sc:citation , "pmcid:PMC6493727", "pubmed:31042738" ; sc:description "Algorithm for automated analysis of high-throughput droplet microfluidic data." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FluoroCellTrack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Manibarathi/FluoroCellTrack" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382, edam:topic_3518 ; sc:citation , , "pmcid:PMC7100978", "pubmed:32126077" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3799 ; sc:license "MIT" ; sc:name "Fly-QMA" ; sc:softwareHelp , , ; sc:url "https://www.sbernasek.com/flyqma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_3304, edam:topic_3382, edam:topic_3474 ; sc:citation , , "pubmed:21129968", "pubmed:31797265" ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_2940, edam:operation_3450 ; sc:name "FlyCircuit" ; sc:url "http://www.flycircuit.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3174, edam:topic_3673 ; sc:author "Jeffrey Yuan", "Mikhail Kolmogorov", "Yu Lin" ; sc:citation , , , "pmcid:PMC10699202", "pmcid:PMC6807382", "pubmed:30936562", "pubmed:31483244", "pubmed:33020656" ; sc: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." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3730 ; sc:name "Flye" ; sc:url "https://github.com/fenderglass/Flye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407, edam:topic_3518 ; sc:description "Formal model checking based pathway analysis (FoPA) - tool for identification of perturbed signaling pathways in clinical conditions using formal methods." ; sc:featureList edam:operation_0533, edam:operation_3501, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:name "FoPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/fmansoori/FoPA" ; biotools:primaryContact "Mansoori F." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2828, edam:topic_3047, edam:topic_3068, edam:topic_3489 ; sc:citation , "pubmed:31686102" ; sc:description "The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422, edam:operation_3454, edam:operation_3695 ; sc:name "FoldamerDB" ; sc:softwareHelp ; sc:url "http://foldamerdb.ttk.hu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3297, edam:topic_3301 ; sc:citation , "pubmed:26704067" ; sc: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)." ; sc:name "FoodMicrobionet" ; sc:softwareVersion "3.1" ; sc:url "http://www.foodmicrobionet.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3168, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6938691", "pubmed:31851693" ; sc: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""" ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3225, edam:operation_3675, edam:operation_3695 ; sc:license "MIT" ; sc:name "ForestQC" ; sc:url "https://github.com/avallonking/ForestQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3050, edam:topic_3489 ; sc:citation , "pmcid:PMC6864098", "pubmed:31745083" ; sc:description "A database for the late quaternary fossil records of Sahul along with data processing scripts." ; sc:name "FosSahul" ; sc:url "https://github.com/GlobalEcologyFlinders/FosSahul" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3382 ; sc:citation , ; sc:description "FossilJ is a ImageJ plugin for fossil data acquisition and semi-automatic measurements by image analysis." ; sc:featureList edam:operation_2409, edam:operation_3435, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "FossilJ" ; sc:url "https://github.com/fionapye/FossilJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0749, edam:topic_3303 ; sc:citation , "pmcid:PMC6301337", "pubmed:30576493" ; sc:description "Message-oriented, horizontally scalable ETL system for scientific data integration and enhancement." ; sc:featureList edam:operation_2422, edam:operation_3436, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Foundry" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/biocaddie/Foundry-ES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3382, edam:topic_3500 ; sc:citation ; sc:description "Automated tool for animal detection in camera trap images." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "FoxMask" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/edevost/foxmask" ; biotools:primaryContact "Eric Devost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0780 ; sc:citation , "pubmed:27794557" ; sc:description "Graphical tool for assessing fractionation bias following polyploidy." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FractBias" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://genomevolution.org/CoGe/SynMap.pl" ; biotools:primaryContact "Eric Lyons" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0593, edam:topic_2258, edam:topic_3314 ; sc:citation , , "pmcid:PMC3961104", "pubmed:24688855" ; sc: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""" ; sc:featureList edam:operation_0249, edam:operation_0479, edam:operation_0480 ; sc:license "BSD-Source-Code" ; sc:name "FragBuilder" ; sc:softwareHelp , ; sc:url "https://github.com/jensengroup/fragbuilder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169, edam:topic_3174, edam:topic_3179 ; sc:citation , "pmcid:PMC8136837", "pubmed:31712779" ; sc: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""" ; sc:featureList edam:operation_0244, edam:operation_3192, edam:operation_3435 ; sc:license "MIT" ; sc:name "FreeHi-C" ; sc:url "https://github.com/keleslab/FreeHiC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1668 ; sc:encodingFormat edam:format_2331 ; sc:name "Z-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pmcid:PMC5428484", "pubmed:28336965" ; sc: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." ; sc:featureList edam:operation_1778, edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Frela" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://frela.eurac.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0632, edam:topic_3168, edam:topic_3293, edam:topic_3512 ; sc:citation ; sc:description "FrogCap is a modular sequence capture probeset for phylogenomics and population genetics for frogs" ; sc:featureList edam:operation_2419, edam:operation_3192, edam:operation_3196 ; sc:name "FrogCap" ; sc:url "https://github.com/chutter/FrogCap-Sequence-Capture" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7523651", "pubmed:31596475" ; sc: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." ; sc:featureList edam:operation_0306, edam:operation_3435 ; sc:name "FullMeSH" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31596475" ; biotools:primaryContact "Shanfeng Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC6612877", "pubmed:31510685" ; sc: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" ; sc:featureList edam:operation_3207, edam:operation_3501 ; sc:name "FunDMDeep-m6A" ; sc:url "https://github.com/NWPU-903PR/DMDeepm6A1.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0218, edam:topic_0602, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31882995" ; sc: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""" ; sc:featureList edam:operation_0306, edam:operation_0362, edam:operation_2495, edam:operation_2939, edam:operation_3208 ; sc:name "FunGeCo" ; sc:url "https://web.rniapps.net/fungeco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0621 ; sc:citation , "pmcid:PMC6376640", "pubmed:30767762" ; sc:description "User-friendly graphical interface that allows to visualize and summarize the functional annotations of one or multiple molecular biology experiments at once." ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FunMappOne" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Greco-Lab/FunMappOne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0769 ; sc:citation , "pubmed:31454647" ; sc: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" ; sc:featureList edam:operation_3501 ; sc:name "FunVar" ; sc:url "https://github.com/lasigeBioTM/FunVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308, edam:topic_3473 ; sc:citation , "pmcid:PMC6377781", "pubmed:30770734" ; sc:description "Automated and interactive pattern recognition tool to integrate time with multi-omics assays." ; sc:featureList edam:operation_0531, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "Functional Heatmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo-abcc.ncifcrf.gov/Heatmap/" ; biotools:primaryContact "Daniel Watson", "Joshua Williams", "Ruoting Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc: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." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Locating Retinal Blood Vessels on Fundus Images by Kirsch s Template and Fuzzy C-Means" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63116-locating-retinal-blood-vessels-on-fundus-images-by-kirsch-s-template-and-fuzzy-c-means" ; biotools:primaryContact "Jemima Jeba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0202, edam:topic_0625 ; sc:citation , "pmcid:PMC6546077", "pubmed:31183256" ; sc:description "R package for QTL mapping using longitudinal phenotypes." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Funmap2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.4.2" ; sc:url "https://github.com/wzhy2000/Funmap2" ; biotools:primaryContact "N. Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6808644", "pubmed:31610622" ; sc:description """An accurate prediction of fusion genes from RNA-Seq data. Homepage may be broken as of January 4th, 2021.""" ; sc:featureList edam:operation_2454, edam:operation_3192, edam:operation_3359 ; sc:name "FusionScan" ; sc:url "http://biome.ewha.ac.kr/fusionscan/fusionscan.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0749, edam:topic_3382 ; sc:author "Peter Andrews" ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2940 ; sc:license "MIT" ; sc:name "G-Graph" ; sc:url "https://mumdex.com/ggraph/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3382 ; sc:citation , "pmcid:PMC6821377", "pubmed:31070714" ; sc:description "Galaxy-based platform for collaborative annotation of eukaryotic genomes." ; sc:featureList edam:operation_0525, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "G-OnRamp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://gonramp.wustl.edu/" ; biotools:primaryContact "Jeremy Goecks", "Luke Sargent", "Sarah C.R. Elgin", "Wilson Leung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3360, edam:topic_3517 ; sc:citation , , "pmcid:PMC6894795", "pubmed:31805043" ; sc:description "Assessing the performance of genome-wide association studies for predicting disease risk." ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3791 ; sc:name "G-WIZ" ; sc:url "https://github.com/jonaspatronjp/GWIZ-Rscript/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3517 ; sc:citation , "pubmed:30848784" ; sc:description "Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "G2P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/XiaoleiLiuBio/G2P" ; biotools:primaryContact "Xiaolei Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation , "pubmed:31393560" ; sc:description "R package to interactively visualize genetic mutation data using a lollipop-diagram." ; sc:featureList edam:operation_0337, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "G3viz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=g3viz" ; biotools:primaryContact "Xin Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0622, edam:topic_0780, edam:topic_3512 ; sc:citation ; sc:description """A Python script for dividing genome annotation files into feature-based files. A python script for extracting genome features from GTF/GFF3.""" ; sc:featureList edam:operation_0362, edam:operation_2478, edam:operation_3800 ; sc:name "GAD" ; sc:url "https://github.com/bio-projects/GAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3056 ; sc:description "Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data" ; sc:name "GADMA" ; sc:url "https://github.com/ctlab/GADMA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3168, edam:topic_3474 ; sc:citation , ; sc:description "A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction." ; sc:featureList edam:operation_0310, edam:operation_0484, edam:operation_0487, edam:operation_3198, edam:operation_3211 ; sc:name "GAEseq" ; sc:url "https://github.com/WuLoli/GAEseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3520 ; sc:citation , "pmcid:PMC6324007", "pubmed:30371822" ; sc:description "Online tool to build 3D models of GAG sequences from GlycoCT codes." ; sc:featureList edam:operation_2422, edam:operation_3561 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GAG builder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://glycan-builder.cermav.cnrs.fr/gag/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0780 ; sc:citation , "pubmed:30926570" ; sc:description "A Docker-based package for genome analysis and visualization." ; sc:featureList edam:operation_0362, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "Genome Annotator Light (GAL)" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "1.1" ; sc:url "https://hub.docker.com/r/cglabiicb/gal" ; biotools:primaryContact "Arijit Panda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3524 ; sc:citation , ; sc:description "GAMA is a modeling and simulation development environment for building spatially explicit agent-based simulations." ; sc:featureList edam:operation_2426 ; sc:name "GAMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gama-platform.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2828, edam:topic_3306, edam:topic_3452 ; sc:citation ; sc: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" ; sc:license "LGPL-2.1" ; sc:name "GAMer" ; sc:softwareHelp ; sc:url "http://github.com/ctlee/gamer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc:description "Collection of commands for working with phylogenetic data." ; sc:featureList edam:operation_0325, edam:operation_0567, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GAPPA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://github.com/lczech/gappa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099, edam:topic_0654, edam:topic_3168 ; sc:citation , , "pmcid:PMC6815017", "pmcid:PMC6862790", "pubmed:31653208", "pubmed:31744474" ; sc: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""" ; sc:featureList edam:operation_0491, edam:operation_0495, edam:operation_0496 ; sc:license "Apache-2.0" ; sc:name "GASAL2" ; sc:url "https://github.com/nahmedraja/GASAL2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3308, edam:topic_3673 ; sc:citation , "pmcid:PMC6289130", "pubmed:29982281" ; sc:description "Customizable computational tool included in Genome Analysis Toolkit (GATK) for the discovery and identification of microbial sequences in libraries from eukaryotic hosts." ; sc:featureList edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "GATK PathSeq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/broadinstitute/gatk" ; biotools:primaryContact "Matthew Meyerson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0780, edam:topic_3050, edam:topic_3277, edam:topic_3303 ; sc:citation , "pmcid:PMC6805691", "pubmed:31656398" ; sc: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." ; sc:featureList edam:operation_2421 ; sc:name "GBIF" ; sc:softwareHelp ; sc:url "https://www.gbif.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_0622, edam:topic_2229 ; sc:citation , "pmcid:PMC6828702", "pubmed:31685817" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_3559 ; sc:name "GBOL" ; sc:url "http://gbol.life" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3518, edam:topic_3673 ; sc:citation , "pmcid:PMC6683502", "pubmed:31387530" ; sc: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" ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "GBS" ; sc:url "http://github.com/malemay/delgbs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3336, edam:topic_3379 ; sc:citation , "pmcid:PMC7394323", "pubmed:30717669" ; sc:description "Galaxy workflow system for predictive model building for virtual screening." ; sc:featureList edam:operation_0482, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GCAC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://toolshed.g2.bx.psu.edu/repository?repository_id=351af44ceb587e54" ; biotools:primaryContact "Andrew M. Lynn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3375, edam:topic_3518 ; sc:citation , "pubmed:31397851" ; sc: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" ; sc:featureList edam:operation_0463, edam:operation_3482, edam:operation_3792 ; sc:name "GCMDR" ; sc:url "https://github.com/xyzx2019/GCMDR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2436, edam:operation_3439, edam:operation_3625 ; sc:name "GCNG" ; sc:url "https://github.com/xiaoyeye/GCNG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0780 ; sc:citation , "pubmed:29420675" ; sc:description "Web tool for guanylyl cyclase functional centre prediction from amino acid sequence." ; sc:featureList edam:operation_0418, edam:operation_0478 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GCPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gcpred.com/" ; biotools:primaryContact "Aloysius Wong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC6902276", "pubmed:31850053" ; sc: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""" ; sc:featureList edam:operation_0292, edam:operation_0362, edam:operation_0524, edam:operation_3227, edam:operation_3644 ; sc:license "MIT" ; sc:name "GEAN" ; sc:url "https://github.com/baoxingsong/GEAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC6624217", "pubmed:31100356" ; sc:description "GEnetic Antibiotic Resistance and Susceptibility Database." ; sc:featureList edam:operation_3196, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GEAR-base" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gear-base.com" ; biotools:primaryContact "Andreas E. Posch", "Andreas Keller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC6883002", "pubmed:31824573" ; sc:description """Graph Embedding Deep Learning Guides Microbial Biomarkers' Identification. graph embedding deep learning guide microbial biomarkers' identification.""" ; sc:featureList edam:operation_2940, edam:operation_3439 ; sc:name "GEDFN" ; sc:url "https://github.com/MicroAVA/GEDFN.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3629, edam:operation_3800 ; sc:name "GEDIT" ; sc:url "http://webtools.mcdb.ucla.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3314, edam:topic_3489 ; sc:citation , "pmcid:PMC6661976", "pubmed:31404233" ; sc: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" ; sc:name "GEM-NET" ; sc:url "http://gem-net.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3303, edam:topic_3398 ; sc:citation , "pmcid:PMC6805226", "pubmed:31406981" ; sc: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" ; sc:featureList edam:operation_0331 ; sc:name "GEMME" ; sc:url "http://www.lcqb.upmc.fr/GEMME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3382 ; sc:citation , "pmcid:PMC9881680", "pubmed:29401212" ; sc: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." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GEMMER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gemmer.barberislab.com" ; biotools:primaryContact "Matteo Barberis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3382, edam:topic_3407 ; sc:citation ; sc:description """Extracting Views into Genome-scale Metabolic Models. The GEMtractor a platform for trimming and extracting genome-scale metabolic models (GEMs).""" ; sc:featureList edam:operation_3192, edam:operation_3280, edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "GEMtractor" ; sc:url "http://sbi.uni-rostock.de/gemtractor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6796420", "pubmed:31619158" ; sc: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""" ; sc:featureList edam:operation_0571, edam:operation_2436, edam:operation_2939, edam:operation_3435, edam:operation_3891 ; sc:name "GENAVi" ; sc:url "https://junkdnalab.shinyapps.io/GENAVi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0769 ; sc:citation , , , , "pmcid:PMC3431492", "pmcid:PMC3431493", "pmcid:PMC6323946", "pmcid:PMC7778937", "pubmed:22955987", "pubmed:22955988", "pubmed:30357393", "pubmed:33270111" ; sc: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." ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GENCODE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , , , ; sc:url "https://www.gencodegenes.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , , ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0292, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "GENOMICUS" ; sc:softwareHelp ; sc:url "http://www.genomicus.biologie.ens.fr/genomicus/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3192, edam:operation_3223, edam:operation_3435 ; sc:name "GEO2RNAseq" ; sc:softwareHelp ; sc:url "https://anaconda.org/xentrics/r-geo2rnaseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0204, edam:topic_0218, edam:topic_0219 ; sc:citation , "pubmed:31617460" ; sc: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)""" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_2495, edam:operation_3431 ; sc:name "GEREDB" ; sc:url "http://www.thua45.cn/geredb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293, edam:topic_3299 ; sc:author "Agata Kilar" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GERONIMO" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/amkilar/GERONIMO.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0736, edam:topic_2640, edam:topic_3170 ; sc:citation , "pubmed:31630971" ; sc: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.""" ; sc:featureList edam:operation_0264, edam:operation_2238, edam:operation_2495 ; sc:name "GESUR" ; sc:url "http://gesur.cancer-pku.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3361, edam:topic_3489 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_3435 ; sc:name "GET-IT" ; sc:url "http://get-it.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3421, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6857918", "pubmed:31730620" ; sc: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.""" ; sc:featureList edam:operation_0571, edam:operation_2454, edam:operation_3891 ; sc:name "GE LDA Survival" ; sc:url "https://github.com/nitsanluke/GE-LDA-Survival" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3474, edam:topic_3517 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3659, edam:operation_3891 ; sc:name "GFA" ; sc:url "https://cran.r-project.org/web/packages/GFA/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3172 ; sc:citation , "pmcid:PMC6901079", "pubmed:31077287" ; sc:description "Exact hypothesis testing for shrinkage based Gaussian Graphical Models." ; sc:featureList edam:operation_2238, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GGMs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/V-Bernal/GGM-Shrinkage" ; biotools:primaryContact "Peter Horvatovich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6517830", "pubmed:31089686" ; sc:description "Knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal (GI) cancer." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GIDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bmtongji.cn/GIDB/index.html" ; biotools:primaryContact "Xiaoyan Zhang", "Ying Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3315 ; sc:citation ; sc: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" ; sc:name "GISA" ; sc:url "https://github.com/ceegeeCode/GISA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3656 ; sc:citation , "pmcid:PMC6364044", "pubmed:30553884" ; sc: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." ; sc:featureList edam:operation_1812, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GITAR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://genomegitar.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0781, edam:topic_3050, edam:topic_3174 ; sc:citation , "pmcid:PMC6936153", "pubmed:31884971" ; sc: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""" ; sc:featureList edam:operation_0362, edam:operation_3198, edam:operation_3460 ; sc:name "GL-UVAB" ; sc:url "https://sourceforge.net/projects/gluvab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2269, edam:topic_3304 ; sc:citation , , "pmcid:PMC6914332", "pubmed:31841564" ; sc: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)" ; sc:featureList edam:operation_3436 ; sc:license "MIT" ; sc:name "GLAMbox" ; sc:url "https://glambox.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation , "pmcid:PMC6355098", "pubmed:28541490" ; sc:description "Genomic loci annotation and enrichment tool." ; sc:featureList edam:operation_3197, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GLANET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/burcakotlu/GLANET" ; biotools:primaryContact "Burçak Otlu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6927135", "pubmed:31870412" ; sc: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.""" ; sc:featureList edam:operation_2939, edam:operation_3563, edam:operation_3891 ; sc:license "Artistic-2.0" ; sc:name "GLM-PCA" ; sc:url "https://cran.r-project.org/web/packages/glmpca/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3174 ; sc:citation , "pmcid:PMC6266928", "pubmed:30497362" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GLOSSary" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.szn.it/glossary/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0781, edam:topic_3305 ; sc:citation , "pmcid:PMC6299651", "pubmed:30563445" ; sc: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." ; sc:featureList edam:operation_0499, edam:operation_0564, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "GLUE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.glue.cvr.ac.uk/#/home" ; biotools:primaryContact "Josh Singer", "Robert Gifford" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3518 ; sc:citation ; sc:description "Web-based tool to visualize, analyze, present and mine glycan microarray data." ; sc:featureList edam:operation_1812, edam:operation_3218, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GLycan Array Dashboard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://glycotoolkit.com/Tools/GLAD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31070732" ; sc:description "Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/chaoning/GMA" ; biotools:primaryContact "Jian-Feng Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pubmed:31825885" ; sc: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.""" ; sc:featureList edam:operation_0346 ; sc:name "GMCLDA" ; sc:url "https://github.com/bioinfomaticsCSU/GMCLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3385, edam:topic_3810 ; sc:citation , "pmcid:PMC6711351", "pubmed:31467803" ; sc: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" ; sc:name "GMpi" ; sc:url "https://github.com/BrandinGrindstaff/GMpi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0625, edam:topic_3174 ; sc:citation , "pubmed:31504765" ; sc: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" ; sc:featureList edam:operation_0362 ; sc:name "GMrepo" ; sc:url "https://gmrepo.humangut.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC8424702", "pubmed:31874639" ; sc: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""" ; sc:featureList edam:operation_2492, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "GO2Vec" ; sc:url "https://github.com/xszhong/GO2Vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0196, edam:topic_0622, edam:topic_0780, edam:topic_3316 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3672 ; sc:name "GOMAP" ; sc:softwareHelp ; sc:url "https://dill-picl.org/projects/gomap/gomap-datasets/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0632, edam:topic_0749 ; sc:citation , "pmcid:PMC6332836", "pubmed:30642251" ; sc:description "Generator of probes for capture Hi-C experiments at high resolution." ; sc:featureList edam:operation_0309, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GOPHER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/TheJacksonLaboratory/Gopher" ; biotools:primaryContact "The Jackson Laboratory" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3474, edam:topic_3489 ; sc:citation , "pubmed:31804928" ; sc: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""" ; sc:featureList edam:operation_3436 ; sc:name "GOT-10k" ; sc:url "http://got-10k.aitestunion.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_3518 ; sc:citation , "pmcid:PMC6330489", "pubmed:30634902" ; sc:description "Tool to navigate through branches of gene ontology hierarchy." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GOTrapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BioGeneTools/GOTrapper" ; biotools:primaryContact "Hezha Hassan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_3518 ; sc:citation , "pmcid:PMC6695228", "pubmed:31415589" ; sc:description "Advances in gene ontology utilization improve statistical power of annotation enrichment | Welcome to GOcats’ documentation! — GOcats 1.1.5 documentation" ; sc:featureList edam:operation_3352, edam:operation_3501, edam:operation_3559 ; sc:name "GOcats" ; sc:url "https://gocats.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0602 ; sc:citation , "pmcid:PMC6286514", "pubmed:30526489" ; sc:description "Tool for interactive Gene Ontology analysis." ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "GOnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.dice-database.org/GOnet/" ; biotools:primaryContact "Mikhail Pomaznoy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0209, edam:topic_0593, edam:topic_0820, edam:topic_3892 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0269, edam:operation_2476, edam:operation_2995, edam:operation_3891 ; sc:name "GPCRmd" ; sc:url "http://gpcrmd.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3334 ; sc:citation , "pmcid:PMC6625143", "pubmed:31127708" ; sc:description "Inherited glycophosphatidylinositol deficiency variant database." ; sc:featureList edam:operation_0417, edam:operation_3225, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GPI-anchor biosynthesis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.gpibiosynthesis.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0622, edam:topic_0780, edam:topic_3170, edam:topic_3500 ; sc:citation , "pmcid:PMC6929509", "pubmed:31874598" ; sc: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.""" ; sc:featureList edam:operation_0430, edam:operation_0476, edam:operation_2454 ; sc:name "GPRED-GC" ; sc:url "https://sourceforge.net/projects/gpred-gc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2259, edam:topic_3068 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0267, edam:operation_2489, edam:operation_3461 ; sc:name "GPSRdocker" ; sc:url "https://webs.iiitd.edu.in/gpsrdocker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3314 ; sc:citation , "pubmed:31145605" ; sc:description "Implementation of the Molecular Electrostatic Potential over Graphics Processing Units." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GPUAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/gpuam/binaries.git" ; biotools:primaryContact "Jorge Garza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3512, edam:topic_3676 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_2421, edam:operation_2422, edam:operation_3802 ; sc:name "GPress" ; sc:url "https://github.com/qm2/gpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC7703763", "pubmed:31608923" ; sc: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""" ; sc:featureList edam:operation_0313, edam:operation_0337, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "GPseudoClust" ; sc:url "https://github.com/magStra/GPseudoClust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC6742416", "pubmed:31469829" ; sc: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" ; sc:featureList edam:operation_0331, edam:operation_0441, edam:operation_3232 ; sc:name "GRAM" ; sc:url "https://github.com/gersteinlab/GRAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3067 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GRANAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://granar.github.io" ; biotools:primaryContact "Guillaume Lobet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC3287830", "pubmed:22373025" ; sc: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." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:name "GRANVIL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.geenivaramu.ee/en/tools/granvil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6749106", "pubmed:31530648" ; sc: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)" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3798 ; sc:name "GRASE" ; sc:url "http://adsteen.shinyapps.io/grase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3431 ; sc:name "GRASS" ; sc:url "http://grass.osgeo.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6527554", "pubmed:31110304" ; sc:description "Interactive Web Platform for Re-analyzing Gene Expression Omnibus (GEO) RNA-seq Data." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GREIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://shiny.ilincs.org/grein" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC6416924", "pubmed:30866794" ; sc:description "Guide RNA Identifier for Balancer Chromosome Generation (GRIBCG) - software for selection of sgRNAs in the design of balancer chromosomes." ; sc:isAccessibleForFree true ; sc:name "GRIBCG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bmerritt1762/GRIBCG" ; biotools:primaryContact "B. Merritt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "GRN" ; sc:url "https://dcolin.shinyapps.io/CancerGRN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0749, edam:topic_3368 ; sc:citation , "pubmed:31065808" ; sc:description "GROMACS to LAMMPS (GRO2LAM) - converter for molecular dynamics software." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GRO2LAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hernanchavezthielemann/GRO2LAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_3068, edam:topic_3295 ; sc:citation , "pmcid:PMC5750854", "pubmed:31725863" ; sc: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""" ; sc:featureList edam:operation_0283, edam:operation_0305, edam:operation_3196, edam:operation_3431 ; sc:name "GRONS" ; sc:url "http://bioinfo.tmu.edu.cn/GRONS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3172, edam:topic_3300, edam:topic_3697 ; sc:citation , "pubmed:31638380" ; sc: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.""" ; sc:featureList edam:operation_2940, edam:operation_3463, edam:operation_3659, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "GRaMM" ; sc:url "https://github.com/chentianlu/GRaMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0625 ; sc:citation ; sc:description "Gene Set Annotation - an alternative to enrichment analysis for annotating gene sets." ; sc:featureList edam:operation_2942, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GSAn" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gsan.labri.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0634, edam:topic_3410 ; sc:citation , "pubmed:31437915" ; sc: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" ; sc:featureList edam:operation_3559 ; sc:license "Apache-2.0" ; sc:name "GSSO" ; sc:url "https://github.com/Superraptor/GSSO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3517, edam:topic_3518 ; sc:citation , "pmcid:PMC6507172", "pubmed:31072324" ; sc:description "Package for network-weighted gene-set clustering and network visualization." ; sc:featureList edam:operation_2436, edam:operation_2492, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GScluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/unistbig/GScluster" ; biotools:primaryContact , "Seon-Young Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0623, edam:topic_3293 ; sc:citation , "pmcid:PMC6821227", "pubmed:31560374" ; sc: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" ; sc:featureList edam:operation_3431, edam:operation_3501 ; sc:license "MIT" ; sc:name "GTA" ; sc:url "https://github.com/ecg-lab/GTA-Hunter-v1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC6718126", "pubmed:31507629" ; sc: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:" ; sc:featureList edam:operation_3192 ; sc:license "GPL-3.0" ; sc:name "GTACG" ; sc:url "https://github.com/caiorns/GTACG-backend" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:30255462" ; sc:description "Annotation tool for providing image and text annotations to image-based datasets." ; sc:featureList edam:operation_3553 ; sc:isAccessibleForFree true ; sc:name "GTCreator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cvc.uab.es/CVC-Colon/index.php/gtcreator/" ; biotools:primaryContact "CVC-Colon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0637, edam:topic_3174 ; sc:citation , , , , "pmcid:PMC8728215", "pubmed:32341564", "pubmed:34155373", "pubmed:34520557" ; sc: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" ; sc:featureList edam:operation_0544, edam:operation_3432, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "GTDB" ; sc:url "https://gtdb.ecogenomic.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0637, edam:topic_3174, edam:topic_3293, edam:topic_3489 ; sc:citation , "pmcid:PMC7703759", "pubmed:31730192" ; sc: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).""" ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_3182, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "GTDB-Tk" ; sc:url "https://github.com/ecogenomics/gtdbtk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0325, edam:operation_0546, edam:operation_3478 ; sc:name "GTM" ; sc:url "https://github.com/vlasmirnov/GTM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1285 ; sc:encodingFormat edam:format_1996, edam:format_3285 ; sc:name "Gene map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170 ; sc:citation ; sc:description "Software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GUESSmyLT" ; sc:softwareHelp ; sc:softwareVersion "v1.0" ; sc:url "https://github.com/NBISweden/GUESSmyLT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0820, edam:topic_3382 ; sc:citation , "pubmed:30475993" ; sc:description "Multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles." ; sc:featureList edam:operation_3454, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GUV-AP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "https://github.com/AG-Roemer/GUV-AP" ; biotools:primaryContact "Winfried Römer", "Yves Mély" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3489, edam:topic_3520 ; sc:citation , "pubmed:31829415" ; sc:description """Expanding the capillary electrophoresis based glucose unit database of the GUcal app. GUcal 1.1c - Internal / bracketing standard approach with GlycoStore database""" ; sc:featureList edam:operation_3435 ; sc:name "GUcal" ; sc:url "https://www.gucal.hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3315 ; sc:description "GW6 algorithm for multichannel EEG data" ; sc:isAccessibleForFree true ; sc:name "GW6 - Grand-average ERP algorithm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63973-gw6-grand-average-erp-algorithm" ; biotools:primaryContact "marco.bilucaglia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3517 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "GWAS-Flow" ; sc:url "https://github.com/Joyvalley/GWAS_Flow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3517, edam:topic_3574 ; sc:citation , "pmcid:PMC7145571", "pubmed:31612961" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3436, edam:operation_3559, edam:operation_3791 ; sc:name "GWAS Central" ; sc:softwareHelp ; sc:url "https://www.gwascentral.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC6298063", "pubmed:29931045" ; sc:description "Non-local prior based iterative SNP selection tool for genome-wide association studies." ; sc:featureList edam:operation_0484, edam:operation_3659, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GWASinlps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "https://cran.r-project.org/package=GWASinlps" ; biotools:primaryContact "Nilotpal Sanyal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517, edam:topic_3572 ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GWASinspector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.4" ; sc:url "http://gwasinspector.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc: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/)" ; sc:featureList edam:operation_3435, edam:operation_3557, edam:operation_3659 ; sc:name "GWPC" ; sc:url "https://github.com/neuroanatomy/GWPC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3391 ; sc: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." ; sc:name "GalaxEast" ; sc:url "http://www.galaxeast.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091 ; sc: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." ; sc:name "GalaxyCat" ; sc:url "http://galaxycat.france-bioinformatique.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "A wide variety of tools from the Galaxy instance of Institut Pasteur, France." ; sc:name "Galaxy Pasteur" ; sc:url "https://galaxy.pasteur.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Tools provided by the Galaxy workbench." ; sc:isAccessibleForFree true ; sc:license "AFL-2.0" ; sc:name "Galaxy Tools" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/galaxyproject/galaxy/tree/dev/tools" ; biotools:primaryContact "Galaxy Project" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation ; sc: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." ; sc:featureList edam:operation_0571, edam:operation_3563 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "Galaxy scater" ; sc:softwareHelp ; sc:url "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637, edam:topic_0780, edam:topic_3673, edam:topic_3810 ; sc:citation , "pmcid:PMC4958008", "pubmed:27547538" ; sc:description "Tools for genotyping gall-causing phytopathogenic bacteria and identifying strains isolated from Agrobacterium or Rhodococcus-induced galls using MLSA and other methods." ; sc:featureList edam:operation_2421, edam:operation_3192, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "Gall-ID" ; sc:url "http://gall-id.cgrb.oregonstate.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0798 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0417, edam:operation_3715 ; sc:name "GapMind" ; sc:url "https://papers.genomics.lbl.gov/cgi-bin/gapView.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3398, edam:topic_3407 ; sc:citation ; sc:description "Efficient random sampling for constraint-based (COBRA) models." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Gapsplit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jensenlab/gapsplit" ; biotools:primaryContact "Paul A. Jensen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6791524", "pubmed:31501545" ; sc:description "Supervised classification enables rapid annotation of cell atlases | Garnett - Automated cell type identification" ; sc:featureList edam:operation_2495, edam:operation_3233, edam:operation_3501 ; sc:name "Garnett" ; sc:url "https://cole-trapnell-lab.github.io/garnett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3572 ; sc:citation , "pubmed:31735856" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "GazeVisual-Lib" ; sc:url "http://github.com/anuradhakar49/GazeVisual-Lib" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3068, edam:topic_3322, edam:topic_3474, edam:topic_3517 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3280 ; sc:name "GeDex" ; sc:url "https://bitbucket.org/laigen/gedex/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3308 ; sc:citation , "pmcid:PMC6323745", "pubmed:30616521" ; sc: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." ; sc:featureList edam:operation_0277, edam:operation_1781 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GeNeCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://lce.biohpc.swmed.edu/geneck" ; biotools:primaryContact "Minzhe Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3298, edam:topic_3517 ; sc:citation , "pubmed:31393550" ; sc:description "Genome-Phenome Explorer (GePhEx): A tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence." ; sc:featureList edam:operation_0484, edam:operation_2422, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GePhEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gephex.ega-archive.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GemSIM" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/gemsim/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1939 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0622 ; sc:citation ; sc:description "Program for gene presence-absence analysis for series of closely related bacterial genomes from annotated GFF files." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GenAPI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/MigleSur/GenAPI" ; biotools:primaryContact "Migle Gabrielaite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3344 ; sc:description "Read GenBank-formatted flat file into structure" ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:name "GenBank Flat File Reader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/48999-genbank-flat-file-reader" ; biotools:primaryContact "Turner Conrad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0637 ; sc:description "Utilities for manipulations and visualization tasks on GenBank taxonomic information." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GenBank taxonomy tools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/spond/gb_taxonomy_tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6357466", "pubmed:30704396" ; sc:description "Genome exploration open source tool for variants generated from high-throughput sequencing projects." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GenESysV" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/ubccr/genesysv" ; biotools:primaryContact "Center for Computational Research" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0623, edam:topic_0780, edam:topic_3170 ; sc:citation , "pmcid:PMC6892992", "pubmed:31844835" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_3672 ; sc:name "GenFam" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31844835" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC6894214", "pubmed:31653197" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0492, edam:operation_0524, edam:operation_3182 ; sc:license "GPL-3.0" ; sc:name "GenGraph" ; sc:url "https://github.com/jambler24/GenGraph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3489, edam:topic_3571 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3096 ; sc:license "BSD-3-Clause" ; sc:name "GenIE-Sys" ; sc:softwareHelp ; sc:url "https://geniesys.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC5787240", "pubmed:29374474" ; sc: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." ; sc:featureList edam:operation_3196, edam:operation_3229 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GenIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://bioinformatics.ibioba-mpsp-conicet.gov.ar/GenIO/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_3512 ; sc:citation , "pmcid:PMC6442393", "pubmed:30862647" ; sc:description "Integrated resource for analyzing the evolution and function of primate-specific coding genes." ; sc:featureList edam:operation_0487, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GenTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gentree.ioz.ac.cn/index.php" ; biotools:primaryContact "ZhangLab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6360648", "pubmed:30712510" ; sc:description "Machine learning method that utilizes transcriptome-wide gene co-expression to generate a distributed representation of genes." ; sc:featureList edam:operation_0315, edam:operation_3439, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Gene2vec" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/jingcheng-du/Gene2vec" ; biotools:primaryContact "Jingcheng Du" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC7145562", "pubmed:31642496" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3226, edam:operation_3461 ; sc:name "Gene4Denovo" ; sc:url "http://www.genemed.tech/gene4denovo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0203, edam:topic_0621, edam:topic_0625, edam:topic_2229 ; sc:citation , "pmcid:PMC6886503", "pubmed:31754022" ; sc: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.""" ; sc:featureList edam:operation_2436, edam:operation_3557, edam:operation_3672 ; sc:license "GPL-3.0" ; sc:name "GeneBridge" ; sc:url "https://github.com/lihaone/GeneBridge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621 ; sc: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)." ; sc:featureList edam:operation_0310 ; sc:name "GeneMarkS-T" ; sc:url "http://topaz.gatech.edu/GeneMark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6498745", "pubmed:31105932" ; sc:description "Analysis of copy number variation using Illumina Infinium DNA methylation arrays." ; sc:featureList edam:operation_3219, edam:operation_3436, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GenePattern notebook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.genepattern-notebook.org/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3676 ; sc:citation , "pmcid:PMC6524327", "pubmed:31096927" ; sc:description "Score for estimating gene pathogenicity in individuals using next-generation sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GenePy" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/UoS-HGIG/GenePy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0194 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0544, edam:operation_0547, edam:operation_0552 ; sc:license "AGPL-3.0" ; sc:name "GeneRax" ; sc:url "https://github.com/BenoitMorel/GeneRax" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634 ; sc:citation , "pmcid:PMC6503437", "pubmed:31060502" ; sc:description "Network-based identification of disease genes in expression data." ; sc:featureList edam:operation_0277, edam:operation_2436, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GeneSurrounder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/sahildshah1/gene-surrounder" ; biotools:primaryContact "Rosemary Braun", "Sahil Shah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3295 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2495, edam:operation_3659, edam:operation_3890 ; sc:name "GeneSwitches" ; sc:softwareHelp ; sc:url "https://geneswitches.ddnetbio.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325 ; sc:citation , "pmcid:PMC4643620", "pubmed:26209433" ; sc:description "Investigation of the background prevalence (rare, protein altering variants that could be classified as pathogenic) of exonic variation." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GeneVetter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genevetter.org/" ; biotools:primaryContact "Matthew Gordon Sampson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170 ; sc:citation , "pmcid:PMC7852222", "pubmed:33526072" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_2436 ; sc:license "BSD-2-Clause" ; sc:name "GeneWalk" ; sc:url "http://github.com/churchmanlab/genewalk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3676 ; sc:author "David Arenillas", "Zach Maurer" ; sc:citation , "pubmed:25703386" ; sc: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." ; sc:featureList edam:operation_3227, edam:operation_3229, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "GeneYenta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://geneyenta.com/accounts/home/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3512, edam:topic_3912 ; sc:citation , "pmcid:PMC6602503", "pubmed:31127311" ; sc:description "Set of tools for assisting in highly precise genome editing and engineering." ; sc:featureList edam:operation_0420, edam:operation_3096, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Gene Sculpt Suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genesculpt.org" ; biotools:primaryContact , "Jeffrey J. Essner", "Stephen C. Ekker" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:encodingFormat edam:format_2330, edam:format_2350 ; sc:name "Gene identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2848, edam:format_3617, edam:format_3620 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3070, edam:topic_3344, edam:topic_3474, edam:topic_3948 ; sc: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.""" ; sc:featureList edam:operation_2436, edam:operation_3279, edam:operation_3625, edam:operation_3767, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "GeneRecommender" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2 stable" ; sc:url "https://www.generecommender.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC6602493", "pubmed:31114885" ; sc: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" ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Geneshot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://amp.pharm.mssm.edu/geneshot" ; biotools:primaryContact , "Alexander Lachmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC6668410", "pubmed:31366961" ; sc: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" ; sc:featureList edam:operation_0452, edam:operation_3198, edam:operation_3227 ; sc:license "MIT" ; sc:name "Genesis-indel" ; sc:url "https://github.com/mshabbirhasan/Genesis-indel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3068, edam:topic_3168, edam:topic_3305 ; sc:citation , "pubmed:31670023" ; sc: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""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3435 ; sc:name "GenoGeographer" ; sc:url "http://genogeographer.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0622, edam:topic_2815, edam:topic_3489 ; sc:citation , , "pmcid:PMC6902006", "pubmed:31820804" ; sc:contributor , ; sc: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).""" ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_2422, edam:operation_3436 ; sc:name "GenoSurf" ; sc:softwareHelp , ; sc:url "http://gmql.eu/genosurf/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc: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" ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Genoma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.szn.it/genoma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0621, edam:topic_0769 ; sc:citation , "pubmed:31733063" ; sc: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:""" ; sc:featureList edam:operation_0303, edam:operation_2421, edam:operation_2422, edam:operation_3778 ; sc:license "GPL-3.0" ; sc:name "Genome3D" ; sc:softwareHelp ; sc:url "https://www.genome3d.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0654 ; sc:citation , "pmcid:PMC6477968", "pubmed:30215673" ; sc:description "Graphical tool for modeling and analyzing 3D genome structure." ; sc:featureList edam:operation_2429 ; sc:isAccessibleForFree true ; sc:name "GenomeFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/jianlin-cheng/GenomeFlow" ; biotools:primaryContact "Jianlin Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0769, edam:topic_0780, edam:topic_3489 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_3208 ; sc:license "MIT" ; sc:name "GenomeHubs" ; sc:softwareHelp ; sc:url "http://GenomeHubs.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0362, edam:operation_0525, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "GenomeQC" ; sc:url "https://genomeqc.maizegdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0637, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3432 ; sc:name "Genome Constellation" ; sc:url "https://bitbucket.org/berkeleylab/jgi-genomeconstellation/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3263 ; sc:citation , "pmcid:PMC6712716", "pubmed:31455387" ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3891 ; sc:license "MIT" ; sc:name "Genomic GPS" ; sc:url "https://github.com/hanlab-SNU/GenomicGPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3337, edam:topic_3396, edam:topic_3423, edam:topic_3577, edam:topic_3676 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_3227, edam:operation_3436 ; sc:name "GenomicsDB" ; sc:url "http://www.genomicsdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0780, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , , ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-plants" ; sc:url "https://www.genomicus.biologie.ens.fr/genomicus-plants" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-fungi" ; sc:url "http://www.genomicus.biologie.ens.fr/genomicus-fungi/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , , "pmcid:PMC2853686", "pmcid:PMC3531091", "pmcid:PMC4383929", "pmcid:PMC5753199", "pubmed:20185404", "pubmed:23193262", "pubmed:25378326", "pubmed:29087490" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-metazoa" ; sc:url "http://www.genomicus.biologie.ens.fr/genomicus-metazoa/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-protists" ; sc:url "http://www.genomicus.biologie.ens.fr/genomicus-protists/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , "pmcid:PMC5753386", "pmcid:PMC7145539", "pubmed:29149270", "pubmed:31680137" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-tunicates" ; sc:url "https://www.genomicus.biologie.ens.fr/genomicus-tunicates" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3308 ; sc: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)" ; sc:featureList edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genotom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "http://cab.unina.it/genotom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0097, edam:topic_0099, edam:topic_0196, edam:topic_3489 ; sc:citation , "pubmed:31584078" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3431 ; sc:name "Genus biomolecules" ; sc:url "http://genus.fuw.edu.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3489, edam:topic_3855 ; sc:citation ; sc: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:""" ; sc:featureList edam:operation_3436, edam:operation_3760 ; sc:license "GPL-3.0" ; sc:name "GeoNode-Tools4MSP" ; sc:url "http://geonode.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC6943045", "pubmed:31544935" ; sc: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" ; sc:featureList edam:operation_0282, edam:operation_3501 ; sc:name "Gephebase" ; sc:url "http://www.gephebase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3325, edam:topic_3411 ; sc:citation , "pubmed:26065375" ; sc: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." ; sc:featureList edam:operation_3283 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GerOSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.geross.de/Default_en.aspx" ; biotools:primaryContact "Nicholas Lack", "Silvia Berlage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3071 ; sc:citation , , "pmcid:PMC4897896", "pmcid:PMC6511067", "pubmed:27267926", "pubmed:31077313" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3196, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Gigwa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.3" ; sc:url "http://www.southgreen.fr/content/gigwa" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3659 ; sc:name "GiniClust3" ; sc:url "https://github.com/rdong08/GiniClust3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6612808", "pubmed:31510661" ; sc: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)." ; sc:featureList edam:operation_0238, edam:operation_3472, edam:operation_3501 ; sc:name "GkmExplain" ; sc:url "https://github.com/kundajelab/gkmexplain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3444 ; sc:citation , "pubmed:30184055" ; sc:description "Tool for generating structural ensembles of partly disordered proteins from chemical shifts." ; sc:featureList edam:operation_0249, edam:operation_0320, edam:operation_0474 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Glutton" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YeeHo/Glutton" ; biotools:primaryContact "Yi He" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0203, edam:topic_3518 ; sc:citation , "pmcid:PMC7178435", "pubmed:31841142" ; sc:description "Glycan Microarray Database and Analysis Toolset." ; sc:featureList edam:operation_2421, edam:operation_2426, edam:operation_2495 ; sc:name "GlyMDB" ; sc:url "http://www.glycanstructure.org/glymdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3520 ; sc:author "Dr. Ian Walsh" ; sc:citation , "pmcid:PMC6378934", "pubmed:30101321" ; sc:description "Software for automated interpretation of N -glycan profiles after exoglycosidase digestions." ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GlycanAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://glycananalyzer.neb.com/" ; biotools:primaryContact "Dr. Christopher H. Taron", "Dr. Ian Walsh", "Prof. Pauline M. Rudd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0152, edam:topic_0154 ; sc:citation , "pmcid:PMC6612873", "pubmed:30535258" ; sc:description "Conversion tool for translating the complexities of glycans." ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GlycanFormatConverter" ; sc:operatingSystem "Mac" ; sc:url "https://github.com/glycoinfo/GlycanFormatConverter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2815, edam:topic_3520 ; sc:citation , "pubmed:31384044" ; sc: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" ; sc:featureList edam:operation_0417, edam:operation_3501, edam:operation_3799 ; sc:name "Glyco-DIA" ; sc:url "https://github.com/CCGMS/Glyco-DIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_0166, edam:topic_0176, edam:topic_3300 ; sc:citation , "pmcid:PMC6806574", "pubmed:31640540" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_2476, edam:operation_3192 ; sc:name "Glycosylator" ; sc:url "https://github.com/tlemmin/glycosylator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3382, edam:topic_3697 ; sc:citation , "pmcid:PMC6377400", "pubmed:30597007" ; sc:description "Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur." ; sc:featureList edam:operation_3192, edam:operation_3431, edam:operation_3797 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GmT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://galaxyproject.org/use/gmt/" ; biotools:primaryContact "Saskia Hiltemann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3170 ; sc:description "Gmove is a genome annotation tool. This combiner takes as input mapping of RNA-seq or protein or ab initio data." ; sc:featureList edam:operation_0362, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:name "Gmove" ; sc:url "http://www.genoscope.cns.fr/gmove" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2200 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_3000 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_1915 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2200 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1240 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "PCR primers" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_3508 ; sc:name "Protocol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_0601, edam:topic_0632, edam:topic_2533, edam:topic_3361, edam:topic_3895 ; sc:author ; sc:citation , , "pmcid:PMC6662682", "pubmed:31358887" ; sc:contributor ; sc: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." ; sc:featureList edam:operation_0308, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "GoldenMutagenesis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.1" ; sc:url "https://msbi.ipb-halle.de/GoldenMutagenesisWeb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269 ; sc:citation ; sc: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:" ; sc:featureList edam:operation_3659 ; sc:license "MIT" ; sc:name "GpABC" ; sc:url "https://github.com/tanhevg/GpABC.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3305, edam:topic_3673 ; sc:author "Sergio Arredondo-Alonso" ; sc:citation , , , , "pmcid:PMC7320608", "pmcid:PMC7816424", "pubmed:32271863", "pubmed:33472670" ; sc:description """A comprehensive tool for plasmid analysis using short-read graphs. gplas: Binning plasmid-predicted contigs using short-read graphs""" ; sc:featureList edam:operation_0524, edam:operation_0525 ; sc:license "GPL-3.0" ; sc:name "Gplas" ; sc:softwareHelp ; sc:softwareVersion "V0.6.0", "V0.7.0" ; sc:url "https://gitlab.com/sirarredondo/gplas.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "An integrated database for grapevine data" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "GrapeMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "http://urgi.versailles.inra.fr/GrapeMine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0625 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0524, edam:operation_3182, edam:operation_3196, edam:operation_3198, edam:operation_3211 ; sc:license "MIT" ; sc:name "GraphAligner" ; sc:url "https://anaconda.org/bioconda/graphaligner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0659, edam:topic_3170, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC6897289", "pubmed:31808801" ; sc: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.""" ; sc:featureList edam:operation_0278, edam:operation_0302, edam:operation_0502, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "GraphClust2" ; sc:url "https://graphclust.usegalaxy.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6396939", "pubmed:30779737" ; sc:description "Tool for calling transcription factor peaks on graph-based reference genomes using ChIP-seq data." ; sc:featureList edam:operation_0487, edam:operation_3215, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Graph Peak Caller" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/uio-bmi/graph_peak_caller" ; biotools:primaryContact "Biomedical Informatics Research Group (BMI)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0526, edam:operation_3192, edam:operation_3198 ; sc:license "MIT" ; sc:name "Graphmap2" ; sc:url "https://github.com/lbcb-sci/graphmap2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:28945251" ; sc:description "Publicly available novel algorithm and software for discovering and genotyping sequence variants." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Graphtyper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DecodeGenetics/graphtyper" ; biotools:primaryContact "Hannes Pétur Eggertsson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3318, edam:topic_3334, edam:topic_3375 ; sc:citation , "pmcid:PMC6904991", "pubmed:31822261" ; sc: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.""" ; sc:featureList edam:operation_3359 ; sc:name "GreatSPN" ; sc:url "https://github.com/greatspn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0632 ; sc:citation ; sc:description "Web-based tool that rapidly designs custom CRISPR screens targeting sets of genes defined by the user." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Green listed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://greenlisted.cmm.ki.se/" ; biotools:primaryContact "Fredrik Wermeling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3382 ; sc:citation , "pmcid:PMC6764701", "pubmed:31527870" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "GripDL" ; sc:url "https://github.com/2010511951/GripDL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3390, edam:topic_3474 ; sc:citation , "pmcid:PMC6713322", "pubmed:31461459" ; sc: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" ; sc:name "GrowthEstimate" ; sc:url "https://github.com/RungruangsakTorrissenManoonpong/GrowthEstimate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0218, edam:topic_0602, edam:topic_3518 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0277, edam:operation_2436, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "GsVec" ; sc:url "https://github.com/yuumio/GsVec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3343, edam:topic_3369 ; sc:citation , "pmcid:PMC6534830", "pubmed:31127411" ; sc:description "Program for preparing small-molecule libraries for structure-based virtual screening." ; sc:featureList edam:operation_0482 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Gypsum-DL" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://durrantlab.com/gypsum-dl/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3053 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3431, edam:operation_3557, edam:operation_3891 ; sc:name "H3ABioNet" ; sc:url "http://github.io/H3ABionet-SOPs/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation , "pmcid:PMC6893198", "pubmed:31636085" ; sc: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""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:name "HAF-pipe" ; sc:url "https://github.com/petrov-lab/HAFpipe-line" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:30539546" ; sc:description "HAMR (High-throughput Annotation of Modified Ribonucleotides) - web application that allows you to detect and classify modified nucleotides in RNA-seq data." ; sc:featureList edam:operation_0484, edam:operation_3185, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HAMR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2" ; sc:url "http://tesla.pcbi.upenn.edu/hamr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3360 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3501 ; sc:name "HCCPred" ; sc:url "http://webs.iiitd.edu.in/raghava/hccpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC6865732", "pubmed:31403237" ; sc: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" ; sc:name "HD-BET" ; sc:url "https://github.com/NeuroAI-HD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3577 ; sc:citation , "pubmed:31368480" ; sc: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" ; sc:featureList edam:operation_3891 ; sc:name "HD-GMCM" ; sc:url "https://bitbucket.org/cdal/hdgmcm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation ; sc: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" ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3891 ; sc:license "MIT" ; sc:name "HDCytoData" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/HDCytoData" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3295 ; sc:citation , "pmcid:PMC7373178", "pubmed:31504171" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_2495, edam:operation_3439 ; sc:name "HEGIAP" ; sc:url "http://sysomics.com/HEGIAP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3384 ; sc:citation , "pubmed:29993993" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HERMES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hermes.grnet.gr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0218, edam:topic_0621 ; sc:citation , ; sc: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.""" ; sc:featureList edam:operation_2421, edam:operation_2429, edam:operation_3760, edam:operation_3891 ; sc:license "MIT" ; sc:name "HHypermap" ; sc:url "https://github.com/cga-harvard/HHypermap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_3305 ; sc:citation , "pmcid:PMC6947307", "pubmed:31766582" ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_3559 ; sc:license "GPL-3.0" ; sc:name "HIO" ; sc:url "https://bioportal.bioontology.org/ontologies/HIO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3382 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "HIRAC" ; sc:url "https://github.com/priyojitDas/HIRAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0781, edam:topic_0804, edam:topic_3324, edam:topic_3400 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2421, edam:operation_3202, edam:operation_3557 ; sc:name "HIV-1" ; sc:url "http://www.hiv.lanl.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3068, edam:topic_3315, edam:topic_3379 ; sc:citation , "pubmed:31513553" ; sc: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" ; sc:featureList edam:operation_2428, edam:operation_3196, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "HIV-ASSIST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.hivassist.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0804, edam:topic_3168, edam:topic_3379 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_1812, edam:operation_2421, edam:operation_3202, edam:operation_3482 ; sc:name "HIV-DRLink" ; sc:url "https://hivdb.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3305 ; sc:citation , "pmcid:PMC6849208", "pubmed:31718603" ; sc:description "Optimal allocation of HIV resources among geographical regions." ; sc:featureList edam:operation_2426 ; sc:name "HIV-related" ; sc:url "http://hiv.ocds.co" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3474 ; sc:citation , "pubmed:31146118" ; sc:description "Web server for predicting HIV-1 CRF01_AE coreceptor usage." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HIVCoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://codes.bio/hivcor/" ; biotools:primaryContact "Watshara Shoombuatong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885 ; sc:citation , "pubmed:31518964" ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3894 ; sc:name "HIrisPlex-S" ; sc:url "https://hirisplex.erasmusmc.nl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373 ; sc:citation , "pmcid:PMC6884818", "pubmed:31783725" ; sc: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""" ; sc:featureList edam:operation_0321, edam:operation_0337, edam:operation_2421 ; sc:name "HKPocket" ; sc:url "http://zhaoserver.com.cn/HKPocket/HKPocket.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31502156" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3630, edam:operation_3800 ; sc:name "HLA" ; sc:url "https://github.com/ExpressionAnalysis/HLAProfiler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3421 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3891, edam:operation_3893 ; sc:name "HLA Ligand Atlas" ; sc:url "http://www.hla-ligand-atlas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3474 ; sc:citation , "pubmed:31722090" ; sc: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""" ; sc:featureList edam:operation_3222, edam:operation_3435 ; sc:name "HLMethy" ; sc:url "https://github.com/liuze-nwafu/HLMethy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:description "Older version of the HMMER3 program (https://bio.tools/hmmer3) used for searching sequence databases for sequence homologs, and for making sequence alignments." ; sc:featureList edam:operation_2421, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "HMMER2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.1 - 2.4i" ; sc:url "http://hmmer.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0804, edam:topic_3697 ; sc:citation , "pmcid:PMC6650278", "pubmed:31142855" ; sc:description "Collection of workflows that handle processing several different data types assocaited with the IBDMDB (Inflammatory Bowel Disease Multi’omics Database) project." ; sc:featureList edam:operation_3192, edam:operation_3629, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HMP2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/biobakery/hmp2_workflows" ; biotools:primaryContact "Curtis Huttenhower", "Ramnik J. Xavier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_2275 ; sc:citation , "pmcid:PMC6602492", "pubmed:31114906" ; sc:description "Nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures." ; sc:featureList edam:operation_0278, edam:operation_0279, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HNADOCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://huanglab.phys.hust.edu.cn/hnadock/" ; biotools:primaryContact "Lab of Bioinformatics and Molecular Modeling", "Sheng-You Huang", "Yi Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2640, edam:topic_3406 ; sc:citation , "pmcid:PMC6527845", "pubmed:31139565" ; sc:description "Integrated Gene and Drug Database for Head and Neck Cancer." ; sc:featureList edam:operation_0306, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HNCDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hncdb.cancerbio.info" ; biotools:primaryContact "Ankui Yang", "Xiaoqing Pei", "Zhixiang Zuo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3306 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3891 ; sc:name "HNN" ; sc:url "https://hnn.brown.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6521357", "pubmed:31096906" ; sc:description "HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification." ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:name "HOME" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ListerLab/HOME" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC6815001", "pubmed:31653226" ; sc: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""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3791, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "HOPS" ; sc:url "https://github.com/rondolab/HOPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3674 ; sc:citation , "pmcid:PMC6582337", "pubmed:31114922" ; sc:description "Examining the basis of high-occupancy target regions." ; sc:featureList edam:operation_0417, edam:operation_0445, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BIMSBbioinfo/HOT-or-not-examining-the-basis-of-high-occupancy-target-regions" ; biotools:primaryContact , "Verdan Franske" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3308, edam:topic_3382 ; sc:citation , "pmcid:PMC6734269", "pubmed:31500569" ; sc: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" ; sc:featureList edam:operation_2422, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "HPAanalyze" ; sc:url "https://github.com/adussaq/jsHPAanalyze" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3520 ; sc:citation , "pubmed:31729669" ; sc: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""" ; sc:featureList edam:operation_0302, edam:operation_2476, edam:operation_3359 ; sc:name "HPCCS" ; sc:url "https://github.com/cepid-cces/hpccs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0203, edam:topic_0625, edam:topic_0634 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_1777, edam:operation_2429, edam:operation_3280 ; sc:license "GPL-3.0" ; sc:name "HPO2GO" ; sc:url "https://github.com/cansyl/HPO2GO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_2830, edam:topic_3534 ; sc:citation , "pmcid:PMC6872852", "pubmed:31768230" ; sc:description """Discovery of novel helix binding sites at protein-protein interfaces. Helix Positioner a program for locating helix binding sites at protien-protein interfaces.""" ; sc:featureList edam:operation_2464, edam:operation_2476, edam:operation_2492 ; sc:name "Helix Positioner" ; sc:url "https://github.com/proteincraft/HPer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0089, edam:topic_0121, edam:topic_0601, edam:topic_3320 ; sc:citation , "pmcid:PMC8728143", "pubmed:34986596" ; sc: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" ; sc:featureList edam:operation_0224, edam:operation_0417, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Human Proteoform Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://human-proteoform-atlas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31758464" ; sc: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""" ; sc:featureList edam:operation_3431, edam:operation_3443, edam:operation_3799 ; sc:name "HRMAn" ; sc:url "https://hrman.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3517, edam:topic_3518 ; sc:citation , "pmcid:PMC6612810", "pubmed:31510671" ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:license "MIT" ; sc:name "HSIC Lasso" ; sc:url "https://github.com/riken-aip/pyHSICLasso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0324, edam:operation_2426, edam:operation_3658 ; sc:name "HSMRF" ; sc:url "http://github.com/afmagee/hsmrfbdp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6886170", "pubmed:31787073" ; sc: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.""" ; sc:featureList edam:operation_0277, edam:operation_2495, edam:operation_3223 ; sc:name "HTRgene" ; sc:url "http://biohealth.snu.ac.kr/software/HTRgene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6420756", "pubmed:30878035" ; sc:description "Histosketching Using Little Kmers (HULK) - tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis." ; sc:featureList edam:operation_3435, edam:operation_3472, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "HULK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/will-rowe/hulk" ; biotools:primaryContact "Will Rowe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3673 ; sc:citation , "pmcid:PMC6670167", "pubmed:31366358" ; sc: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" ; sc:featureList edam:operation_0523, edam:operation_0525, edam:operation_3216 ; sc:name "HUPAN" ; sc:url "http://cgm.sjtu.edu.cn/hupan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0780, edam:topic_3810 ; sc:citation , "pubmed:31415224" ; sc: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) 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" ; sc:featureList edam:operation_0337, edam:operation_3461 ; sc:license "MIT" ; sc:name "HaGiS" ; sc:url "https://openplantpathology.github.io/hagis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3372 ; sc:citation , "pmcid:PMC6793853", "pubmed:31613890" ; sc: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""" ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3359, edam:operation_3454 ; sc:license "MIT" ; sc:name "HaTSPiL" ; sc:url "https://github.com/dodomorandi/hatspil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC3023673", "pubmed:21192823" ; sc:description "Haloarchaeal genomes database." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Haloarchaeal Genomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://halo.umbc.edu/" ; biotools:primaryContact "Shiladitya DasSarma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC6444579", "pubmed:30940094" ; sc:description "R package for power and sample size calculations in genetic association analyses of family triads and unrelated controls." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Haplin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "7.1.0" ; sc:url "https://cran.r-project.org/package=Haplin" ; biotools:primaryContact "Hakon K. Gjessing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885 ; sc:citation , "pmcid:PMC3245002", "pubmed:22064851" ; sc: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" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196 ; sc:name "HaploReg" ; sc:url "https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0769 ; sc:citation , "pmcid:PMC7178392", "pubmed:31834373" ; sc: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""" ; sc:featureList edam:operation_0487, edam:operation_3227, edam:operation_3454 ; sc:name "HaploTypo" ; sc:url "https://github.com/gabaldonlab/haplotypo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3056, edam:topic_3305 ; sc:citation , "pmcid:PMC3725725", "pubmed:22147662" ; sc:description "Tool for visualizing haplotype diversity, based on a cluster-based model for haplotype variation" ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Haploscope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.4.1" ; sc:url "http://haploscope.scheetlabsoftware.org/" ; biotools:primaryContact "Paul Scheet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3063 ; sc:author "Francesca Cordero", "Marco Becc" ; sc:citation , "pmcid:PMC5701356", "pubmed:29169317" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HashClone" ; sc:operatingSystem "Linux" ; sc:softwareVersion "version 1.2" ; sc:url "http://tanto.unito.it/WebVisual/index.html" ; biotools:primaryContact "Raffaele Calogero" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC6934854", "pubmed:31882769" ; sc: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:.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3227 ; sc:name "Hass" ; sc:url "https://github.com/IHSMFruitCrops/Hass-genotyping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3344, edam:topic_3407, edam:topic_3421 ; sc:citation , "pmcid:PMC6896291", "pubmed:33430999" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3214, edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "HastaLaVista" ; sc:url "https://github.com/jwist/hastaLaVista" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_2275 ; sc:citation , "pmcid:PMC6602443", "pubmed:31106357" ; sc:description "Web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA." ; sc:featureList edam:operation_0482, edam:operation_2492, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HawkDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cadd.zju.edu.cn/hawkdock/" ; biotools:primaryContact "Gaoqi Weng", "Tingjun Hou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0780, edam:topic_0821 ; sc:citation , "pmcid:PMC6821316", "pubmed:31093654" ; sc:description "R package for an Ultra-Fast and Comprehensive Gene Annotation in Plants." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Hayai-Annotation Plants" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kdri-genomics/Hayai-Annotation-Plants" ; biotools:primaryContact "Andrea Ghelfi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6686264", "pubmed:31395005" ; sc:description "A deep learning predictive model for multi-type biological dataset | HetEncs: A Deep Learning Classifier for Integrated Gene Expression Analysis" ; sc:featureList edam:operation_2495, edam:operation_2939, edam:operation_3891 ; sc:name "HetEnc" ; sc:url "https://github.com/seldas/HetEnc_Code" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3321 ; sc:citation ; sc:description "A genetic resource database for rubber tree genomic study | Molecular & Genetic Resources for Hevea tree" ; sc:featureList edam:operation_3216, edam:operation_3431, edam:operation_3766 ; sc:name "HeveaDB" ; sc:url "http://hevea.catas.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC7703765", "pubmed:31697323" ; sc: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""" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "HiCBricks" ; sc:url "http://bioconductor.org/packages/devel/bioc/html/HiCBricks.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2640, edam:topic_3169, edam:topic_3673 ; sc:citation ; sc: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)""" ; sc:featureList edam:operation_0392, edam:operation_3435, edam:operation_3659 ; sc:name "HiCNAtra" ; sc:url "https://github.com/AISKhalil/HiCNAtra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC6821373", "pubmed:31056636" ; sc: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." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HiCNN" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://dna.cs.miami.edu/HiCNN/" ; biotools:primaryContact "Zheng Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169, edam:topic_3170, edam:topic_3295, edam:topic_3382 ; sc:citation , "pmcid:PMC6844183", "pubmed:31749839" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3695, edam:operation_3798 ; sc:license "GPL-2.0" ; sc:name "HiCeekR" ; sc:url "https://github.com/lucidif/HiCeekR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC9883675", "pubmed:31424526" ; sc: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" ; sc:featureList edam:operation_3638, edam:operation_3644, edam:operation_3755 ; sc:name "HiLight-PTM" ; sc:url "https://harrywhitwell.shinyapps.io/hilight-ptm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3385 ; sc:citation , "pmcid:PMC6283589", "pubmed:30521560" ; sc:description "Gradient-based, GPU-accelerated, high-precision contour-segmentation algorithm with application to cell membrane fluctuation spectroscopy." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "HiPFSTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/michaelmell/hipfsta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_2830, edam:topic_3489 ; sc:citation , "pubmed:31855463" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3432 ; sc:name "HiPPO" ; sc:url "http://www.hippopanda.org/hippo.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2840, edam:topic_3520 ; sc:citation , "pubmed:31095696" ; sc:description "Online Crowd-Sourced HR-MS Database for Suspect and Non-targeted Screening of New Psychoactive Substances." ; sc:featureList edam:operation_2929, edam:operation_3431, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "HighResNPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://HighResNPS.com" ; biotools:primaryContact "Marie Mardal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3293 ; sc:citation , "pmcid:PMC6612880", "pubmed:31510674" ; sc: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" ; sc:featureList edam:operation_0567, edam:operation_3478, edam:operation_3629 ; sc:name "Hintra" ; sc:url "https://github.com/sahandk/HINTRA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC7267905", "pubmed:31609046" ; sc: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""" ; sc:featureList edam:operation_3435 ; sc:name "HippMapp3r" ; sc:url "https://hippmapp3r.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2830, edam:topic_3360, edam:topic_3400 ; sc:citation , "pmcid:PMC7243927", "pubmed:31725860" ; sc: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.""" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_2428 ; sc:name "HisgAtlas" ; sc:softwareHelp ; sc:url "http://biokb.ncpsb.org/HisgAtlas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3295, edam:topic_3520 ; sc:citation , "pubmed:31816396" ; sc: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.""" ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3645 ; sc:name "HistoneAnalysisWorkflow" ; sc:url "https://github.com/DenuLab/HistoneAnalysisWorkflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_2229 ; sc:citation , "pmcid:PMC7005629", "pubmed:31821723" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_3227, edam:operation_3461, edam:operation_3778 ; sc:name "HmtVar" ; sc:url "https://www.hmtvar.uniba.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0623, edam:topic_3293, edam:topic_3372 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0539, edam:operation_0540, edam:operation_3478 ; sc:license "MIT" ; sc:name "HogProf" ; sc:url "https://github.com/DessimozLab/HogProf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3379, edam:topic_3474 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:name "Holden" ; sc:url "https://github.com/MSBradshaw/Holden" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3869 ; sc:encodingFormat edam:format_3983 ; sc:name "Simulation" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , "pubmed:28961696" ; sc:description "Graphical tool for development, simulation and analysis of Petri net based models of complex biological systems." ; sc:featureList edam:operation_0244, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "Holmes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html" ; biotools:primaryContact "Piotr Formanowicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , , ; sc:description """A first prototype Python plugin enabling exploratory spatial data analysis into QGIS. A QGIS plugin for hotspot analyis. Hotspot Analysis Plugin for QGIS.""" ; sc:featureList edam:operation_0451, edam:operation_3435 ; sc:name "Hotspot analysis" ; sc:url "https://github.com/danioxoli/HotSpotAnalysis_Plugin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3170, edam:topic_3307, edam:topic_3361, edam:topic_3512, edam:topic_3518, edam:topic_3678 ; sc:citation , "pmcid:PMC7778946", "pubmed:32663312" ; sc: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.""" ; sc:featureList edam:operation_2424, edam:operation_3799, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:name "Housekeeping and Reference Transcript Atlas" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.housekeeping.unicamp.br" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pmcid:PMC8215923", "pubmed:31504157" ; sc:description "Improved representation of sequence Bloom trees | Sequence Bloom Tree, supporting determined/how split filters | Jellyfish (Version 2.2.0 or later)" ; sc:featureList edam:operation_0224 ; sc:license "MIT" ; sc:name "HowDe-SBT" ; sc:url "https://github.com/medvedevgroup/HowDeSBT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0654, edam:topic_0659 ; sc:citation , "pmcid:PMC7402404", "pubmed:30999860" ; sc: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." ; sc:featureList edam:operation_3501, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "HumCFS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/humcfs/index.html" ; biotools:primaryContact "Dr. Gajendra P. S. Raghava" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "HumanMine integrates many types of data for Homo sapiens and Mus musculus" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "HumanMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "6.0 2019 May" ; sc:url "https://www.humanmine.org/humanmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269 ; sc:citation , "pmcid:PMC6684253", "pubmed:31388390" ; sc: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" ; sc:featureList edam:operation_3436, edam:operation_3463, edam:operation_3501 ; sc:name "Hurdle" ; sc:url "https://github.com/amcdavid/HurdleNormal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3315, edam:topic_3673 ; sc:citation , "pubmed:31116364" ; sc: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." ; sc:featureList edam:operation_0578, edam:operation_3482, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HyAsP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/cchauve/HyAsP" ; biotools:primaryContact "Cedric Chauve" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0154, edam:topic_0602 ; sc:author "Art FY Poon", "Sergei L Kosakovsky Pond", "Steven Weaver" ; sc:citation , , "pubmed:15509596", "pubmed:30298394" ; sc:description "Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HyPhy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://hyphy.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0780, edam:topic_3293, edam:topic_3512 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "HybPiper" ; sc:url "https://github.com/mossmatters/HybPiper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209 ; sc:citation , "pubmed:31524396" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3456, edam:operation_3893 ; sc:name "HybridMolDB" ; sc:url "http://www.idruglab.com/HybridMolDB/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3382 ; sc:citation , "pubmed:31569268" ; sc: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:.""" ; sc:featureList edam:operation_3096, edam:operation_3431, edam:operation_3799 ; sc:name "HydroSight" ; sc:url "http://peterson-tim-j.github.io/HydroSight/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "An integrated data warehouse for the Hymenoptera Genome Database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "HymenopteraMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.4" ; sc:url "http://hymenopteragenome.org/hymenopteramine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "HypercubeME" ; sc:url "https://github.com/ivankovlab/HypercubeME.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6530038", "pubmed:31117943" ; sc: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." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Hypergraph Dynamic Correlation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yunchuankong/HypergraphDynamicCorrelation" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31636105" ; sc: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.""" ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3799 ; sc:name "Hypocotyl" ; sc:url "https://github.com/biomag-lab/hypocotyl-UNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3298, edam:topic_3315 ; sc:citation , "pubmed:31647442" ; sc: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""" ; sc:featureList edam:operation_0282, edam:operation_0337, edam:operation_1812, edam:operation_3432, edam:operation_3891 ; sc:name "Hyppo-X" ; sc:url "https://xperthut.github.io/HYPPO-X" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "I-Impute" ; sc:url "https://github.com/xikanfeng2/I-Impute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0769, edam:topic_3056, edam:topic_3574 ; sc:citation , "pmcid:PMC7056857", "pubmed:31765831" ; sc: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""" ; sc:name "I3" ; sc:url "http://suprahex.r-forge.r-project.org/I3.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3374, edam:topic_3382 ; sc:citation , "pmcid:PMC6675096", "pubmed:31369634" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3443 ; sc:license "LGPL-3.0" ; sc:name "IA-Lab" ; sc:url "https://github.com/amcorrigan/ia-lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation , "pmcid:PMC6602435", "pubmed:31127271" ; sc: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." ; sc:featureList edam:operation_3196, edam:operation_3216, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IAMBEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.intec.ugent.be/iambee/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3305, edam:topic_3337 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3211 ; sc:name "IBD" ; sc:url "http://github.com/roohy/IBD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3518 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:name "IBS-privacy" ; sc:url "http://github.com/mdedge/IBS_privacy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0611, edam:topic_2828 ; sc:citation , "pubmed:26092861" ; sc:description "Tool for integrated sequence and 3D structure analysis of large macromolecular complexes." ; sc:featureList edam:operation_0448 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IBiSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ibiss.igbmc.fr/" ; biotools:primaryContact "Bruno P. Klaholz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3172, edam:topic_3308 ; sc:citation , "pmcid:PMC6771121", "pubmed:31500324" ; sc: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" ; sc:featureList edam:operation_2939, edam:operation_3629, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "ICA" ; sc:url "https://github.com/sysbio-curie/ICA-in-Cancer-research-review-materials" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0593, edam:topic_3295, edam:topic_3306, edam:topic_3385 ; sc:citation , "pmcid:PMC6895719", "pubmed:31732142" ; sc: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:""" ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:name "ICCS" ; sc:url "https://github.com/llanzano/ICCS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3500 ; sc:citation , "pmcid:PMC6933885", "pubmed:31878869" ; sc: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.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3359 ; sc:name "ICGRM" ; sc:url "https://github.com/mingfang618/CLGRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3304, edam:topic_3474 ; sc:citation , "pmcid:PMC6592775", "pubmed:31103785" ; sc:description "Automated electroencephalographic independent component classifier, dataset, and website." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ICLabel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://iclabel.ucsd.edu/" ; biotools:primaryContact "Luca Pion-Tonachini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3403, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:license "GPL-3.0" ; sc:name "ICU readmissions" ; sc:url "http://github.com/deepphong/icu-readmission" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3399 ; sc:citation , "pubmed:31087665" ; sc:description "Web server for adult age estimation of human skeletal remains." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IDADE2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bass.uib.es/~jaume/IDADE2/https/index.html" ; biotools:primaryContact "Allysha Winburn", "Carme Rissech Badallo", "Marta San-Millán" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_1915, edam:format_2333, edam:format_3244, edam:format_3245, edam:format_3654 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3621 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3301, edam:topic_3336, edam:topic_3697 ; sc:author ; sc:citation , , "pmcid:PMC5949002", "pmcid:PMC7204650", "pubmed:29686101", "pubmed:31157770" ; sc:description "A MALDI bioinformatics platform for analyzing protein and small molecule MALDI-TOF MS data (with a particular focus on mic organism analysis )" ; sc:featureList edam:operation_0567, edam:operation_2409, edam:operation_2939, edam:operation_3214, edam:operation_3432, edam:operation_3694, edam:operation_3744 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IDBac" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.10" ; sc:url "https://chasemc.github.io/IDBac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0736, edam:topic_0749, edam:topic_0780, edam:topic_3306 ; sc:citation , "pmcid:PMC6933863", "pubmed:31642121" ; sc: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""" ; sc:featureList edam:operation_0303, edam:operation_0337, edam:operation_3904 ; sc:name "IDDomainSpotter" ; sc:url "http://www.bio.ku.dk/sbinlab/IDDomainSpotter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3360 ; sc:citation , "pmcid:PMC6777501", "pubmed:31608326" ; sc: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.""" ; sc:featureList edam:operation_2428, edam:operation_3503, edam:operation_3659 ; sc:name "IDH-wild-type" ; sc:url "https://gcioffi.shinyapps.io/Nomogram_For_IDH_Wildtype_GBM_H_Gittleman/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:encodingFormat edam:format_3790 ; sc:name "Query script" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3255, edam:format_3256, edam:format_3261, edam:format_3464, edam:format_3475, edam:format_3752, edam:format_3956 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "SPARQL endpoint", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3343, edam:topic_3369 ; sc:author , ; sc:citation , , "pmcid:PMC6599361", "pmcid:PMC8117646", "pubmed:31254167", "pubmed:33980298" ; sc:description "Integrated Database of Small Molecules" ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "IDSM" ; sc:softwareHelp ; sc:url "https://idsm.elixir-czech.cz/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3384 ; sc:citation , "pmcid:PMC6663300", "pubmed:31410382" ; sc: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:" ; sc:featureList edam:operation_3216, edam:operation_3658 ; sc:license "GPL-3.0" ; sc:name "IDTxl" ; sc:url "https://github.com/pwollstadt/IDTxl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3063, edam:topic_3324 ; sc:citation , "pmcid:PMC6933616", "pubmed:31881820" ; sc: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.""" ; sc:featureList edam:operation_0303 ; sc:name "IILLS" ; sc:url "http://bioinformatics.csu.edu.cn/IILLS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3301, edam:topic_3837 ; sc:citation , "pmcid:PMC6886165", "pubmed:31787095" ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3439 ; sc:name "ILMF-VH" ; sc:url "https://github.com/liudan111/ILMF-VH.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_0804, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC8734366", "pubmed:34991455" ; sc:description "The ImmunoDataAnalyzer (IMDA) pipeline provides various methods for analysing immunological next-generation sequencing (NGS) data." ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3200, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "ImmunoDataAnalyzer" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://bioinformatics.fh-hagenberg.at/immunoanalyzer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3297, edam:topic_3407 ; sc:citation , "pmcid:PMC7145673", "pubmed:31665416" ; sc:description """An update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. The public IMG/ABC site has limited features and tools.""" ; sc:featureList edam:operation_2454, edam:operation_3216, edam:operation_3432 ; sc:name "IMG-ABC" ; sc:url "https://img.jgi.doe.gov/abc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , , , , "pmcid:PMC3038005", "pubmed:10745995", "pubmed:15089751", "pubmed:17949886", "pubmed:21099347", "pubmed:22654892" ; sc: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." ; sc:featureList edam:operation_3501 ; sc:name "IMGT-ONTOLOGY" ; sc:softwareHelp ; sc:url "http://www.imgt.org/IMGTindex/ontology.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology concept" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC4383898", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0564, edam:operation_2416 ; sc:isAccessibleForFree true ; sc:name "IMGT 2Dstructure-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0804 ; sc:citation , "pmcid:PMC4383898", "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description "IMGT/Allele-Align is the IMGT® tool for the comparison of two alleles highlighting the nucleotide and amino acid differences." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "IMGT Allele-Align" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.imgt.org/Allele-Align/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2331 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation , "pmcid:PMC4383898", "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description "IMGT/CloneSearch is the IMGT® tool allowing the search of a clone in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT CloneSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/LocusView" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2331 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation "pubmed:11862387", "pubmed:18208865", "pubmed:21632776", "pubmed:25378316" ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "IMGT Collier-de-Perles" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/cgi/Collier-de-Perles.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3510, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC4383898", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT DomainDisplay" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/cgi/DomainDisplay.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3154 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation , , , "pmcid:PMC2808948", "pmcid:PMC4383898", "pubmed:19900967", "pubmed:21632775", "pubmed:25378316" ; sc: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." ; sc:featureList edam:operation_0491, edam:operation_2479 ; sc:isAccessibleForFree true ; sc:name "IMGT DomainGapAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2331 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation , "pmcid:PMC4383898", "pubmed:25378316" ; sc: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." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT DomainSuperimpose" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/cgi/DomainSuperimpose.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology concept" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation , , "pmcid:PMC4383898", "pmcid:PMC539964", "pubmed:15608191", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "IMGT GENE-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://www.imgt.org/genedb/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2058 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2331 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2331 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3053, edam:topic_3930, edam:topic_3948 ; sc:citation , , "pmcid:PMC1482724", "pmcid:PMC4383898", "pubmed:15972004", "pubmed:16640788", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT GeneFrequency" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/genefrequency/query" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2331 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1278 ; sc:encodingFormat edam:format_2331 ; sc:name "Genetic map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , , , "pmcid:PMC1482724", "pmcid:PMC308775", "pmcid:PMC4383898", "pubmed:14681357", "pubmed:16640788", "pubmed:25378316" ; sc: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." ; sc:featureList edam:operation_0224 ; sc:name "IMGT GeneInfo" ; sc:softwareHelp ; sc:url "http://www.imgt.org/GeneInfoServlets/htdocs/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2331 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC4383898", "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description "IMGT/GeneSearch is the IMGT® tool allowing the search of a gene in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT GeneSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/LocusView/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2331 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC4383898", "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description "IMGT® tool providing the view of a gene in IMGT/LocusView. Display is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT GeneView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/LocusView/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3779 ; sc:encodingFormat edam:format_3752 ; sc:name "Annotated text" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , , , "pmcid:PMC4383898", "pubmed:22665256", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0292, edam:operation_0448, edam:operation_2478, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:name "IMGT HighV-QUEST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.imgt.org/HighV-QUEST/home.action" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2200 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , , , "pmcid:PMC4383898", "pubmed:15262823", "pubmed:21632777", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0292, edam:operation_0448, edam:operation_2478 ; sc:isAccessibleForFree true ; sc:name "IMGT JunctionAnalysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/IMGT_jcta" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1103 ; sc:encodingFormat edam:format_2330 ; sc:name "EMBL/GenBank/DDBJ ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology concept" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation , , "pmcid:PMC1347451", "pmcid:PMC4383898", "pubmed:16381979", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0338, edam:operation_0361, edam:operation_0564 ; sc:isAccessibleForFree true ; sc:name "IMGT LIGM-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/ligmdb/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2969 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation , "pmcid:PMC5018401", "pubmed:15089751", "pubmed:15972004", "pubmed:25972004" ; sc: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.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT LocusView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/LocusView/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC4383898", "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0361 ; sc:isAccessibleForFree true ; sc:name "IMGT PRIMER-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/IMGTPrimerDB/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology concept" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:encodingFormat edam:format_2331 ; sc:name "Phylogenetic data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_1929, edam:format_2331 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , , "pmcid:PMC4383898", "pubmed:12818634", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0292, edam:operation_0499 ; sc:isAccessibleForFree true ; sc:name "IMGT PhyloGene" ; sc:softwareHelp ; sc:url "http://www.imgt.org/IMGTPhylogeny/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:author "Safa Aouinti" ; sc:citation , , "pmcid:PMC4634997", "pmcid:PMC4711580", "pubmed:26540440", "pubmed:26731095" ; sc: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." ; sc:featureList edam:operation_0315, edam:operation_2238 ; sc:isAccessibleForFree true ; sc:name "IMGT StatClonotype" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.imgt.org/StatClonotype/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_2331 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0804 ; sc:citation , , "pmcid:PMC308776", "pmcid:PMC4383898", "pubmed:14681396", "pubmed:15089751", "pubmed:25378316" ; sc: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." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT StructuralQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3400, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC4383898", "pubmed:25378316" ; sc: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.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT mAb-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.imgt.org/mAb-DB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0804, edam:topic_3172, edam:topic_3302 ; sc:citation , "pmcid:PMC7145572", "pubmed:31691834" ; sc:description """Extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. IUPHAR Guide to IMMUNOPHARMACOLOGY. The IUPHAR/BPS Guide to IMMUNOPHARMACOLOGY. Description.""" ; sc:featureList edam:operation_0224, edam:operation_0252 ; sc:name "IMMUNOPHARMACOLOGY" ; sc:url "http://www.guidetoimmunopharmacology.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3794 ; sc:citation , "pmcid:PMC6345043", "pubmed:30678641" ; sc:description "Aligner for mapping noisy long reads to the reference genome." ; sc:featureList edam:operation_0337, edam:operation_0495 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "IMOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Mosjava/IMOS" ; biotools:primaryContact "Hadadian Nejad Youesfi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:29993787" ; sc:description "Inferring MiRNA Targets based on Restricted Boltzmann Machines (IMTRBM) for prediction of miRNA-target interactions (MTIs)." ; sc:featureList edam:operation_0463 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IMTRBM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liuying201705/IMTRBM" ; biotools:primaryContact "Y. Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3360 ; sc:author "Zhenzhi Li" ; sc:citation , "pmcid:PMC6549230", "pubmed:31179159" ; sc:description "R package for network based differential expression analysis." ; sc:featureList edam:operation_3463, edam:operation_3741, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "INDEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "https://bioconductor.org/packages/release/bioc/html/INDEED.html" ; biotools:primaryContact "Yiming Zuo", "Zhenzhi Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0218, edam:topic_0602 ; sc:citation , "pmcid:PMC6821420", "pubmed:31070726" ; sc:description "Interactive pathway modeling using natural language with automated assembly." ; sc:featureList edam:operation_0533, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "INDRA-IPM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pathwaymap.indra.bio/" ; biotools:primaryContact "Peter Sorger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_3810 ; sc:citation , "pmcid:PMC6820601", "pubmed:31535162" ; sc: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 .." ; sc:featureList edam:operation_2426, edam:operation_3196, edam:operation_3557 ; sc:name "INLA" ; sc:url "http://www.r-inla.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0218, edam:topic_3474 ; sc:citation , "pubmed:31883904" ; sc: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.""" ; sc:featureList edam:operation_0418, edam:operation_3631, edam:operation_3767 ; sc:name "INSP" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/INSP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC3004884", "pubmed:21114820" ; sc:description "Software generated to aid in MRS analysis to achieve a specific diagnosis for brain lesions." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "INTERPRET DSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.2" ; sc:url "http://gabrmn.uab.es/dss" ; biotools:primaryContact "Biomedical Applications of Magnetic Resonance research group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31509381" ; sc: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" ; sc:featureList edam:operation_3803 ; sc:name "IPA" ; sc:url "https://github.com/francescodc87/IPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3056 ; sc:citation , "pmcid:PMC6427891", "pubmed:30936940" ; sc:description "R package for iterative pruning to capture population structure." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IPCAPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.5" ; sc:url "https://cran.r-project.org/package=IPCAPS" ; biotools:primaryContact "Kridsadakorn Chaichoompu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0199, edam:topic_0621, edam:topic_2830, edam:topic_3489 ; sc:citation , "pubmed:31641782" ; sc: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.""" ; sc:featureList edam:operation_0416, edam:operation_3197, edam:operation_3431 ; sc:name "IPD project" ; sc:url "https://www.ebi.ac.uk/ipd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc: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." ; sc:featureList edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "IPEV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "V4" ; sc:url "https://github.com/basehc/IPEV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3322 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3501, edam:operation_3629 ; sc:name "IPF" ; sc:url "http://IPFCellAtlas.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6664791", "pubmed:31362694" ; sc: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" ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_3472 ; sc:name "IRESpy" ; sc:url "https://irespy.shinyapps.io/IRESpy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0804, edam:topic_3512 ; sc:citation , "pmcid:PMC5091335", "pubmed:31414702" ; sc: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" ; sc:featureList edam:operation_0463, edam:operation_2495, edam:operation_3501 ; sc:name "IRNdb" ; sc:url "http://irndb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3382, edam:topic_3417 ; sc:citation , "pmcid:PMC6553792", "pubmed:31125331" ; sc: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." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ISETBIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://isetbio.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3077, edam:topic_3372 ; sc:citation , "pmcid:PMC6832938", "pubmed:31635039" ; sc: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) and Dillingham, P.W., Alsaedi, B.S.O. and McGraw, C.M. (2017) """ ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "ISEtools" ; sc:url "https://CRAN.R-project.org/package=ISEtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31736404" ; sc: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.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "ISIMA" ; sc:url "https://www.ilastik.org/download.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3403, edam:topic_3474 ; sc:citation , "pubmed:31430550" ; sc: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" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "ISeeU" ; sc:url "https://github.com/williamcaicedo/ISeeU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0749, edam:topic_3295 ; sc:citation ; sc:description "Modeling methylation dynamics with simultaneous changes in CpG islands." ; sc:featureList edam:operation_0417, edam:operation_0430, edam:operation_3186 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IWEPoissonPaper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com//statgenlmu//IWEPoissonPaper" ; biotools:primaryContact "Dirk Metzler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0632, edam:topic_0804, edam:topic_3360 ; sc:citation , "pmcid:PMC6901697", "pubmed:31849974" ; sc: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.""" ; sc:featureList edam:operation_0291, edam:operation_2421, edam:operation_2495 ; sc:name "IgM" ; sc:url "https://github.com/ansts/IgMimoPap1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3382, edam:topic_3892 ; sc:citation , "pmcid:PMC6834899", "pubmed:31519398" ; sc: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" ; sc:featureList edam:operation_0337 ; sc:name "Illustrate" ; sc:url "https://github.com/ccsb-scripps/Illustrate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31780825" ; sc:description """An open-source computational platform for the deep learning era. ImJoy -- Deep Learning Made Easy!""" ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:name "ImJoy" ; sc:softwareHelp ; sc:url "https://imjoy.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0140, edam:topic_2640, edam:topic_3360, edam:topic_3382 ; sc:citation , "pubmed:31804670" ; sc: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""" ; sc:featureList edam:operation_0418, edam:operation_0477, edam:operation_2489, edam:operation_3436, edam:operation_3552 ; sc:name "ImPLoc" ; sc:url "https://github.com/yl2019lw/ImPloc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3170, edam:topic_3400 ; sc:citation , "pmcid:PMC7703782", "pubmed:31665245" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:name "ImSpectR" ; sc:url "https://github.com/martijn-cordes/ImSpectR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_1964, edam:format_3475, edam:format_3752 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1147 ; sc:name "GEO accession number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3308 ; sc:author ; sc:citation , "pubmed:30137226" ; sc: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." ; sc:featureList edam:operation_0531, edam:operation_3223, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ImaGEO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://imageo.genyo.es" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3056, edam:topic_3474 ; sc:citation , "pmcid:PMC6873651", "pubmed:31757205" ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3799, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "ImaGene" ; sc:url "https://github.com/mfumagalli/ImaGene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3314, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31714792" ; sc:description """A Tool To Extract and Quantify Data from Microscopy Images. Extract relevant images using ChemDataExtractor. Identify regions corresponding to individual particles""" ; sc:featureList edam:operation_0306, edam:operation_3458, edam:operation_3799 ; sc:license "MIT" ; sc:name "ImageDataExtractor" ; sc:url "http://www.imagedataextractor.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC6841823", "pubmed:31388864" ; sc: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" ; sc:name "Imager-4D" ; sc:url "https://jeffreyleal.wixsite.com/jleal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC6525208", "pubmed:31101851" ; sc:description "Characterization of inner shell colour variations in Pinctada margaritifera assessed by HSV colour quantification." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ImaginR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/ImaginR/index.html" ; biotools:primaryContact "Chin-Long Ky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3400 ; sc:citation ; sc:description "An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets." ; sc:featureList edam:operation_2436, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImmClass2019" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KlinkeLab/ImmClass2019" ; biotools:primaryContact "David J. Klinke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation , "pmcid:PMC5827693", "pubmed:29485622" ; sc:description "Data repository with analysis tools that is mainly focused on cytometry and immunology." ; sc:featureList edam:operation_0224, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImmPort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.immport.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2830, edam:topic_3168 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3432, edam:operation_3625 ; sc:license "CC-BY-SA-4.0" ; sc:name "Immcantation" ; sc:url "http://www.immcantation.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2269, edam:topic_2640, edam:topic_3070, edam:topic_3400 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3659 ; sc:name "ImmuCellAI" ; sc:url "http://bioinfo.life.hust.edu.cn/ImmuCellAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_3517 ; sc:citation , "pmcid:PMC6602512", "pubmed:31114925" ; sc:description "Web-based tool for identifying human immune regulatory elements." ; sc:featureList edam:operation_0441, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImmuneRegulation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://immuneregulation.mssm.edu" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2830 ; sc:citation , "pubmed:31396940" ; sc:description "Structural Modeling of Lymphocyte Receptors and Their Antigens" ; sc:featureList edam:operation_0416, edam:operation_0477, edam:operation_0478 ; sc:name "ImmuneScape" ; sc:url "https://sysimm.org/immune-scape/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830 ; sc:citation ; sc:description "Tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImmunomeBrowser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.iedb.org/immunomebrowser/" ; biotools:primaryContact "Sandeep Kumar Dhanda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3376, edam:topic_3419 ; sc:citation , "pmcid:PMC6693182", "pubmed:31412887" ; sc: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" ; sc:featureList edam:operation_3435 ; sc:name "ImpRes" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31412887" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3300, edam:topic_3398 ; sc:citation , "pmcid:PMC6462781", "pubmed:31011536" ; sc:description "Python package for writing data analysis workflows to interpret microbial physiology." ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Impact framework" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.5.0" ; sc:url "https://github.com/lmse/impact" ; biotools:primaryContact "Laboratory for Metabolic Systems Engineering" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293, edam:topic_3474 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0557, edam:operation_3478, edam:operation_3557 ; sc:name "ImputeDistances" ; sc:url "https://github.com/Ananya-Bhattacharjee/ImputeDistances" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3934 ; sc:description "MATLAB script for importing images and metadata using the LOCI Bioformats package." ; sc:isAccessibleForFree true ; sc:name "Imread for multiple life science image file formats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.7.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/32920-imread-for-multiple-life-science-image-file-formats" ; biotools:primaryContact "Christoph Moehl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC6614062", "pubmed:31284879" ; sc:description "Database and software for mitochondrial imperfect interspersed repeats annotation." ; sc:featureList edam:operation_0237, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImtRDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfodbs.kantiana.ru/ImtRDB/" ; biotools:primaryContact "Konstantin Gunbin", "Viktor Shamansky" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "IndigoMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.1" ; sc:url "http://www.cbrc.kaust.edu.sa/indigo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC6777010", "pubmed:31608148" ; sc: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" ; sc:license "MIT" ; sc:name "InferAMP" ; sc:url "http://inferamp.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475, edam:format_3620, edam:format_3752, edam:format_3758 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3579, edam:format_3603 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation , "pmcid:PMC2692489", "pubmed:18453552" ; sc:description "InfernoRDN can perform various downstream data analysis, data reduction, and data comparison tasks including normalization, hypothesis testing, clustering, and heatmap generation." ; sc:featureList edam:operation_0337, edam:operation_0531, edam:operation_2238, edam:operation_2939, edam:operation_3432, edam:operation_3435, edam:operation_3557, edam:operation_3630 ; sc:license "Apache-2.0" ; sc:name "InfernoRDN" ; sc:url "https://omics.pnl.gov/software/infernordn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3360, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:31769783" ; sc: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.""" ; sc:featureList edam:operation_3204, edam:operation_3435, edam:operation_3629 ; sc:name "InfiniumPurify-R" ; sc:url "https://github.com/Xiaoqizheng/InfiniumPurify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_3307 ; sc:citation , "pubmed:31756362" ; sc: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""" ; sc:featureList edam:operation_3659 ; sc:name "InfoMating" ; sc:url "http://acraaj.webs6.uvigo.es/InfoMating/Infomating.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3673 ; sc:citation , "pmcid:PMC4702856", "pubmed:26578584" ; sc:description "Comprehensive genetic resource and analysis platform of insects." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "InsectBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.insect-genome.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3512, edam:topic_3519 ; sc:citation , "pmcid:PMC7178424", "pubmed:31834359" ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "IntMTQ" ; sc:url "https://github.com/CompbioLabUcf/IntMTQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0484, edam:operation_3227, edam:operation_3675 ; sc:name "Intelli-NGS" ; sc:url "https://www.github.com/aditya-88/intelli-ngs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_2275 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0267, edam:operation_2464, edam:operation_2492, edam:operation_3899, edam:operation_3904 ; sc:name "InterPep2" ; sc:url "http://wallnerlab.org/InterPep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3172 ; sc:citation , "pmcid:PMC6648201", "pubmed:31459550" ; sc: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" ; sc:featureList edam:operation_3215, edam:operation_3637, edam:operation_3642 ; sc:name "InterSpin" ; sc:url "http://dmar.riken.jp/interspin/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3305, edam:topic_3411, edam:topic_3418 ; sc:citation , "pmcid:PMC6818104", "pubmed:31648624" ; sc: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.""" ; sc:featureList edam:operation_2409, edam:operation_3503 ; sc:license "GPL-3.0" ; sc:name "InterVA-5" ; sc:url "http://www.interva.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3384, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0321, edam:operation_3659 ; sc:license "MIT" ; sc:name "InteractionTransformer" ; sc:softwareHelp ; sc:url "https://github.com/jlevy44/InteractionTransformer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC6612871", "pubmed:31510675" ; sc: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" ; sc:featureList edam:operation_3891 ; sc:name "IonSpattern" ; sc:url "https://github.com/Vitek-Lab/IonSpattern" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3172, edam:topic_3955 ; sc:citation , "pubmed:30903185" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IsoCor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MetaSys-LISBP/IsoCor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_3315 ; sc:citation , "pmcid:PMC6855200", "pubmed:31737449" ; sc: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""" ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:name "IsoPOPd" ; sc:url "https://cwhl.vet.cornell.edu/tools/isopopd" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3713 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2332 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation , "pubmed:21067241" ; sc: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)." ; sc:featureList edam:operation_3435, edam:operation_3630, edam:operation_3635, edam:operation_3639, edam:operation_3641, edam:operation_3694, edam:operation_3705, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "IsobariQ" ; sc:url "http://norwegian-proteomics-society.uio.no/isobariq/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3955 ; sc:citation , , , , "pubmed:15256408", "pubmed:16002431", "pubmed:17000750", "pubmed:31893378" ; sc: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." ; sc:featureList edam:operation_2426 ; sc:license "Freeware" ; sc:name "Isodyn" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/seliv55/isodyn" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3955 ; sc:citation , "pubmed:31893378" ; sc: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." ; sc:featureList edam:operation_3214 ; sc:license "Freeware" ; sc:name "Isoform" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.0.1.0" ; sc:url "https://github.com/seliv55/ramidcor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2885, edam:topic_3577 ; sc:citation , "pmcid:PMC6699389", "pubmed:31467902" ; sc: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" ; sc:featureList edam:operation_0331, edam:operation_0463, edam:operation_0484 ; sc:name "IsomiR_Find" ; sc:url "https://github.com/wangying0128/IsomiR_Find" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation , "pmcid:PMC6396427", "pubmed:30674557" ; sc:description "Analysis package for processing counts from genome-wide CRISPR/Cas9 screens." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "JACKS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/felicityallen/JACKS" ; biotools:primaryContact "F. Allen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_3315, edam:topic_3382 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3629, edam:operation_3659, edam:operation_3891 ; sc:name "JACOBI4" ; sc:url "https://jacobi4.ru/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0632, edam:topic_2275 ; sc:citation , "pubmed:31140800" ; sc:description "Characterization of Hydration Properties in Structural Ensembles of Biomolecules." ; sc:featureList edam:operation_0244, edam:operation_0478, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "JAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mspc.bii.a-star.edu.sg/minhn/jal.html" ; biotools:primaryContact "Chandra S. Verma", "Minh N. Nguyen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0632, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0450, edam:operation_0487, edam:operation_3192, edam:operation_3196, edam:operation_3200 ; sc:name "JAMP" ; sc:url "https://github.com/VascoElbrecht/JAMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC6408804", "pubmed:30849961" ; sc: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." ; sc:featureList edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:name "JOA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://joa.readthedocs.org" ; biotools:primaryContact "Burcak Otlu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2258 ; sc:citation , "pmcid:PMC6645593", "pubmed:31457399" ; sc: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" ; sc:featureList edam:operation_1812 ; sc:name "JRgui" ; sc:url "https://github.com/curieshicy/JRgui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3489 ; sc:citation , "pmcid:PMC7868055", "pubmed:31882996" ; sc: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.""" ; sc:license "MIT" ; sc:name "JUDI" ; sc:url "https://github.com/ncbi/JUDI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_2275 ; sc:citation , "pmcid:PMC7007192", "pubmed:31390206" ; sc: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" ; sc:featureList edam:operation_0387, edam:operation_0482, edam:operation_3899 ; sc:license "GPL-3.0" ; sc:name "JabberDock" ; sc:url "http://github.com/degiacom/JabberDock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_2269, edam:topic_3292, edam:topic_3301 ; sc:citation , "pmcid:PMC6929325", "pubmed:31874610" ; sc: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.""" ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "Jaccard" ; sc:url "https://cran.r-project.org/package=jaccard" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1477, edam:format_1915, edam:format_1929, edam:format_1938, edam:format_1939, edam:format_1947, edam:format_1948, edam:format_1961, edam:format_1982, edam:format_1984, edam:format_1997, edam:format_3015, edam:format_3016, edam:format_3311, edam:format_3313, edam:format_3774 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0886 ; sc:encodingFormat edam:format_1476 ; sc:name "Structure alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_1915, edam:format_2331, edam:format_3466, edam:format_3603, edam:format_3604 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929, edam:format_1947, edam:format_1948, edam:format_1961, edam:format_1982, edam:format_1997, edam:format_3015, edam:format_3313, edam:format_3464, edam:format_3774 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092 ; sc:citation , "pmcid:PMC2672624", "pubmed:19151095" ; sc:description "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation." ; sc:featureList edam:operation_0324, edam:operation_0564, edam:operation_3081 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Jalview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "2.11.4.1" ; sc:url "https://www.jalview.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3855 ; sc:citation , "pubmed:31310719" ; sc:description "Extensible open-source software package for adaptive quantum mechanics/molecular mechanics (QM/MM) Methods." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Janus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/CCQC/janus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3170 ; sc:citation , "pmcid:PMC7703784", "pubmed:31681943" ; sc: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""" ; sc:featureList edam:operation_3198, edam:operation_3435, edam:operation_3792 ; sc:name "Jasmine" ; sc:url "https://bitbucket.org/bipous/jasmine/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3384 ; sc:citation , "pmcid:PMC7380699", "pubmed:31841400" ; sc: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.""" ; sc:featureList edam:operation_3659 ; sc:name "Joint Multi-Modal Longitudinal Regression Classification" ; sc:url "https://github.com/minds-mines/jmmlrc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Aeschynomene evenia genomic data from the Legume Information System" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "JointvetchMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "2.1" ; sc:url "https://mines.legumeinfo.org/jointvetchmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830 ; sc:citation ; sc:description "General approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "K-TOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mlpaull/KTOPE" ; biotools:primaryContact "Michael L. Paull", "Patrick S. Daugherty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0632 ; sc:citation , "pmcid:PMC6735863", "pubmed:30624621" ; sc:description "In vitro and in silico PCR analysis tool for high-throughput SNP genotyping." ; sc:featureList edam:operation_0282, edam:operation_0308, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KASPspoon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon" ; biotools:primaryContact "Dr. Shafik D. Ibrahim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0659, edam:topic_3172, edam:topic_3173, edam:topic_3298 ; sc:citation , "pmcid:PMC6923931", "pubmed:31856718" ; sc: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""" ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_2939, edam:operation_2940 ; sc:name "KBCommons" ; sc:url "http://kbcommons.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_3375 ; sc:citation , "pubmed:31381336" ; sc: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" ; sc:name "KBbox" ; sc:url "https://kbbox.h-its.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_2840 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "KDDANet" ; sc:url "https://github.com/huayu1111/KDDANet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3263, edam:topic_3474 ; sc:citation , "pmcid:PMC6776354", "pubmed:31581246" ; sc: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""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3659 ; sc:name "KETOS" ; sc:url "https://ketos.ai/hb/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3068, edam:topic_3489 ; sc:citation , "pmcid:PMC6790968", "pubmed:31608948" ; sc: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""" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3778 ; sc:name "KOFFI" ; sc:url "http://www.koffidb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation , "pmcid:PMC6889754", "pubmed:31794015" ; sc: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.""" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3228 ; sc:name "KOREF" ; sc:url "http://koref.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3421 ; sc:citation , "pmcid:PMC6538268", "pubmed:31054501" ; sc:description "KPDGUI (Kidney Paired Donation Graphical User Interface) - interactive application for optimization and management of a virtual kidney paired donation program." ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "KPDGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mathieubray/KPDGUI" ; biotools:primaryContact "Mathieu Bray" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_3407 ; sc:citation ; sc:description "Hidden Markov Model generator for detecting KEGG PATHWAY-specific genes." ; sc:featureList edam:operation_3092, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "KPHMMER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/suecharo/KPHMMER" ; biotools:primaryContact "Hirotaka Suetake" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3295 ; sc:citation , "pubmed:31392309" ; sc:description "Online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas." ; sc:featureList edam:operation_0420, edam:operation_2495, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "KRAB ZNF explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mi2.mini.pw.edu.pl:8080/KRAB_ZNF/" ; biotools:primaryContact "Urszula Oleksiewicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3379 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2436, edam:operation_3799 ; sc:name "KRASi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://manciaslab.shinyapps.io/KRASi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068 ; sc:citation , "pmcid:PMC5860163", "pubmed:28655153" ; sc:description "Kinase-Substrate Enrichment Analysis (KSEA) App - web-based tool for kinase activity inference from quantitative phosphoproteomics." ; sc:featureList edam:operation_0337, edam:operation_3501, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "KSEA App" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://casecpb.shinyapps.io/ksea/" ; biotools:primaryContact "Danica D. Wiredja", "Mark R. Chance" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830, edam:topic_3301, edam:topic_3305, edam:topic_3673 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0525, edam:operation_2421, edam:operation_3431, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "Kaptive" ; sc:url "http://kaptive.holtlab.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2830, edam:topic_3411, edam:topic_3518, edam:topic_3673 ; sc:citation , "pubmed:31862729" ; sc: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)""" ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3891 ; sc:name "KataegisPortal" ; sc:url "https://github.com/MeichunCai/Kataegisportal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:31583639" ; sc: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.""" ; sc:featureList edam:operation_3083, edam:operation_3439, edam:operation_3501 ; sc:name "KeyPathwayMiner" ; sc:url "https://keypathwayminer.compbio.sdu.dk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3517 ; sc:author "Dr. Ehsan Ullah" ; sc:citation , "pmcid:PMC6931347", "pubmed:30590437" ; sc:description "Visualization tool to detect cryptic relatedness in genetic datasets." ; sc:featureList edam:operation_3196, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "KinVis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shiny-vis.qcri.org/public/kinvis/" ; biotools:primaryContact "Dr. Ehsan Ullah", "Dr. Halima Bensmail" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0820, edam:topic_0821, edam:topic_3314, edam:topic_3570 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0270, edam:operation_2995 ; sc:name "Kirchhoff polynomials" ; sc:url "https://gitlab.com/csb.ethz/KirchPy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC3358658", "pubmed:22537044" ; sc:description "KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome." ; sc:featureList edam:operation_3227, edam:operation_3258 ; sc:name "KisSplice" ; sc:url "http://kissplice.prabi.fr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1975 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_3665 ; sc:name "Position frequency matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3475 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1975 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1975 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_3665 ; sc:name "Position frequency matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_3665 ; sc:name "Position frequency matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2914 ; sc:encodingFormat edam:format_1975 ; sc:name "Sequence features metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1975 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0780, edam:topic_0797, edam:topic_3511 ; sc:author , , , "Markus Schwalbe" ; sc:citation , "pubmed:31823436" ; sc:contributor , "Markus Schwalbe" ; sc: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." ; sc:featureList edam:operation_0237, edam:operation_0379, edam:operation_0463, edam:operation_2428, edam:operation_2451, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Kmasker" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.1.0", "1.1.1" ; sc:url "https://kmasker.ipk-gatersleben.de/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0780, edam:topic_3673, edam:topic_3912 ; sc:citation , "pubmed:31823436" ; sc: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.""" ; sc:featureList edam:operation_0368, edam:operation_0525, edam:operation_3196, edam:operation_3211, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "Kmasker plants" ; sc:url "https://kmasker.ipk-gatersleben.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6943067", "pubmed:31598675" ; sc: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""" ; sc:featureList edam:operation_0315, edam:operation_2436, edam:operation_2942 ; sc:name "KnockTF" ; sc:url "http://www.licpathway.net/KnockTF/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation , "pmcid:PMC9883683", "pubmed:31504154" ; sc: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" ; sc:featureList edam:operation_3890 ; sc:license "GPL-3.0" ; sc:name "Knot_pull" ; sc:url "http://github.com/dzarmola/knot_pull" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0736, edam:topic_3315 ; sc:citation , "pubmed:29722808" ; sc:description "Tool to study the entanglement of open protein chains using the concept of knotoids." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Knoto-ID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.vital-it.ch/software/Knoto-ID" ; biotools:primaryContact "Julien Dorier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625 ; sc:citation , "pmcid:PMC6690010", "pubmed:31428111" ; sc: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" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:name "KnowPulse" ; sc:url "https://knowpulse.usask.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3315, edam:topic_3318 ; sc:citation , "pubmed:31120584" ; sc:description "Rate constant method for prediction of the diffusion of sorbates inside nanoporous materials at different loadings." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KoBra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/kobra/" ; biotools:primaryContact "Panagiotis D. Kolokathis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_0621, edam:topic_0623 ; sc:citation , "pmcid:PMC7141845", "pubmed:31742321" ; sc: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.""" ; sc:featureList edam:operation_0533, edam:operation_2421, edam:operation_3092 ; sc:name "KofamKOALA" ; sc:url "https://www.genome.jp/tools/kofamkoala/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3324, edam:topic_3673, edam:topic_3837 ; sc:citation , "pmcid:PMC6897419", "pubmed:31756192" ; sc:description "Identification and quantitation of clinically relevant microbes in patient samples." ; sc:featureList edam:operation_2428, edam:operation_3460, edam:operation_3472, edam:operation_3799 ; sc:license "MIT" ; sc:name "KrakenUniq" ; sc:url "https://github.com/hurwitzlab/krakenuniq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC4722636", "pubmed:26801218" ; sc:description "Matlab implementation of the Kronecker Regularized Least Squares with multiple kernels algorithm." ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "KronRLS-MKL" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/andrecamara/kronrlsmkl" ; biotools:primaryContact "André C. A. Nascimento" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6692109", "pubmed:31405451" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "KymoButler" ; sc:url "http://kymobutler.deepmirror.ai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8215917", "pubmed:31584629" ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3198, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "L1EM" ; sc:url "https://github.com/FenyoLab/L1EM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3293, edam:topic_3361 ; sc:citation , "pubmed:31374334" ; sc: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" ; sc:name "LABiocin database" ; sc:url "http://labiocin.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_2640, edam:topic_3336 ; sc:citation , "pubmed:31799600" ; sc: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""" ; sc:featureList edam:operation_2476, edam:operation_2495 ; sc:name "LARMD" ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/LARMD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3325 ; sc:citation , "pubmed:22682917" ; sc: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." ; sc:name "LAS database" ; sc:url "http://catalogue.rd-connect.eu/web/liege-acromegaly-survey-las-database" ; biotools:primaryContact "Patrick Petrossians" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3435, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "LASHiS" ; sc:url "https://github.com/thomshaw92/LASHiS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2229, edam:topic_3047 ; sc:citation , "pmcid:PMC6822780", "pubmed:31634364" ; sc: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.""" ; sc:featureList edam:operation_2949, edam:operation_3454, edam:operation_3893 ; sc:name "LASSI" ; sc:url "https://github.com/Pappulab/LASSI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0749, edam:topic_0781, edam:topic_3676 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3192, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "LAVA" ; sc:url "https://github.com/michellejlin/lava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3474 ; sc:citation , "pmcid:PMC6853662", "pubmed:31038689" ; sc:description "Label Ambiguous Domain Adaptation (LAmbDA) - species- and dataset-independent transfer learning framework (LAmbDA) to train models on multiple datasets." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LAmbDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/tsteelejohnson91/LAmbDA" ; biotools:primaryContact "Jie Zhang", "Kun Huang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2310 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091 ; sc:author ; sc:citation , "pubmed:26406767" ; sc: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." ; sc:featureList edam:operation_0252 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LBEEP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/brsaran/LBEEP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31683145" ; sc: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.""" ; sc:featureList edam:operation_3359 ; sc:name "LCA-CNN" ; sc:url "https://github.com/billzyx/LCA-CNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3518, edam:topic_3673 ; sc:citation , "pmcid:PMC6889475", "pubmed:31850063" ; sc: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""" ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3216, edam:operation_3661 ; sc:license "GPL-3.0" ; sc:name "LD-annot" ; sc:url "https://github.com/ArnaudDroitLab/LD-annot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3172, edam:topic_3314, edam:topic_3520 ; sc:citation , "pmcid:PMC6882832", "pubmed:31780665" ; sc: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".""" ; sc:featureList edam:operation_0337, edam:operation_3646, edam:operation_3801, edam:operation_3803 ; sc:name "LDB" ; sc:url "https://gnps.ucsd.edu/ProteoSAFe/gnpslibrary.jsp?library=LDB_POSITIVE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632 ; sc:citation ; sc:description "Improved read/write cost tradeoff in DNA-based data storage using LDPC codes | LDPC codes for Illumina sequencing-based DNA storage" ; sc:featureList edam:operation_3192 ; sc:name "LDPC" ; sc:url "https://github.com/shubhamchandak94/LDPC_DNA_storage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3305, edam:topic_3517 ; sc:citation , "pmcid:PMC6030966", "pubmed:28968746" ; sc:description "Tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LDassoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ldlink.nci.nih.gov/?%20tab=ldassoc" ; biotools:primaryContact "Mitchell J. Machiela" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC7703752", "pubmed:31584626" ; sc: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.""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0478 ; sc:name "LDmotif" ; sc:url "https://github.com/tanviralambd/LD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3168, edam:topic_3174, edam:topic_3175, edam:topic_3697 ; sc:citation , "pmcid:PMC6933643", "pubmed:31881904" ; sc: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""" ; sc:featureList edam:operation_0495, edam:operation_3228, edam:operation_3359, edam:operation_3802 ; sc:name "LEMON" ; sc:url "https://github.com/lichen2018/LEMON" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3518 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2499, edam:operation_3196, edam:operation_3680, edam:operation_3800 ; sc:license "MIT" ; sc:name "LESSeq" ; sc:url "https://github.com/gersteinlab/LESSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:30525483" ; sc: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." ; sc:featureList edam:operation_2929, edam:operation_3631, edam:operation_3634 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "LFAQ" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://lfaq.github.io/LFAQ/" ; biotools:primaryContact "Cheng Chang", "Zhiqiang Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31657565" ; sc: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""" ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3557, edam:operation_3634, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "LFQ-Analyst" ; sc:softwareHelp ; sc:url "https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3168 ; sc:citation , "pmcid:PMC6855649", "pubmed:31725736" ; sc: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""" ; sc:name "LFastqC" ; sc:url "https://github.uconn.edu/sya12005/LFastqC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6837623", "pubmed:31658247" ; sc: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.""" ; sc:featureList edam:operation_0244, edam:operation_0455, edam:operation_2426 ; sc:name "LGE" ; sc:url "https://github.com/GabrielBalabanResearch/lgemri_scar_metrics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_2640 ; sc:citation , "pmcid:PMC7229246", "pubmed:31621885" ; sc: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])""" ; sc:featureList edam:operation_2428, edam:operation_3503, edam:operation_3659 ; sc:name "LGG" ; sc:url "https://hgittleman.shinyapps.io/LGG_Nomogram_H_Gittleman/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3489 ; sc:citation ; sc:description "LIBR Methamphetamine and Opioid Cue Database (LIBR MOCD) | Repository for the LIBR Meth Opioid Cue Reactivity Database | This project contains two folders:" ; sc:name "LIBR MOCD" ; sc:url "https://github.com/rkuplicki/LIBR_MOCD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0621, edam:topic_2640, edam:topic_3384, edam:topic_3452 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_3435, edam:operation_3553 ; sc:name "LIDC" ; sc:url "https://pylidc.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3314, edam:topic_3315 ; sc:citation ; sc:description "Toolkit for Simulating Lignin Biosynthesis." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LIGNIN-KMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/michaelorella/lignin-kmc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pubmed:31804675" ; sc:description """A tool for comparing species partition. We are pleased to announce the launch of Limes!.""" ; sc:name "LIMES" ; sc:url "http://www.limes.cnrs.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3840 ; sc:name "LINbase" ; sc:url "http://www.LINbase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0153, edam:topic_3306 ; sc:citation , "pmcid:PMC6541037", "pubmed:31141612" ; sc:description "Web-based ontology enrichment tool for lipidomic data analysis." ; sc:featureList edam:operation_0335, edam:operation_3501, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LION-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lipidontology.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_0780 ; sc:citation ; sc:description "Software for identifying lipids in LC-MS/MS-based lipidomics data." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "LIQUID" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/PNNL-Comp-Mass-Spec/LIQUID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_0625, edam:topic_3172, edam:topic_3518 ; sc:citation , "pmcid:PMC6902471", "pubmed:31822265" ; sc: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""" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3463, edam:operation_3659 ; sc:name "LLCT" ; sc:url "https://github.com/its-likeli-jeff/LLCT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3172, edam:topic_3292, edam:topic_3336, edam:topic_3382, edam:topic_3518 ; sc:citation , , "pmcid:PMC6719194", "pubmed:31443278", "pubmed:33657805" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3435, edam:operation_3891 ; sc:name "LM-GlycomeAtlas" ; sc:url "https://glycosmos.gitlab.io/lm-glycomeatlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3382 ; sc:citation , "pubmed:31860062" ; sc: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.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "LOBSTER" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31860062" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3325, edam:topic_3360 ; sc:citation , "pmcid:PMC6527418", "pubmed:31119199" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "LOINC2HPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/monarch-initiative/loinc2hpo" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0160, edam:topic_3399 ; sc:citation , "pmcid:PMC6602514", "pubmed:31081035" ; sc:description "LOMETS (Local Meta-Threading Server) is meta-threading method for template-based protein structure prediction." ; sc:featureList edam:operation_0267, edam:operation_0302, edam:operation_0474 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LOMETS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://zhanglab.ccmb.med.umich.edu/LOMETS/" ; biotools:primaryContact "Yang Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6722229", "pubmed:31555116" ; sc: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" ; sc:featureList edam:operation_3180, edam:operation_3218, edam:operation_3431 ; sc:name "LONI-QC" ; sc:url "http://qc.loni.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6786659", "pubmed:31568528" ; sc: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""" ; sc:featureList edam:operation_2454, edam:operation_3436, edam:operation_3439 ; sc:name "LOTUS" ; sc:url "https://github.com/LOTUSproject/LOTUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3063, edam:topic_3378, edam:topic_3379 ; sc:citation , "pmcid:PMC6918608", "pubmed:31849321" ; sc: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:.""" ; sc:featureList edam:operation_3435, edam:operation_3907 ; sc:name "LP-SDA" ; sc:url "https://github.com/ruoqi-liu/LP-SDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31860024" ; sc: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""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3557, edam:operation_3658, edam:operation_3659 ; sc:name "LPM" ; sc:url "https://github.com/mingjingsi/LPM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196 ; sc:citation , "pubmed:29036421" ; sc:description "Tool for evaluating Long Reads Correction methods." ; sc:featureList edam:operation_3195, edam:operation_3198, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LRCstats" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cchauve/lrcstats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC6902338", "pubmed:31818249" ; sc: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""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:name "LRScaf" ; sc:url "https://github.com/shingocat/lrscaf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3318 ; sc:citation , "pmcid:PMC6879002", "pubmed:31769805" ; sc: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.""" ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_0525, edam:operation_3211, edam:operation_3216 ; sc:license "MIT" ; sc:name "LRTK-SIM" ; sc:url "https://github.com/zhanglu295/LRTK-SIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:22119648" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.statistical-modeling.de/lst.html" ; biotools:primaryContact "Mark Mühlau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31502974" ; sc: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" ; sc:name "LSTD" ; sc:url "https://github.com/Cassie94/LSTD/tree/lstd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31443043" ; sc: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" ; sc:featureList edam:operation_0303, edam:operation_0463 ; sc:name "LSTM" ; sc:url "https://github.com/rajkumar1501/sequence-prediction-using-CNN-and-LSTMs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31634636" ; sc: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).""" ; sc:featureList edam:operation_1781, edam:operation_2495, edam:operation_3439 ; sc:license "MIT" ; sc:name "LSTrAP-Lite" ; sc:url "https://github.com/mutwil/LSTrAP-Lite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293, edam:topic_3500 ; sc:citation , "pmcid:PMC6693147", "pubmed:31409290" ; sc: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" ; sc:license "GPL-3.0" ; sc:name "LSX" ; sc:url "https://github.com/carlosj-rr/LSx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610 ; sc:description "Webpage dedicated to the visualization and management of environmental and planktonic data collected at the LTER-MC station in the Gulf of Naples." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LTER-MARECHIARA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://szn.macisteweb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6765121", "pubmed:31372654" ; sc: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" ; sc:featureList edam:operation_0441, edam:operation_2495, edam:operation_3223 ; sc:name "LTMG" ; sc:url "https://github.com/zy26/LTMGSCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6702745", "pubmed:31429720" ; sc: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" ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3766 ; sc:license "GPL-3.0" ; sc:name "LUAD LUSC" ; sc:url "https://github.com/ELELAB/LUAD_LUSC_TCGA_comparison" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3172, edam:topic_3360 ; sc:citation , "pmcid:PMC7986585", "pubmed:31504184" ; sc: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" ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "LUCIDus" ; sc:url "https://CRAN.R-project.org/package=LUCIDus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3797 ; sc:license "LGPL-3.0" ; sc:name "LULU" ; sc:url "https://github.com/tobiasgf/lulu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description "Using Transcriptional Signatures to Find Cancer Drivers with LURE | LURE (Learning UnRealized Events)" ; sc:featureList edam:operation_3501 ; sc:name "LURE" ; sc:url "https://sysbiowiki.soe.ucsc.edu/lure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3489 ; sc:citation ; sc: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...""" ; sc:name "LaMMA" ; sc:url "http://dati.lamma.toscana.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation , "pubmed:31653717" ; sc: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").""" ; sc:featureList edam:operation_2940, edam:operation_3196, edam:operation_3432 ; sc:license "Apache-2.0" ; sc:name "La isla de tomato" ; sc:url "https://github.com/mmjulkowska/La_isla_de_tomato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6526094", "pubmed:31106360" ; sc:description "Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species." ; sc:featureList edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LanceletDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genome.bucm.edu.cn/lancelet/" ; biotools:primaryContact "Anlong Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0279, edam:operation_0337, edam:operation_3802 ; sc:name "LandScape" ; sc:url "http://bio.oviz.org/demo-project/analyses/landscape" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service", "Workbench" ; sc:author , ; sc:citation , , "pmcid:PMC7136032", "pmcid:PMC8574934", "pubmed:32252069", "pubmed:34749633" ; sc:contributor , , , ; sc: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)." ; sc:license "GPL-3.0" ; sc:name "Laniakea" ; sc:provider "ELIXIR-ITA-INFN" ; sc:softwareHelp ; sc:softwareVersion "2.0.0" ; sc:url "https://laniakea-elixir-it.github.io/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:31425100" ; sc: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" ; sc:name "LassoNet" ; sc:url "https://lassonet.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0780, edam:topic_3172, edam:topic_3308 ; sc:citation , "pubmed:31605615" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3625 ; sc:name "LeGOO" ; sc:url "https://www.legoo.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6286150", "pubmed:30179717" ; sc:description "MATLAB-toolbox facilitating deep brain stimulation electrode locations and connectomic imaging." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Lead-DBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2" ; sc:url "https://www.lead-dbs.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303, edam:topic_3337 ; sc:citation ; sc:description "Open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research." ; sc:featureList edam:operation_0224, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "Leaf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/uwrit/leaf" ; biotools:primaryContact "Sean D. Mooney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269 ; sc:citation ; sc:description "A QGIS plugin for automated landscape ecology analysis." ; sc:featureList edam:operation_3799 ; sc:name "LecoS" ; sc:url "http://plugins.qgis.org/plugins/LecoS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3056 ; sc:citation , "pmcid:PMC6819480", "pubmed:31660852" ; sc: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.""" ; sc:featureList edam:operation_2426, edam:operation_3659 ; sc:name "Legofit" ; sc:url "https://github.com/alanrogers/legofit" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Multi-organism mine integrates data from legume species: string bean, soybean, peanut and barrel medic" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "LegumeMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "11" ; sc:url "https://mines.legumeinfo.org/legumemine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pubmed:30552881" ; sc:description "Leishmania Inhibitor Database" ; sc:featureList edam:operation_0004 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "LeishInDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://leishindb.biomedinformri.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0820, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0269, edam:operation_0418, edam:operation_2241 ; sc:name "LiGIoNs" ; sc:url "http://bioinformatics.biol.uoa.gr/ligions/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3474 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "LiPLike" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.com/Gustafsson-lab/liplike" ; biotools:primaryContact "Mika Gustafsson", "Rasmus Magnusson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6354030", "pubmed:30597002" ; sc:description "Scalable k-mer-based tool for massive all-vs-all metagenome comparisons." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Libra" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/iychoi/libra" ; biotools:primaryContact "Illyoung Choi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:encodingFormat edam:format_2331 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:encodingFormat edam:format_2331 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3275 ; sc:encodingFormat edam:format_2331 ; sc:name "Phenotype name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2331 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1935, edam:format_2330, edam:format_2571 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1048 ; sc:encodingFormat edam:format_2331 ; sc:name "Database ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1192 ; sc:encodingFormat edam:format_2331 ; sc:name "Tool name (BLAST)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3723 ; sc:encodingFormat edam:format_2330 ; sc:name "Morphology parameter" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3752 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1868 ; sc:encodingFormat edam:format_2331 ; sc:name "Taxon" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_1333, edam:format_2330, edam:format_2331, edam:format_3547 ; sc:name "Sequence report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0621, edam:topic_0622, edam:topic_3071, edam:topic_3302, edam:topic_3387, edam:topic_3810 ; sc:author , "Sea Lice Research Centre (SLRC)", "Wei Zhang" ; sc: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." ; sc:featureList edam:operation_0305, edam:operation_0346, edam:operation_2421, edam:operation_2422, edam:operation_3208 ; sc:funder "The Research Council of Norway" ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "LiceBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Bergen" ; sc:softwareHelp , , , ; sc:url "https://licebase.org/" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_1910 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3299 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_0567, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "Lifemap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://lifemap.univ-lyon1.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3673 ; sc:citation , "pmcid:PMC6513517", "pubmed:31084602" ; sc:description "Multi-view CpG sites detection on single-cell whole genome sequence data." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LightCpG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/guofei-tju/LightCpG" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0654 ; sc:citation , "pubmed:27416618" ; sc:description "Tool to determine DNA profile weight of evidence." ; sc:featureList edam:operation_2937, edam:operation_3196, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LikeLTD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "6.3.0" ; sc:url "https://sites.google.com/site/baldingstatisticalgenetics/" ; biotools:primaryContact "Christopher Steele" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172 ; sc:citation , "pmcid:PMC6290884", "pubmed:30535020" ; sc:description "R package for personalized pathway-based classification modeling using metabolomics data." ; sc:featureList edam:operation_0533, edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Lilikoi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/lilikoi/index.html" ; biotools:primaryContact "Fadhl Alakwaa" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2978 ; sc:encodingFormat edam:format_2330 ; sc:name "Reaction data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3314, edam:topic_3520 ; sc:citation , "pubmed:33657806" ; sc:description "LinX is a Java language-based program designed for fast assignment, evaluation, and validation of mass spectrometric datasets from chemical cross-linking." ; sc:featureList edam:operation_0389, edam:operation_2945, edam:operation_3767, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LinX" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://peterslab.org/downloads.php" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2182, edam:format_2200 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1235 ; sc:name "Sequence cluster" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080, edam:topic_0623, edam:topic_3174 ; sc:citation , "pmcid:PMC6026198", "pubmed:29959318" ; sc: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." ; sc:featureList edam:operation_0291 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Linclust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://mmseqs.com" ; biotools:primaryContact "Söding Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3512, edam:topic_3542 ; sc:citation , "pmcid:PMC6681470", "pubmed:31510672" ; sc: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" ; sc:featureList edam:operation_0278, edam:operation_0481, edam:operation_1812 ; sc:name "LinearFold" ; sc:url "http://linearfold.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0780 ; sc:citation , "pmcid:PMC7141858", "pubmed:31738392" ; sc: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""" ; sc:featureList edam:operation_3501, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "Link-HD" ; sc:url "https://github.com/lauzingaretti/LinkHD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0602, edam:topic_2229, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0269, edam:operation_0417, edam:operation_3439 ; sc:name "LinkPhinder" ; sc:url "https://LinkPhinder.insight-centre.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_2830 ; sc:citation , "pmcid:PMC6571408", "pubmed:31124967" ; sc: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." ; sc:featureList edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LinkeDomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.linkedomics.org" ; biotools:primaryContact "Xiaohua Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325 ; sc:citation , "pmcid:PMC5682045", "pubmed:29214177" ; sc:description "Connects rare diseases patient registries through a Semantic Web Layer." ; sc:featureList edam:operation_2422, edam:operation_3283 ; sc:isAccessibleForFree true ; sc:name "Linked Registries" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.ua.pt/linked-registries-app/#" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0153, edam:topic_0593, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC6921604", "pubmed:31867556" ; sc: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.""" ; sc:featureList edam:operation_3215, edam:operation_3799, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "LipMat" ; sc:url "https://github.com/MarJakubec/LipMat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0736 ; sc:citation , "pubmed:31545554" ; sc: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" ; sc:featureList edam:operation_0303, edam:operation_3431, edam:operation_3798 ; sc:name "Lipase Engineering Database" ; sc:url "https://led.biocatnet.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0821, edam:topic_3534 ; sc:citation ; sc:description "Deposit and classification of lipolytic enzymes based on the proposed classification system in Hitch and Clavel (TBP)." ; sc:featureList edam:operation_0483, edam:operation_3431, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Lipase reclassification" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/thh32/Lipase_reclassification" ; biotools:primaryContact "Thomas C. A. Hitch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_3314, edam:topic_3407 ; sc:citation , "pubmed:31729667" ; sc: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.""" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3860 ; sc:name "LipidIMMS" ; sc:url "http://imms.zhulab.cn/LipidIMMS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3337, edam:topic_3520 ; sc:citation , "pubmed:30500173" ; sc:description "R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LipidMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://cran.r-project.org/package=LipidMS" ; biotools:primaryContact "M Isabel Alcoriza-Balaguer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC6489209", "pubmed:31035918" ; sc:description "Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values." ; sc:featureList edam:operation_3629, edam:operation_3633, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LipidMatch Normalizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "http://secim.ufl.edu/secim-tools/lipidmatch-normalizer/" ; biotools:primaryContact "Jason Cochran", "Jeremy Koelmel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0153 ; sc:citation ; sc:description "Lipid Mining and Ontology (Lipid Mini-On) - mining and ontology tool for enrichment analysis of lipidomic data." ; sc:featureList edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "Lipid Mini-On" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://omicstools.pnnl.gov/shiny/lipid-mini-on/" ; biotools:primaryContact "Geremy Clair", "Jennifer E. Kyle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3068 ; sc:citation , "pmcid:PMC7145649", "pubmed:31617563" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3208, edam:operation_3503, edam:operation_3659 ; sc:name "LnCeVar" ; sc:url "http://www.bio-bigdata.net/LnCeVar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3068 ; sc:citation , "pubmed:29850816" ; sc:description "ab initio lncRNA identification and functional annotation tool based on deep learning." ; sc:featureList edam:operation_0476, edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LncADeep" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cyang235/LncADeep/" ; biotools:primaryContact "Huaiqiu Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0634, edam:topic_0659 ; sc:citation , "pubmed:31524988" ; sc: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." ; sc:featureList edam:operation_0314, edam:operation_0417, edam:operation_2495, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "LncBook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://ngdc.cncb.ac.cn/lncbook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3295, edam:topic_3360 ; sc:citation , "pmcid:PMC7145524", "pubmed:31713618" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_3439, edam:operation_3446 ; sc:name "LncTarD" ; sc:url "http://biocc.hrbmu.edu.cn/LncTarD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2885 ; sc:citation , , "pubmed:27605101", "pubmed:30539556" ; sc:description "Database of genetic variations associated with long noncoding genes." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:name "LncVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ibp.ac.cn/LncVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:30401722" ; sc:description "Automated eukaryotic genome annotation based on long-read cDNA sequencing." ; sc:featureList edam:operation_0308, edam:operation_0362, edam:operation_0476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LoReAn" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/lfaino/LoReAn" ; biotools:primaryContact "Luigi Faino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0140, edam:topic_0602, edam:topic_0749, edam:topic_2229 ; sc:citation , "pmcid:PMC6886211", "pubmed:31787091" ; sc:description """Integrating protein localization with automated signaling pathway reconstruction. Are you sure you want to delete this graph?""" ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:name "LocPL" ; sc:url "http://graphspace.org/graphs/?query=tags:LocPL" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "An integrated Omics data warehouse for Locust, Locusta migratoria" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "LocustMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.2" ; sc:url "http://locustmine.org:8080/locustmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3512, edam:topic_3855 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Logomaker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/jbkinney/logomaker" ; biotools:primaryContact "Ammar Tareen", "Justin Kinney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2885 ; sc:citation , "pubmed:31287494" ; sc:description "de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models." ; sc:featureList edam:operation_3359, edam:operation_3472, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:name "Look4TRs" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/TulsaBioinformaticsToolsmith/Look4TRs" ; biotools:primaryContact "Hani Z. Girgis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0632, edam:topic_2885, edam:topic_3068, edam:topic_3168 ; sc:citation , "pubmed:31674643" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_0487, edam:operation_3192 ; sc:name "Loxodonta Localizer" ; sc:url "http://www.loxodontalocalizer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_3067, edam:topic_3172, edam:topic_3382 ; sc:citation , "pmcid:PMC6814058", "pubmed:31651362" ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3352, edam:operation_3553 ; sc:name "LungMAP" ; sc:url "http://www.lungmap.net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "White and narrow-leaf lupin data from the Legume Information System" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "LupinMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "2" ; sc:url "https://mines.legumeinfo.org/lupinmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:31719438" ; sc: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.""" ; sc:name "LutzoDexTM" ; sc:url "https://play.google.com/store/apps/details?id=max.com.lutzodexhl=pt_BR." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3179, edam:topic_3519 ; sc:citation , "pubmed:31745565" ; sc: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.""" ; sc:featureList edam:operation_0308, edam:operation_0335, edam:operation_0435, edam:operation_0440, edam:operation_3222 ; sc:name "LuxR" ; sc:url "https://github.com/Juliacvk/LuxR_H-NS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation , "pmcid:PMC6823652", "pubmed:31673810" ; sc: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.""" ; sc:featureList edam:operation_2426, edam:operation_3659, edam:operation_3799 ; sc:name "LyoPRONTO" ; sc:url "https://sites.google.com/view/rgdart/Research/lyopronto-lyophilization-processoptimization-tool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3295 ; sc:citation , "pubmed:31493278" ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3557 ; sc:name "M-GCTA" ; sc:url "https://github.com/uqzqiao/M-GCTA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3295, edam:topic_3300, edam:topic_3382 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3216, edam:operation_3443, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "M-TRACK" ; sc:url "https://github.com/opnumten/M-TRACK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3473, edam:topic_3697 ; sc:citation , "pmcid:PMC6602433", "pubmed:31114912" ; sc:description "Web server for the analysis of large-scale microbial genomics data." ; sc:featureList edam:operation_0306, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "M1CR0B1AL1Z3R" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://microbializer.tau.ac.il/" ; biotools:primaryContact "Tal Pupko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6923906", "pubmed:31861972" ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3664 ; sc:name "M3S" ; sc:url "https://github.com/zy26/M3S" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3489 ; sc:citation , "pubmed:31634642" ; sc: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.""" ; sc:featureList edam:operation_3196 ; sc:name "MAC-INMV-SSR" ; sc:url "http://mac-inmv.tours.inra.fr/0_macinmv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_0199, edam:topic_3306 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_2492 ; sc:name "MACV" ; sc:url "https://github.com/clauswilke/MACV_SMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_0154, edam:topic_2814 ; sc:citation , "pmcid:PMC6929402", "pubmed:31870277" ; sc: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.""" ; sc:featureList edam:operation_0360, edam:operation_0491, edam:operation_0503, edam:operation_0510, edam:operation_3454 ; sc:name "MADOKA" ; sc:url "http://madoka.denglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168, edam:topic_3518 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3501 ; sc:name "MADloy" ; sc:url "https://github.com/isglobal-brge/MADloy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , , , , , "pmcid:PMC3603318", "pmcid:PMC548345", "pmcid:PMC6041967", "pmcid:PMC6781576", "pubmed:15661851", "pubmed:23329690", "pubmed:24170399", "pubmed:28968734", "pubmed:29506019" ; sc:description "MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program." ; sc:featureList edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "BSD-Source-Code" ; sc:name "MAFFT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mafft.cbrc.jp/alignment/server/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0097, edam:topic_0154 ; sc:citation , "pmcid:PMC6602451", "pubmed:31062021" ; sc:description "Multiple alignment program for amino acid or nucleotide sequences." ; sc:featureList edam:operation_0503, edam:operation_0504, edam:operation_0509 ; sc:isAccessibleForFree true ; sc:license "GPL-1.0" ; sc:name "MAFFT-DASH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mafft.cbrc.jp/alignment/server/" ; biotools:primaryContact , "Daron M. Standley" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:18372315" ; sc:description "High speed multiple sequence alignment program." ; sc:featureList edam:operation_0492 ; sc:name "MAFFT API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/msa/mafft_rest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625, edam:topic_0659, edam:topic_3334 ; sc:citation , "pmcid:PMC6815046", "pubmed:31653223" ; sc: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.""" ; sc:featureList edam:operation_3196, edam:operation_3439, edam:operation_3501 ; sc:name "MAGI-S" ; sc:url "https://github.com/jchow32/magi-s" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_3174, edam:topic_3316, edam:topic_3697 ; sc:citation , "pmcid:PMC6993843", "pubmed:31633780" ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3798 ; sc:name "MAGO" ; sc:url "http://mago.fe.uni-lj.si" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2640, edam:topic_2885, edam:topic_3676 ; sc:citation ; sc:description """Discovering Subclones in Tumors Sequenced at Standard Depths. MAGOS: Model-based Adaptive Grouping of Subclones""" ; sc:featureList edam:operation_3196, edam:operation_3432, edam:operation_3435 ; sc:name "MAGOS" ; sc:url "https://github.com/liliulab/magos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0798, edam:topic_3301 ; sc:citation , "pmcid:PMC5860071", "pubmed:28498899" ; sc:description "Microbial Assessment by Genome-wide Tn-Seq Analysis (MAGenTA) - Galaxy implemented tool for complete Tn-Seq analysis and data visualization." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MAGenTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://vanopijnenlab.github.io/MAGenTA/" ; biotools:primaryContact "Tim van Opijnen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3170, edam:topic_3320 ; sc:citation , "pmcid:PMC7263396", "pubmed:28968636" ; sc:description "Web-tool to interrogate classical and complex splicing variations from RNA-Seq data." ; sc:featureList edam:operation_0308, edam:operation_3237, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MAJIQ-SPEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "http://majiq.biociphers.org/majiq-spel" ; biotools:primaryContact "Yoseph Barash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3334, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC7198352", "pubmed:31691160" ; sc: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""" ; sc:featureList edam:operation_2428, edam:operation_3283, edam:operation_3435 ; sc:license "MIT" ; sc:name "MALINI" ; sc:url "https://github.com/pradlanka/malini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0602, edam:topic_0736, edam:topic_0821, edam:topic_3407 ; sc:citation , "pmcid:PMC6812854", "pubmed:31648227" ; sc: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.""" ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3660 ; sc:name "MANET" ; sc:url "http://manet.illinois.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6796874", "pubmed:31636953" ; sc: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""" ; sc:featureList edam:operation_2429, edam:operation_2495, edam:operation_3638, edam:operation_3659 ; sc:name "MAP" ; sc:url "http://bioinfo.sibs.ac.cn/shaolab/MAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC6483256", "pubmed:30986246" ; sc: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." ; sc:featureList edam:operation_2429, edam:operation_3222, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:name "MAPS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ijuric/MAPS" ; biotools:primaryContact "Ivan Juric", "Ming Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500, edam:topic_3524 ; sc:citation , "pmcid:PMC6876843", "pubmed:31765421" ; sc: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.""" ; sc:featureList edam:operation_3435, edam:operation_3450 ; sc:name "MARGO" ; sc:url "https://github.com/de-Bivort-Lab/margo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3474 ; sc:citation , "pmcid:PMC7075463", "pubmed:31611695" ; sc: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.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2454, edam:operation_3439 ; sc:name "MARIA" ; sc:url "https://maria.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3520 ; sc:citation , "pubmed:31097673" ; sc:description "Extracting Publication-ready Mass Spectrometry Metadata from RAW Files." ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3627 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MARMoSET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.molgen.mpg.de/loosolab/MARMoSET_C" ; biotools:primaryContact "Johannes Graumann", "Mario Looso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3306, edam:topic_3810 ; sc:citation ; sc: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:""" ; sc:featureList edam:operation_2426 ; sc:license "Apache-2.0" ; sc:name "MARSHAL" ; sc:url "https://plantmodelling.shinyapps.io/marshal/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_1915, edam:format_2330, edam:format_3651, edam:format_3834 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_1915, edam:format_3244, edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3834 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2332, edam:format_3247, edam:format_3651, edam:format_3681, edam:format_3713, edam:format_3752 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pmcid:PMC3108832", "pubmed:10612281", "pubmed:12422359", "pubmed:21447708" ; sc:description "The leading software package for protein identification and characterisation using mass spectrometry data." ; sc:featureList edam:operation_2929, edam:operation_3639, edam:operation_3641, edam:operation_3643, edam:operation_3646, edam:operation_3647, edam:operation_3649, edam:operation_3767, edam:operation_3801 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Mascot Server" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.matrixscience.com/server.html" ; biotools:primaryContact "see publication" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0736, edam:topic_3169 ; sc:citation , "pmcid:PMC7703792", "pubmed:31742324" ; sc: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.""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0240 ; sc:license "MIT" ; sc:name "MASSIF" ; sc:url "https://github.com/SchulzLab/MASSIF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_3196, edam:operation_3211 ; sc:name "MAtCHap" ; sc:url "https://sourceforge.net/projects/matchap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_2269, edam:topic_3324 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2426, edam:operation_3659 ; sc:name "MBITES" ; sc:url "https://github.com/dd-harp/MBITES/tree/v1.0/MBITES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC7145604", "pubmed:31624841" ; sc: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.""" ; sc:featureList edam:operation_0484, edam:operation_2421, edam:operation_2429, edam:operation_3196, edam:operation_3227 ; sc:name "MBKbase rice" ; sc:softwareHelp ; sc:url "http://www.mbkbase.org/rice" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2830, edam:topic_3315 ; sc:citation , "pmcid:PMC6644659", "pubmed:31458826" ; sc: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" ; sc:featureList edam:operation_0478, edam:operation_2492 ; sc:name "MCMap" ; sc:url "http://www.bisb.uni-bayreuth.de/index.php?page=downloads" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6868382", "pubmed:31750523" ; sc: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""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_2492 ; sc:name "MCOT" ; sc:url "https://gitlab.sysbio.cytogen.ru/academiq/mcot-kernel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3407 ; sc:citation , "pmcid:PMC6612898", "pubmed:31510702" ; sc: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" ; sc:featureList edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "MCS2" ; sc:url "https://github.com/RezaMash/MCS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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." ; sc:name "MCScan" ; sc:url "https://github.com/tanghaibao/mcscan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3168, edam:topic_3173, edam:topic_3674 ; sc:citation , "pmcid:PMC6795852", "pubmed:31619715" ; sc: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.""" ; sc:featureList edam:operation_0308, edam:operation_3196, edam:operation_3204 ; sc:name "MCSeEd" ; sc:url "https://bitbucket.org/capemaster/mcseed/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2640, edam:topic_3315 ; sc:citation , "pmcid:PMC6612807", "pubmed:31510657" ; sc: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" ; sc:featureList edam:operation_0555, edam:operation_0557, edam:operation_3478 ; sc:name "MCT" ; sc:url "https://github.com/elkebir-group/MCT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3372 ; sc:citation , "pubmed:31659696" ; sc: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""" ; sc:featureList edam:operation_0394, edam:operation_3436, edam:operation_3659, edam:operation_3891 ; sc:name "MD-LOVIs" ; sc:url "http://tomocomd.com/md-lovis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3047, edam:topic_3335, edam:topic_3512 ; sc:citation , "pmcid:PMC6786093", "pubmed:31632446" ; sc: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.""" ; sc:featureList edam:operation_0463, edam:operation_2428, edam:operation_3792 ; sc:name "MDCAP" ; sc:url "https://github.com/cuppeanuts/MDCAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0749 ; sc:citation , "pmcid:PMC7394328", "pubmed:30717647" ; sc:description "Web server for identifying glutarylation sites." ; sc:featureList edam:operation_0417, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "MDDGlutar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cse.yzu.edu.tw/MDDGlutar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2258, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:31745704" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3893 ; sc:license "MIT" ; sc:name "MDFPtools" ; sc:url "https://github.com/rinikerlab/mdfptools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_3068, edam:topic_3332 ; sc:citation , "pubmed:31660624" ; sc: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""" ; sc:featureList edam:operation_0477, edam:operation_2476, edam:operation_3893 ; sc:license "MIT" ; sc:name "MDMS" ; sc:url "https://github.com/szymonzaczek/MDMS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_3746 ; sc:name "Count matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_3033 ; sc:name "Mathematical model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3905 ; sc:encodingFormat edam:format_3508 ; sc:name "Histogram" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_2269, edam:topic_3301, edam:topic_3474 ; sc:author ; sc:citation ; sc:contributor ; sc: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." ; sc:featureList edam:operation_0004, edam:operation_0335, edam:operation_0337, edam:operation_3432, edam:operation_3480, edam:operation_3695, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MDPBiome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/beatrizgj/MDPbiome" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3170, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC7075537", "pubmed:31697315" ; sc: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.""" ; sc:featureList edam:operation_3562, edam:operation_3659 ; sc:name "MDiNE" ; sc:url "https://github.com/kevinmcgregor/mdine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0602 ; sc:citation , "pubmed:31418769" ; sc: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" ; sc:featureList edam:operation_1816 ; sc:license "GPL-3.0" ; sc:name "MEPSAnd" ; sc:url "http://bioweb.cbm.uam.es/software/MEPSAnd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0625, edam:topic_2885, edam:topic_3305 ; sc:citation , "pubmed:31683007" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3482 ; sc:name "MERCAT" ; sc:url "https://github.com/zaandahl/mercat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6755101", "pubmed:31428793" ; sc: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" ; sc:featureList edam:operation_3478, edam:operation_3557, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "MERLoT" ; sc:url "https://github.com/soedinglab/merlot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0736, edam:topic_0820 ; sc:citation , "pmcid:PMC6602572", "pubmed:31106328" ; sc:description "Web server to prepare and run coarse-grained membrane protein dynamics." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MERMAID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://molsim.sci.univr.it/mermaid/" ; biotools:primaryContact "Alejandro Giorgetti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0623, edam:topic_0821 ; sc:citation , "pmcid:PMC6750024", "pubmed:31524991" ; sc: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" ; sc:featureList edam:operation_3092 ; sc:name "MESSA" ; sc:url "http://prodata.swmed.edu/MESSA/MESSA.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:name "Spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172 ; sc: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.""" ; sc:featureList edam:operation_3801, edam:operation_3803 ; sc:name "MESSAR (MEtabolite SubStructure Auto-Recommender)" ; sc:url "https://messar.biodatamining.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3407 ; sc:citation , "pmcid:PMC6735823", "pubmed:30657869" ; sc:description "R package for context-specific expression analysis of metabolic gene clusters." ; sc:featureList edam:operation_0313, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "METACLUSTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mbanf/METACLUSTER" ; biotools:primaryContact "EducatedGuess.ai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_2640 ; sc:citation , "pubmed:31432076" ; sc: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:" ; sc:featureList edam:operation_1812, edam:operation_3501 ; sc:name "MEXCOwalk" ; sc:url "https://github.com/abu-compbio/MEXCOwalk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_3168, edam:topic_3174, edam:topic_3308 ; sc:citation , "pmcid:PMC6842160", "pubmed:31703549" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_0362, edam:operation_3192 ; sc:name "MG-RAST API explorer" ; sc:url "https://explorer.mg-rast.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_0798 ; sc:citation , "pmcid:PMC6515669", "pubmed:31114637" ; sc:description "Mobile Genetic Elements Retrieving Tool Pipeline (MGERT) for retrieving coding sequences of mobile genetic elements from genome assemblies." ; sc:featureList edam:operation_0427, edam:operation_0525, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MGERT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/andrewgull/MGERT" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3297, edam:topic_3303, edam:topic_3697, edam:topic_3837 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_3431, edam:operation_3472, edam:operation_3731 ; sc:license "GPL-3.0" ; sc:name "MGLEX" ; sc:url "http://pypi.python.org/pypi/mglex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885 ; sc:citation , "pmcid:PMC9158227", "pubmed:35650523" ; sc:description "Parameter estimation and classification for Gaussian Mixture Models (GMMs) in the presence of missing data." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MGMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zrmacc/MGMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_3293 ; sc:citation , "pmcid:PMC6904324", "pubmed:31397853" ; sc: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" ; sc:featureList edam:operation_3208, edam:operation_3216, edam:operation_3501 ; sc:name "MGOB" ; sc:url "http://mgob.ucd.ie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_2229, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC7145632", "pubmed:31696235" ; sc: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.""" ; sc:featureList edam:operation_0310, edam:operation_3184, edam:operation_3731 ; sc:name "MGnify" ; sc:url "http://www.ebi.ac.uk/metagenomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0781, edam:topic_0804, edam:topic_3292 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0482 ; sc:name "MHCII" ; sc:url "http://tools.iedb.org/mhci/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2830 ; sc:citation , "pmcid:PMC6540523", "pubmed:31138107" ; sc:description "Deep neural network model for universal Major Histocompatibility Complex (MHC) binding prediction." ; sc:featureList edam:operation_0252, edam:operation_3227, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MHCSeqNet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cmbcu/MHCSeqNet" ; biotools:primaryContact "Computational Molecular Biology Group, Chulalongkorn University" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_2830, edam:topic_3520 ; sc:citation , "pubmed:31589052" ; sc:description """Automated and Reproducible Data Analysis for Immunopeptidomics. MHCquant: Identify and quantify peptides from mass spectrometry raw data.""" ; sc:featureList edam:operation_3634, edam:operation_3643, edam:operation_3649 ; sc:name "MHCquant" ; sc:url "https://www.openms.de/mhcquant/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:31647522" ; sc: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.""" ; sc:featureList edam:operation_3435 ; sc:name "MIAmS" ; sc:url "https://github.com/bialimed/miams" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0610, edam:topic_2269 ; sc:citation , "pmcid:PMC6854112", "pubmed:31832144" ; sc: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.""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3664 ; sc:name "MIAmaxent" ; sc:url "https://biodiversityinformatics.amnh.org/open_source/maxent/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0140, edam:topic_0605, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC6815465", "pubmed:31655541" ; sc: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)""" ; sc:featureList edam:operation_0321, edam:operation_2489, edam:operation_3092 ; sc:name "MIC_Locator" ; sc:url "https://github.com/ProteinLocator/MIC_Locator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0605, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC6829817", "pubmed:31684860" ; sc: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""" ; sc:featureList edam:operation_0463, edam:operation_2436, edam:operation_3792 ; sc:name "MIENTURNET" ; sc:url "http://userver.bio.uniroma1.it/apps/mienturnet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3056, edam:topic_3500 ; sc:citation , , "pmcid:PMC2870966", "pmcid:PMC6442577", "pubmed:20176979", "pubmed:30867282" ; sc: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." ; sc:featureList edam:operation_0487, edam:operation_0547, edam:operation_3446 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MIGRATE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://peterbeerli.com/migrate-html5/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31443048" ; sc: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" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_2492 ; sc:name "MILAMP" ; sc:url "http://faculty.pieas.edu.pk/fayyaz/software.html#MILAMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3489 ; sc:citation , "pmcid:PMC6908718", "pubmed:31831740" ; sc: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""" ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:name "MIMIC-CXR" ; sc:url "https://mimic-cxr.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC7523682", "pubmed:31400192" ; sc: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" ; sc:featureList edam:operation_3232, edam:operation_3629, edam:operation_3658 ; sc:name "MIND" ; sc:url "https://github.com/randel/MIND" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3342, edam:topic_3391 ; sc:citation , , , , , "pmcid:PMC4932659", "pmcid:PMC5516855", "pmcid:PMC6821317", "pmcid:PMC7373180", "pubmed:27441714", "pubmed:28725475", "pubmed:30991279", "pubmed:31074494", "pubmed:31273380" ; sc:description """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. MINERVA is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java 8. 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 JSF and PrimeFaces. The displayed content is visualized by OpenLayers or Google Maps API, dedicated JavaScript and CSS.""" ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "MINERVA Platform" ; sc:softwareVersion "13.1.3", "13.2.0", "14.0.13", "15.0.3" ; sc:url "https://minerva-web.lcsb.uni.lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6913132", "pubmed:31624092" ; sc: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.""" ; sc:featureList edam:operation_0239, edam:operation_0417, edam:operation_3644 ; sc:name "MINES" ; sc:url "https://github.com/YeoLab/MINES.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6923819", "pubmed:31861975" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3096 ; sc:name "MIRIA" ; sc:url "https://mammal.deepomics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3300, edam:topic_3305, edam:topic_3335, edam:topic_3382 ; sc:citation , "pmcid:PMC6830040", "pubmed:31688939" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3454 ; sc:name "MIRKB" ; sc:url "http://sysbio.org.cn/MIRKB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_0632, edam:topic_2885, edam:topic_3305 ; sc:citation , "pubmed:31603462" ; sc: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.""" ; sc:featureList edam:operation_0310, edam:operation_3196, edam:operation_3227 ; sc:license "MIT" ; sc:name "MIRUReader" ; sc:url "https://github.com/phglab/MIRUReader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3375, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6335810", "pubmed:30651067" ; sc:description "Generic open-source framework for model fits and their exploration in medical imaging - design, implementation and application on the example of DCE-MRI." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MITK-ModelFit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mitk.org/wiki/MITK-ModelFit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC6721208", "pubmed:31477162" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "MITRE" ; sc:url "https://github.com/gerberlab/mitre/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6561249", "pubmed:31113885" ; sc:description "Mismatching Isoform eXon Remover." ; sc:featureList edam:operation_0499, edam:operation_0544, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MIXR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/hawkjo/mixr" ; biotools:primaryContact "Sara L. Sawyer", "William H. Press" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3384, edam:topic_3577 ; sc:citation , "pmcid:PMC7523642", "pubmed:31693075" ; sc: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.""" ; sc:name "MKpLMM" ; sc:url "https://github.com/YaluWen/OmicPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0176, edam:topic_0621 ; sc:citation , "pmcid:PMC6880518", "pubmed:31775608" ; sc: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.""" ; sc:featureList edam:operation_2476 ; sc:name "ML-Force" ; sc:url "https://git.informatik.uni-rostock.de/mosi/ml-force-publication" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3298, edam:topic_3382 ; sc:citation ; sc: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" ; sc:name "ML-morph" ; sc:url "https://github.com/agporto/ml-morph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Metric Learning on Expression Data for Gene Function Prediction." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MLC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.github.com/stamakro/MLC" ; biotools:primaryContact "Stavros Makrodimitris" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0157, edam:topic_0654 ; sc:citation , "pubmed:31584616" ; sc:description """A Fast and Memory Efficient MLCS Algorithm by Character Merging for DNA Sequences Alignment. 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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""" ; sc:featureList edam:operation_3227, edam:operation_3431, edam:operation_3840 ; sc:license "MIT" ; sc:name "MLSTar" ; sc:url "http://github.com/iferres/MLSTar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_2885, edam:topic_3519, edam:topic_3673 ; sc:citation , "pmcid:PMC6905556", "pubmed:31825986" ; sc: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).""" ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_2404 ; sc:name "MLVAType" ; sc:url "https://github.com/dpchris/MLVA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC6493971", "pubmed:31042284" ; sc:description "Microbiome Learning Repo (ML Repo) - public repository of microbiome regression and classification tasks" ; sc:featureList edam:operation_3192, edam:operation_3431, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ML Repo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://knights-lab.github.io/MLRepo/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3474, edam:topic_3570 ; sc:citation , "pubmed:31219626" ; sc:description "Program package for quantum chemical research assisted by machine learning." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MLatom" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://mlatom.com/" ; biotools:primaryContact "Dr. Pavlo O. Dral" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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." ; sc:name "MLME: Machine Learning Made Easy" ; sc:url "https://github.com/FunctionalUrology/MLme" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6839613", "pubmed:31446280" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3891 ; sc:name "MM-WHS" ; sc:url "http://www.sdspeople.fudan.edu.cn/zhuangxiahai/0/mmwhs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3443, edam:operation_3454 ; sc:name "MM3" ; sc:url "https://piazza.com/ucsd/fall2019/mm3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3315, edam:topic_3384, edam:topic_3398, edam:topic_3452 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3435 ; sc:name "MMCL" ; sc:url "http://mcx.space/#mmc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2182, edam:format_2200 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2182, edam:format_2200 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2182, edam:format_2200 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1235 ; sc:name "Sequence cluster" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080, edam:topic_0623, edam:topic_0637, edam:topic_3174 ; sc:citation , , , , , , , "pmcid:PMC6026198", "pmcid:PMC6691333", "pmcid:PMC8479651", "pubmed:29035372", "pubmed:29959318", "pubmed:30615063", "pubmed:33734313" ; sc: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 GPL-licensed 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.""" ; sc:featureList edam:operation_0291, edam:operation_0292, edam:operation_0346, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MMseqs2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://mmseqs.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc: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!" ; sc:featureList edam:operation_0337 ; sc:license "Proprietary" ; sc:name "MNE-Python" ; sc:softwareHelp ; sc:url "http://python.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3336 ; sc:citation , "pmcid:PMC6589129", "pubmed:31125569" ; sc:description "Mother of All Databases (MOAD) - Polypharmacology Tools and Their Utility in Drug Repurposing." ; sc:featureList edam:operation_0482, edam:operation_2575, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MOAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.BindingMOAD.org" ; biotools:primaryContact "Heather A. Carlson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3673 ; sc:citation ; sc:description "Efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool." ; sc:featureList edam:operation_1812, edam:operation_3227, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MOAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://moat.gersteinlab.org/" ; biotools:primaryContact "Mark Gerstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model" ; sc:name "MOBFinder" ; sc:url "https://github.com/FengTaoSMU/MOBFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0623 ; sc:citation , "pubmed:31584171" ; sc: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""" ; sc:featureList edam:operation_0578, edam:operation_2421, edam:operation_3192 ; sc:name "MOBscan" ; sc:url "https://castillo.dicom.unican.es/mobscan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3303, edam:topic_3697 ; sc:citation , "pmcid:PMC6419911", "pubmed:30165396" ; sc:description "Web-application to collect, manage, analyze, visualize and share large and complex biomedical datasets, without the need for advanced bioinformatics skills." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MOLGENIS Research" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wiki.gcc.rug.nl/wiki/research" ; biotools:primaryContact "Morris A. Swertz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6612815", "pubmed:31510700" ; sc: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" ; sc:featureList edam:operation_3557 ; sc:name "MOLI" ; sc:url "https://github.com/hosseinshn/MOLI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3360 ; sc:citation ; sc:description "Toolbox integrating top-performing methods for NEtwork MOdularisation." ; sc:featureList edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MONET" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/BergmannLab/MONET.git" ; biotools:primaryContact "Mattia Tomasoni", "Sven Bergmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3895 ; sc:citation ; sc: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:" ; sc:featureList edam:operation_2425, edam:operation_3745 ; sc:license "MIT" ; sc:name "MOODA" ; sc:url "http://mooda.stracquadaniolab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3315, edam:topic_3407 ; sc:citation , "pmcid:PMC9883724", "pubmed:31504164" ; sc: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" ; sc:featureList edam:operation_3223, edam:operation_3501, edam:operation_3660 ; sc:license "MIT" ; sc:name "MOOMIN" ; sc:url "http://github.com/htpusa/moomin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3295 ; sc:citation , "pmcid:PMC6698707", "pubmed:31049575" ; sc:description "Multi-Omic and Survival pathway analysis for the identification of survival associated gene and module." ; sc:featureList edam:operation_0417, edam:operation_0533, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "MOSClip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cavei/MOSClip" ; biotools:primaryContact "Paolo Martini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3407 ; sc:citation , "pubmed:28430868" ; sc:description "Software for producing automated textbook-style maps of genome-scale metabolic networks." ; sc:featureList edam:operation_0533, edam:operation_3660, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MOST-visualization" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://most.ccib.rutgers.edu/" ; biotools:primaryContact "Desmond S. Lun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0634 ; sc:citation , "pmcid:PMC6789201", "pubmed:31620462" ; sc: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….""" ; sc:license "Apache-2.0" ; sc:name "MOTS" ; sc:url "https://github.com/motech-implementations/mots" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2269, edam:topic_3474 ; sc:citation , "pubmed:31851308" ; sc: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""" ; sc:license "MIT" ; sc:name "MPF-BML" ; sc:url "https://github.com/ahmedaq/MPF-BML-GUI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3068, edam:topic_3360, edam:topic_3379 ; sc:citation , "pmcid:PMC6759478", "pubmed:31620162" ; sc: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""" ; sc:featureList edam:operation_2428, edam:operation_2495 ; sc:name "MPIC" ; sc:url "http://www.mpic-app.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC6717970", "pubmed:31477158" ; sc: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" ; sc:featureList edam:operation_3200, edam:operation_3501, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "MPRAnalyze" ; sc:url "https://bioconductor.org/packages/release/bioc/html/MPRAnalyze.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3518 ; sc:citation , "pmcid:PMC5198521", "pubmed:27605100" ; sc:description "Web-based tool for the design of massively parallel reporter assay experiments." ; sc:featureList edam:operation_0438 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MPRAnator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.sanger.ac.uk/science/tools/mpranator" ; biotools:primaryContact "Ilias Georgakopoulos-Soares", "Martin Hemberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pubmed:31359027" ; sc: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" ; sc:name "MPRAscore" ; sc:url "https://github.com/abhisheknrl/MPRAscore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_2275 ; sc:citation , "pubmed:31086984" ; sc:description "Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models." ; sc:featureList edam:operation_0477, edam:operation_0482, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MPRDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://huanglab.phys.hust.edu.cn/mprdock/" ; biotools:primaryContact "Lab of Bioinformatics and Molecular Modeling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_3360 ; sc:citation , "pmcid:PMC4349052", "pubmed:25755929" ; sc: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""" ; sc:featureList edam:operation_3096, edam:operation_3359 ; sc:name "MPS" ; sc:url "http://campagnelab.org/software/bdval-for-mps/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3375, edam:topic_3379 ; sc:citation ; sc: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)" ; sc:featureList edam:operation_3436 ; sc:name "MPS-Db" ; sc:url "https://mps.csb.pitt.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_3517 ; sc:citation , , "pmcid:PMC5976434", "pmcid:PMC6694718", "pubmed:29846171", "pubmed:31448343" ; sc: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" ; sc:featureList edam:operation_0488, edam:operation_3659 ; sc:license "MIT" ; sc:name "MR-Base" ; sc:url "http://www.mrbase.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2885, edam:topic_3305, edam:topic_3517 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3432, edam:operation_3659, edam:operation_3791 ; sc:name "MR-Clust" ; sc:url "https://github.com/cnfoley/mrclust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3517 ; sc:citation , "pmcid:PMC5755684", "pubmed:28911207" ; sc: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." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MR-MEGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "beta 0.1.5" ; sc:url "https://www.geenivaramu.ee/en/tools/mr-mega" ; biotools:primaryContact "Andrew P Morris", "Reedik Magi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6609486", "pubmed:31037800" ; sc:description "Multi‐Atlas Label Fusion Tool for Neonatal Brain MRI Parcellation and Quantification." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MRICloud" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://braingps.mricloud.org" ; biotools:primaryContact "Kenichi Oishi", "Kumiko Oishi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3384, edam:topic_3422, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC6790816", "pubmed:31607099" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "MRIcron" ; sc:url "https://www.nitrc.org/projects/mricron" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3512, edam:topic_3519 ; sc:citation , "pmcid:PMC6602510", "pubmed:31045205" ; sc:description "Tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MRPrimerW2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://MRPrimerW2.com" ; biotools:primaryContact , "Min-Soo Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3520, edam:topic_3673 ; sc:citation , "pubmed:27993788" ; sc:description "Tool for de novo peptide sequencing utilizing the hadoop distributed computing framework." ; sc:featureList edam:operation_0476, edam:operation_3202, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MRUniNovo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.hupo.org.cn/MRUniNovo/index.php" ; biotools:primaryContact "Kenli Li", "Tao Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31473352" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:name "MRtrix3" ; sc:url "https://github.com/MRtrix3/mrtrix3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6330434", "pubmed:30634897" ; sc: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." ; sc:featureList edam:operation_0417, edam:operation_2939, edam:operation_2940 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MS-Helios" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.8" ; sc:url "https://sourceforge.net/projects/ms-helios/" ; biotools:primaryContact "Harald Marx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC6929458", "pubmed:31874640" ; sc: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""" ; sc:featureList edam:operation_3643, edam:operation_3646, edam:operation_3767, edam:operation_3801, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "MS2CNN" ; sc:url "https://github.com/changlabtw/MS2CNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31120050" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'MotifDB' | Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra | Python code for running single file and multi-file LDA | A web application developed in Django+D3 to visualise how topics inferred from Latent Dirichlet Allocation can be used to assist in the unsupervised characterisation of fragmented (LC-MS-MS) metabolomics data | Demo available at www.ms2lda.org (please email us to gain access) | Go to Experiments Quick Decomposition | 25th November 2018: We have introduced many new features to make interpreting Mass2Motifs in MS2LDA.org easier | The last command inserts the gensim lda results into the database" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_2929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MS2LDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ms2lda.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , , , "pmcid:PMC4489309", "pmcid:PMC5994937", "pmcid:PMC6602496", "pubmed:24078703", "pubmed:25990723", "pubmed:31028400" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MS2PIP Server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://iomics.ugent.be/ms2pip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_2885, edam:topic_3305, edam:topic_3489 ; sc:citation , "pmcid:PMC6943038", "pubmed:31599331" ; sc: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.""" ; sc:featureList edam:operation_0237, edam:operation_0337, edam:operation_0543, edam:operation_3840 ; sc:name "MSDB" ; sc:url "http://minisatellites.u-psud.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_2640, edam:topic_3373, edam:topic_3676 ; sc:citation , "pubmed:31802092" ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3439 ; sc:name "MSDRP" ; sc:url "https://github.com/shimingwang1994/MSDRP.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3682 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3591 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3752 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:27542771" ; sc:description "Tool to visualize biological indices from mass spectrometry imaging data." ; sc:featureList edam:operation_0337, edam:operation_3627, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MSIdV" ; sc:operatingSystem "Windows" ; sc:url "https://sourceforge.net/projects/msidv/" ; biotools:primaryContact "Eisuke Hayakawa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3295, edam:topic_3676 ; sc:citation , "pmcid:PMC6277498", "pubmed:30510242" ; sc:description "Python package for tumor microsatellite instability classification from tumor mutation annotation data using a support vector machine." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MSIpred" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/wangc29/MSIpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3077, edam:topic_3520 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3644, edam:operation_3646, edam:operation_3860 ; sc:name "MSMS-Chooser" ; sc:url "https://ccms-ucsd.github.io/GNPSDocumentation/msmschooser/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3673 ; sc:citation ; sc: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." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MTBGT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KamelaNg/MTBGT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC6794379", "pubmed:31649730" ; sc: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""" ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3432, edam:operation_3463 ; sc:license "GPL-3.0" ; sc:name "MTGO-SC" ; sc:url "https://github.com/ne1s0n/MTGOsc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0202, edam:topic_0749, edam:topic_0781, edam:topic_3297 ; sc:citation , "pubmed:31686495" ; sc:description """A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells. Code and sequence files used in MTK manuscript""" ; sc:featureList edam:operation_0308, edam:operation_0310 ; sc:name "MTK" ; sc:url "https://github.com/jpfon/MTK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation , "pubmed:31403410" ; sc: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" ; sc:featureList edam:operation_3659 ; sc:name "MTMR-Net" ; sc:url "https://github.com/CaptainWilliam/MTMR-NET" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_3816 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3814, edam:format_3816 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pmcid:PMC4489289", "pubmed:25855812" ; sc:description "Docking into a user-defined binding site or blind docking using AutoDock 4.2." ; sc:featureList edam:operation_0482 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MTiAutoDock" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDock" ; biotools:primaryContact "Maria A. Miteva" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3814, edam:format_3816 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_3816 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3343 ; sc:citation , , "pmcid:PMC4489289", "pmcid:PMC6769597", "pubmed:25855812", "pubmed:31546814" ; sc:description "Automated virtual screening with AutoDock Vina." ; sc:featureList edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MTiOpenScreen" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiOpenScreen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780 ; sc:citation , "pubmed:31061104" ; sc:description "Multivariate analysis application for streamlined data analysis and curation." ; sc:featureList edam:operation_2939, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MVApp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mvapp.kaust.edu.sa/MVApp/" ; biotools:primaryContact "Magdalena Julkowska" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC6751173", "pubmed:31534156" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3436 ; sc:name "MVIAm" ; sc:url "https://github.com/must-bio-team/MVIAm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0634, edam:topic_3444 ; sc:citation , "pubmed:31407400" ; sc: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" ; sc:featureList edam:operation_3501, edam:operation_3799 ; sc:name "MWI" ; sc:url "https://sourceforge.net/projects/mwi-spinal-cord-atlases/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC10046854", "pubmed:36979426" ; sc:description "A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses" ; sc:featureList edam:operation_3214 ; sc:name "MaCProQC" ; sc:softwareVersion "1" ; sc:url "https://workflowhub.eu/workflows/343?version=1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0769, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC7145696", "pubmed:31665439" ; sc:description """A functional genomics hub for Malvaceae plants. Pipelines of data analysis for MaGenDB""" ; sc:featureList edam:operation_0308, edam:operation_2422, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "MaGenDB" ; sc:url "http://magen.whu.edu.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0166, edam:topic_2275, edam:topic_3172, edam:topic_3474 ; sc:citation , "pubmed:31819266" ; sc: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""" ; sc:featureList edam:operation_2492, edam:operation_2929, edam:operation_3092 ; sc:license "Apache-2.0" ; sc:name "MaSIF" ; sc:url "https://github.com/lpdi-epfl/masif" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0821, edam:topic_3421 ; sc:citation , "pmcid:PMC6853642", "pubmed:31681953" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_0477, edam:operation_0478 ; sc:name "Mabellini" ; sc:url "http://www.mabellinidb.science" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_3382 ; sc:citation , "pmcid:PMC6724615", "pubmed:31555312" ; sc: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" ; sc:featureList edam:operation_0282, edam:operation_3232, edam:operation_3553 ; sc:name "MaizeDIG" ; sc:url "http://www.maizegdb.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "An integrated data warehouse for MaizeGDB" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "MaizeMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.3" ; sc:url "http://maizemine.rnet.missouri.edu:8080/maizemine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3293, edam:topic_3489 ; sc:citation , "pmcid:PMC6861670", "pubmed:31762961" ; sc: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.""" ; sc:featureList edam:operation_0282, edam:operation_2422, edam:operation_3196, edam:operation_3431 ; sc:name "MaizeSNPDB" ; sc:url "https://github.com/venyao/MaizeSNPDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_3047, edam:topic_3292, edam:topic_3306 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0480, edam:operation_2476, edam:operation_3891 ; sc:name "Making Soup" ; sc:url "http://github.com/dspoel/soup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3305, edam:topic_3518 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3211, edam:operation_3629, edam:operation_3891 ; sc:name "MalariaGEN" ; sc:url "http://www.malariagen.net/projects" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3305 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0337 ; sc:name "Malaria Data District" ; sc:url "https://seantomlinson30.shinyapps.io/shiny-map-prize/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3500, edam:topic_3517 ; sc:citation , "pmcid:PMC6882345", "pubmed:31775616" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3661 ; sc:name "Manhattan" ; sc:url "https://genome.sph.umich.edu/wiki/Code_Sample:_Generating_Manhattan_Plots_in_R" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC6330393", "pubmed:30634901" ; sc:description "Tool for automatically detecting and characterizing peaks from GWAS output files (Manhattan Plots)." ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Manhattan Harvester" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.geenivaramu.ee/en/tools/manhattan-harvester" ; biotools:primaryContact "T. Haller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3168 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0452, edam:operation_3198, edam:operation_3227 ; sc:license "MIT" ; sc:name "MapCaller" ; sc:url "https://github.com/hsinnan75/MapCaller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3382 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MapOptics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FadyMohareb/mapoptics" ; biotools:primaryContact "Fady Mohareb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3263, edam:topic_3489 ; sc:citation ; sc:description "The opendata geoportal of the Lamma Consortium." ; sc:featureList edam:operation_3454, edam:operation_3695 ; sc:license "CC-BY-4.0" ; sc:name "MapStore" ; sc:url "http://geoportale.lamma.rete.toscana.it/MapStore/public/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3067, edam:topic_3304 ; sc:citation , "pmcid:PMC6663211", "pubmed:31410377" ; sc: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" ; sc:featureList edam:operation_3463, edam:operation_3562, edam:operation_3766 ; sc:name "Mapper" ; sc:url "https://github.com/alpatania/AHBA_microarray_Mapper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179, edam:topic_3295, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0440, edam:operation_0441, edam:operation_2575 ; sc:license "MIT" ; sc:name "MariaOsmala" ; sc:url "https://github.com/MariaOsmala/preprint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC7243925", "pubmed:31725857" ; sc: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""" ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3280 ; sc:name "MarkerHub" ; sc:url "http://markerhub.iis.sinica.edu.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "Mascot Daemon is a Microsoft Windows client application that automates the submission of data files to Mascot server." ; sc:featureList edam:operation_3762, edam:operation_3763 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "Mascot Daemon" ; sc:operatingSystem "Windows" ; sc:url "http://www.matrixscience.com/daemon.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330, edam:format_3244, edam:format_3654, edam:format_3710, edam:format_3712, edam:format_3858 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331, edam:format_2332 ; sc:name "Protein report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3651, edam:format_3652, edam:format_3834 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc: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. 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This is a joint project between CRG bioinformatics core and Epitranscriptomics and RNA Dynamics research group.""" ; sc:featureList edam:operation_0428, edam:operation_3185, edam:operation_3218 ; sc:license "MIT" ; sc:name "MasterOfPores" ; sc:url "https://github.com/biocorecrg/master_of_pores" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3324, edam:topic_3400 ; sc:citation , "pmcid:PMC8215913", "pubmed:31609421" ; sc: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).""" ; sc:featureList edam:operation_0491, edam:operation_0496, edam:operation_2421 ; sc:license "MIT" ; sc:name "Mat_Peptide" ; sc:url "https://github.com/VirusBRC/vipr_mat_peptide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3474 ; sc:citation , "pubmed:31621830" ; sc: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. 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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. 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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." ; sc:featureList edam:operation_0234, edam:operation_0238, edam:operation_0239, edam:operation_0364, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MatrixMotif" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "https://peterslab.org/downloads.php" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0749, edam:topic_3168, edam:topic_3577 ; sc:citation , "pmcid:PMC6827219", "pubmed:31679514" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3227, edam:operation_3431 ; sc:license "CC-BY-4.0" ; sc:name "MaveDB" ; sc:url "https://www.mavedb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3489 ; sc:citation , "pubmed:31504189" ; sc:description "An integrated resource for metalloenzyme-ligand associations | The Metalloenzyme-Ligand Association Database (MeLAD)" ; sc:featureList edam:operation_0482, edam:operation_3501, edam:operation_3898 ; sc:name "MeLAD" ; sc:url "https://melad.ddtmlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3233, edam:operation_3435 ; sc:license "MIT" ; sc:name "Mecan4CNA" ; sc:url "https://pypi.org/project/mecan4cna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2840, edam:topic_3292, edam:topic_3378 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3501, edam:operation_3642 ; sc:license "MIT" ; sc:name "MechSpy" ; sc:url "https://github.com/ignaciot/MechSpy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "MedicMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.3.0" ; sc:url "http://medicmine.jcvi.org/medicmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3295 ; sc:citation "pmcid:PMC6247925", "pubmed:29931280" ; sc:description """algorithms for analyzing DNA methylation data generated using Infinium HumanMethylation450 or MethylationEPIC BeadChips Epigenome-Wide Association Studies (EWAS)""" ; sc:featureList edam:operation_1812, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "Meffil" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/perishky/meffil" ; biotools:primaryContact "Matthew Suderman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3293, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6843070", "pubmed:31749830" ; sc: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.""" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3731 ; sc:name "MegaGTA" ; sc:url "https://github.com/HKU-BAL/megagta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3175, edam:topic_3673 ; sc:citation , "pmcid:PMC8215921", "pubmed:31584621" ; sc: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""" ; sc:featureList edam:operation_3216, edam:operation_3227, edam:operation_3233, edam:operation_3478 ; sc:license "MIT" ; sc:name "Meltos" ; sc:url "https://github.com/ih-lab/Meltos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0820, edam:topic_3306 ; sc:citation , "pubmed:31564100" ; sc: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" ; sc:license "GPL-3.0" ; sc:name "MemSurfer" ; sc:url "https://bbs.llnl.gov/MemSurfer-data.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1915 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_1317 ; sc:author ; sc:citation , , , , "pubmed:22038510", "pubmed:25261217", "pubmed:27428000", "pubmed:30382245" ; sc:description "Analysis tool for protein-protein cross-linking using MS-cleavable cross-lining reagents such as DSBU, DSSO, CDI or PIR linker" ; sc:featureList edam:operation_0004 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MeroX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0 (2.0.0.7)" ; sc:url "https://www.stavrox.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation , "pmcid:PMC4939962", "pubmed:27400279" ; sc: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.""" ; sc:name "MetAML" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://segatalab.cibio.unitn.it/tools/metaml/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31429549" ; sc: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" ; sc:featureList edam:operation_3431, edam:operation_3501, edam:operation_3629 ; sc:name "MetGem" ; sc:url "https://github.com/metgem/metgem/releases" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3056 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "MetHis" ; sc:url "https://github.com/romain-laurent/MetHis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3360 ; sc:citation , "pmcid:PMC6572057", "pubmed:31130635" ; sc:description "Metabolite Pipeline Consisting of Metabolite Identification and Biomarker Discovery Under the Control of Two-Dimensional FDR." ; sc:featureList edam:operation_3659, edam:operation_3803, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MetPC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jjs3098/CNU-Bioinformatics-Lab" ; biotools:primaryContact "Jaesik Jeong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3343 ; sc:citation , "pubmed:31369240" ; sc: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" ; sc:featureList edam:operation_3627, edam:operation_3629, edam:operation_3803 ; sc:name "MetWork" ; sc:url "https://metwork.pharmacie.parisdescartes.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC6540332", "pubmed:31146255" ; sc:description "Sequence-Based Meta-Predictor for Accurate DNA 4mC Site Prediction Using Effective Feature Representation." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Meta-4mCpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://thegleelab.org/Meta-4mCpred" ; biotools:primaryContact "Balachandran Manavalan", "Gwang Lee", "Leyi Wei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3373, edam:topic_3379, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6888698", "pubmed:31731751" ; sc: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""" ; sc:featureList edam:operation_0252, edam:operation_3436, edam:operation_3631 ; sc:name "Meta-iAVP" ; sc:url "http://codes.bio/meta-iavp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation , , "pmcid:PMC4556158", "pmcid:PMC6662567", "pubmed:26336640", "pubmed:31388474" ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3798 ; sc:name "MetaBAT 2" ; sc:url "https://bitbucket.org/berkeleylab/metabat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC5592083", "pubmed:28894651" ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "MetaCRAST" ; sc:url "https://github.com/molleraj/MetaCRAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6710874", "pubmed:31451112" ; sc: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" ; sc:featureList edam:operation_0524, edam:operation_2495, edam:operation_3216 ; sc:license "MIT" ; sc:name "MetaCarvel" ; sc:url "https://github.com/marbl/MetaCarvel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6790056", "pubmed:31604482" ; sc: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.""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3799 ; sc:name "MetaCell" ; sc:url "https://tanaylab.github.io/metacell/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6807170", "pubmed:31737256" ; sc: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""" ; sc:featureList edam:operation_0232, edam:operation_3219, edam:operation_3435 ; sc:name "MetaDEGalaxy" ; sc:url "http://203.101.224.202/galaxy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0736 ; sc:citation , "pmcid:PMC6772141", "pubmed:31116477" ; sc:description "Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains." ; sc:featureList edam:operation_0303, edam:operation_3197, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MetaDome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://stuart.radboudumc.nl/metadome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0160, edam:topic_0602, edam:topic_3174 ; sc:citation , "pmcid:PMC6803454", "pubmed:31681429" ; sc: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)""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3083, edam:operation_3439, edam:operation_3460 ; sc:name "MetaErg" ; sc:url "https://github.com/xiaoli-dong/metaerg" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3174 ; sc:citation , , "pmcid:PMC7126354", "pubmed:32245390" ; sc:description "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics" ; sc:featureList edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaEuk" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1-ea903e5", "2-ddf2742" ; sc:url "https://metaeuk.soedinglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2640 ; sc:author "Benjamin Haibe-Kains", "Deena M.A. Gen-doo" ; sc:description "A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium." ; sc:featureList edam:operation_0441, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "MetaGxBreast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/release/data/experiment/html/MetaGxBreast.html" ; biotools:primaryContact "Benjamin Haibe-Kains", "Michael Zon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3295, edam:topic_3308, edam:topic_3390, edam:topic_3407 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2495 ; sc:name "MetaMEx" ; sc:url "http://www.metamex.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3303, edam:topic_3697 ; sc:citation , "pmcid:PMC6787565", "pubmed:31594829" ; sc: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""" ; sc:featureList edam:operation_3432, edam:operation_3660, edam:operation_3803 ; sc:name "MetaMed" ; sc:url "http://metamed.rwebox.com/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_3174, edam:topic_3520, edam:topic_3697 ; sc:citation , "pmcid:PMC6952069", "pubmed:31629686" ; sc: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.""" ; sc:featureList edam:operation_3755, edam:operation_3803 ; sc:name "MetaMiner" ; sc:url "https://github.com/mohimanilab/MetaMiner" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929, edam:format_3770 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3651, edam:format_3712 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247, edam:format_3475 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520, edam:topic_3922 ; sc:citation , , "pmcid:PMC6733628", "pmcid:PMC8377504", "pubmed:31378069", "pubmed:33683901" ; sc: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" ; sc:featureList edam:operation_2421, edam:operation_3215, edam:operation_3629, edam:operation_3631, edam:operation_3649, edam:operation_3755, edam:operation_3767 ; sc:license "MIT" ; sc:name "MetaMorpheus" ; sc:url "https://github.com/smith-chem-wisc/MetaMorpheus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3308 ; sc:citation , "pmcid:PMC6499246", "pubmed:30304367" ; sc:description "Analysis pipeline and browser-based software suite for transcriptomic meta-analysis." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MetaOmics" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/metaOmics/metaOmics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308, edam:topic_3697 ; sc:citation , "pmcid:PMC6821265", "pubmed:31116375" ; sc:description "Integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MetaQUBIC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/OSU-BMBL/metaqubic" ; biotools:primaryContact "Qin Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3170, edam:topic_3372, edam:topic_3676 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0555, edam:operation_2422, edam:operation_2495 ; sc:name "MetaR" ; sc:url "http://metaR.campagnelab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0769, edam:topic_3382, edam:topic_3697 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0362, edam:operation_2422, edam:operation_2489 ; sc:license "GPL-3.0" ; sc:name "MetaSanity" ; sc:url "https://github.com/cjneely10/MetaSanity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:28065898" ; sc:description "Spark-based distributed processing tool to recruit metagenomic reads to reference genomes." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MetaSpark:" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/zhouweiyg/metaspark" ; biotools:primaryContact "Beifang Niu", "Jing Luo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6710406", "pubmed:31481973" ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "MetaTOR" ; sc:url "https://github.com/koszullab/metaTOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC6780920", "pubmed:31533242" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3803 ; sc:license "GPL-2.0" ; sc:name "MetaboList" ; sc:url "https://CRAN.R-project.org/package=MetaboList" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:description "Graphical visualization tool for metabolomics and genomic data within metabolic pathways" ; sc:featureList edam:operation_3660 ; sc:name "MetaboPath View" ; sc:url "https://prf.jcu.cz/mpv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0769, edam:topic_3047, edam:topic_3407 ; sc:citation , "pmcid:PMC6929434", "pubmed:31870296" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_0533, edam:operation_3439 ; sc:license "MIT" ; sc:name "Metabolic Disassembler" ; sc:url "https://github.com/the-metabolic-disassembler/metadisassembler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219 ; sc:description "FAIR metadata editor for guiding the user through the creation of FAIR Data Point metadata." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Metadata Editor" ; sc:url "https://editor.fair-dtls.surf-hosted.nl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3174, edam:topic_3407 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "Metage2Metabo" ; sc:softwareHelp ; sc:url "https://github.com/AuReMe/metage2metabo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc: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" ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Metagenomic read binning using sparse coding" ; sc:operatingSystem "Linux" ; sc:url "https://gitlab.com/kyrgyzov/lsa_slurm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC6814207", "pubmed:31623721" ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3803 ; sc:name "Metandem" ; sc:url "http://metandem.com/web/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3056 ; sc:citation , "pmcid:PMC6469578", "pubmed:30362291" ; sc:description "Individual-based model for simulating the evolution of tree populations in spatially and temporally heterogeneous landscapes." ; sc:featureList edam:operation_0282, edam:operation_2426, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Metapop" ; sc:softwareHelp ; sc:url "https://quercusportal.pierroton.inra.fr/index.php?p=METAPOP" ; biotools:primaryContact "Antoine Kremer", "Armel Thöni", "Jean-Paul Soularue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3172 ; sc:citation , "pmcid:PMC6447622", "pubmed:30944313" ; sc:description "Portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Metascape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:url "http://metascape.org/gp/index.html#/main/step1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3295 ; sc:citation , "pmcid:PMC3855694", "pubmed:24324667" ; sc:description "A reference methylome database for different organisms that is created from public BS-seq datasets." ; sc:featureList edam:operation_0564, edam:operation_3204 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MethBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://smithlabresearch.org/software/methbase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6698668", "pubmed:31049595" ; sc: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)" ; sc:featureList edam:operation_0417, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MethylCal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lb664/MethylCal" ; biotools:primaryContact "Leonardo Bottolo", "Verena Zuber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC7846147", "pubmed:31107532" ; sc:description "Framework for Methyl-Seq genome-wide power calculation and study design issues." ; sc:featureList edam:operation_0417, edam:operation_3186, edam:operation_3206 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MethylSeqDesign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/liupeng2117/MethylSeqDesign" ; biotools:primaryContact "George Tseng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC6923858", "pubmed:31861999" ; sc: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:""" ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3186, edam:operation_3196, edam:operation_3661 ; sc:name "MethylToSNP" ; sc:url "https://github.com/elnitskilab/MethylToSNP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31596440" ; sc: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""" ; sc:featureList edam:operation_3627, edam:operation_3767, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "MetumpX" ; sc:url "https://github.com/hasaniqbal777/MetumpX-bin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382, edam:topic_3518 ; sc:citation , "pubmed:31785415" ; sc: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.""" ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3501, edam:operation_3659 ; sc:name "MiCA" ; sc:url "http://irzamsarfraz.com/mica/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3301 ; sc:citation , "pmcid:PMC6784143", "pubmed:31480341" ; sc: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" ; sc:featureList edam:operation_3192, edam:operation_3196 ; sc:name "MiDRMpol" ; sc:url "https://github.com/neogilab/MiDRMPol" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2182 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2830 ; sc:description "Mapper for full-length T- and B-cell repertoire sequencing." ; sc:featureList edam:operation_2403, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MiGMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mikessh/migmap" ; biotools:primaryContact "Mikhail Shugay" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3306, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6842143", "pubmed:31703551" ; sc: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""" ; sc:featureList edam:operation_0436, edam:operation_3659, edam:operation_3792 ; sc:name "MiPepid" ; sc:url "https://github.com/MindAI/MiPepid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3400, edam:topic_3524 ; sc:citation , "pmcid:PMC6498635", "pubmed:31046789" ; sc:description "Agent-based simulation tool to study the self-nonself discrimination of the adaptive immune response." ; sc:featureList edam:operation_0478, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MiStImm" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kerepesi/mistimm" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2182 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2830 ; sc:citation ; sc:description "Software for extraction of T- and B-cell receptor repertoires from any type of sequencing data." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MiXCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://milaboratory.com/software/mixcr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3301 ; sc:citation , "pubmed:30368088" ; sc:description "Software tool for predictive microbiology and microbial risk assessment in foods." ; sc:featureList edam:operation_2426, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MicroHibro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.microhibro.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6683435", "pubmed:31387630" ; sc: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:" ; sc:featureList edam:operation_0362, edam:operation_2495, edam:operation_3730 ; sc:license "GPL-3.0" ; sc:name "MicroPro" ; sc:url "https://github.com/zifanzhu/MicroPro" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1098 ; sc:name "RefSeq accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1098 ; sc:name "RefSeq accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2166 ; sc:name "Sequence composition plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1936 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1936 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_1929, edam:format_1936 ; sc:name "Sequence report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1936 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0219, edam:topic_0621, edam:topic_0797, edam:topic_2259, edam:topic_3301 ; sc:author "LABGeM - CEA/Genosocope - UMR8030" ; sc:citation , , , , , , "pubmed:28968784", "pubmed:31647104" ; sc: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." ; sc:featureList edam:operation_0258, edam:operation_0291, edam:operation_0292, edam:operation_0305, edam:operation_0337, edam:operation_0346, edam:operation_0349, edam:operation_0362, edam:operation_2421, edam:operation_2422, edam:operation_2454, edam:operation_2495, edam:operation_2945, edam:operation_3197, edam:operation_3208, edam:operation_3209, edam:operation_3223, edam:operation_3227, edam:operation_3431, edam:operation_3660, edam:operation_3672, edam:operation_3680, edam:operation_3925, edam:operation_3926, edam:operation_3928, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:name "MicroScope platform" ; sc:provider "LABGeM - CEA/Genosocope - UMR8030" ; sc:softwareHelp , , ; sc:url "https://mage.genoscope.cns.fr/microscope/" ; biotools:primaryContact "LABGeM - CEA/Genosocope - UMR8030" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc: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:" ; sc:featureList edam:operation_0362, edam:operation_2939, edam:operation_3891 ; sc:license "MIT" ; sc:name "MicroWineBar" ; sc:url "https://github.com/klincke/MicroWineBar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0780, edam:topic_3324, edam:topic_3697 ; sc:citation ; sc: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!.""" ; sc:featureList edam:operation_2422, edam:operation_3200 ; sc:name "Microbe Directory" ; sc:url "https://microbe.directory" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0610, edam:topic_3063, edam:topic_3810 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2492, edam:operation_3439, edam:operation_3461 ; sc:name "MicrobioLink" ; sc:url "https://github.com/korcsmarosgroup/HMIpipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697 ; sc:author ; sc:citation ; sc: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." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MicrobiomeR" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6.1" ; sc:url "https://microbiomer.vallenderlab.science/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3063, edam:topic_3473 ; sc:citation , "pubmed:31531513" ; sc: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" ; sc:featureList edam:operation_3644 ; sc:license "GPL-3.0" ; sc:name "Microdatasus" ; sc:url "http://datasus.saude.gov.br/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3955 ; sc:citation , , "pmcid:PMC5291980", "pubmed:28158972", "pubmed:31893378" ; sc: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." ; sc:featureList edam:operation_3860 ; sc:license "Freeware" ; sc:name "Midcor" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.0.1.0" ; sc:url "https://github.com/seliv55/ramidcor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3293, edam:topic_3301, edam:topic_3305, edam:topic_3673 ; sc:citation , "pmcid:PMC6841976", "pubmed:31704961" ; sc: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:.""" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3644 ; sc:name "MinION" ; sc:url "https://github.com/jvolkening/minion_bacterial" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6314158", "pubmed:30523036" ; sc:description "Alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics." ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Minerva" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dcdanko/minerva_barcode_deconvolution" ; biotools:primaryContact "David C. Danko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC6833143", "pubmed:31694525" ; sc: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""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3185, edam:operation_3219, edam:operation_3644 ; sc:name "MiniScrub" ; sc:url "https://bitbucket.org/berkeleylab/jgi-miniscrub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172 ; sc:citation , "pubmed:30726876" ; sc:description "R Package for Multiple Isotope Labeling Assisted Metabolomics Data Analysis." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Miso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.1" ; sc:url "https://cran.r-project.org/package=Miso" ; biotools:primaryContact "Yonghui Dong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC6732850", "pubmed:31523131" ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3557 ; sc:license "MIT" ; sc:name "MitoIMP" ; sc:url "https://github.com/omics-tools/mitoimp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3384, edam:topic_3518 ; sc:citation ; sc:description "Snakemake pipeline for imputation of mitochondrial genetic variants using Impute2 Chromosome X protocol." ; sc:featureList edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MitoImpute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sjfandrews/MitoImpute" ; biotools:primaryContact "Shea J. Andrews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3697, edam:topic_3855 ; sc:citation , "pmcid:PMC6612855", "pubmed:31510709" ; sc: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\":" ; sc:featureList edam:operation_2937, edam:operation_3192 ; sc:name "MixMPLN" ; sc:url "https://github.com/sahatava/MixMPLN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:30730249" ; sc:description "Image-processing software developed for counting cells in photographs of blood smears." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Mizutama" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://datadryad.org/resource/doi:10.5061/dryad.bk2690n?show=full" ; biotools:primaryContact "Gregorio Moreno-Rueda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3297 ; sc:citation ; sc: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)""" ; sc:featureList edam:operation_3196, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "MoBPS" ; sc:url "https://github.com/tpook92/MoBPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0654, edam:topic_3399, edam:topic_3518 ; sc:citation "pmcid:PMC6846495" ; sc: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).""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3454 ; sc:name "MoChA" ; sc:url "https://github.com/freeseek/mocha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3175, edam:topic_3512 ; sc:citation , "pmcid:PMC6833150", "pubmed:31690272" ; sc: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:""" ; sc:featureList edam:operation_3182, edam:operation_3198, edam:operation_3208, edam:operation_3227 ; sc:license "MIT" ; sc:name "MoMI-G" ; sc:url "https://github.com/MoMI-G/MoMI-G" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3474, edam:topic_3538 ; sc:citation , "pubmed:31504193" ; sc: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" ; sc:featureList edam:operation_0253, edam:operation_0303, edam:operation_3904 ; sc:name "MoRF" ; sc:url "https://gsponerlab.msl.ubc.ca/software/morf_chibi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0749, edam:topic_2269 ; sc:citation , "pmcid:PMC6819637", "pubmed:31660849" ; sc: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.""" ; sc:featureList edam:operation_0250, edam:operation_0303, edam:operation_3904 ; sc:name "MoRFMPM" ; sc:url "https://github.com/HHJHgithub/MoRFs_MPM/tree/master/github_code_MPM_MoRFs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3520 ; sc:citation , "pubmed:30649115" ; sc:description "Programfor calculation of ion or molecule collision cross sections on parallelized computing architectures." ; sc:featureList edam:operation_0386 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MobCal-MPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://uwaterloo.ca/hopkins-lab/mobcal-mpi" ; biotools:primaryContact "C. Ieritano", "W. S. Hopkins" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3407 ; sc:citation , "pubmed:30201314" ; sc:description "Strain design framework for modular cell engineering." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ModCell2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://modcell2.readthedocs.io/en/latest/" ; biotools:primaryContact "TrinhLab - University of Tennessee Knoxville" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0218, edam:topic_0602, edam:topic_2640, edam:topic_3169 ; sc:citation , "pubmed:31857203" ; sc: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""" ; sc:featureList edam:operation_0306, edam:operation_1781, edam:operation_3439 ; sc:license "MIT" ; sc:name "ModEx" ; sc:url "https://github.com/samanfrm/modex" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "A data warehouse for the modENCODE project" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "ModMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "33 28JUL2014" ; sc:url "http://intermine.modencode.org/release-33" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3407 ; sc:citation , "pmcid:PMC6348647", "pubmed:30691403" ; sc:description "Software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ModelExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "https://almaaslab.nt.ntnu.no/index.php/resources/metabolic-modeling/" ; biotools:primaryContact "Eivind Almaas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3293, edam:topic_3316 ; sc:citation , "pmcid:PMC6984357", "pubmed:31432070" ; sc: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" ; sc:featureList edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "ModelTest-NG" ; sc:url "https://github.com/ddarriba/modeltest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0659, edam:topic_2275, edam:topic_3512 ; sc:citation , "pmcid:PMC6900601", "pubmed:31732673" ; sc: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.""" ; sc:featureList edam:operation_3216, edam:operation_3899, edam:operation_3900, edam:operation_3901, edam:operation_3902 ; sc:name "ModelX" ; sc:url "http://modelx.crg.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0601 ; sc:citation , "pmcid:PMC6247942", "pubmed:29931246" ; sc:description "MolArt (MOLeculAR structure annoTator) - molecular structure annotation and visualization tool." ; sc:featureList edam:operation_0564, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MolArt" ; sc:softwareHelp ; sc:url "https://cusbg.github.io/MolArt/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0990 ; sc:encodingFormat edam:format_1964 ; sc:name "Compound name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3068, edam:topic_3292, edam:topic_3332 ; sc:author , "Jakub Juračka" ; sc:citation ; sc:contributor , , "Michaela Melíková" ; sc:description "MolMeDB is an open chemistry database about interactions of molecules with membranes." ; sc:featureList edam:operation_2422, edam:operation_3431 ; sc:funder "Czech Grant Agency" ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MolMeDB" ; sc:softwareHelp , ; sc:url "http://molmedb.upol.cz" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2814 ; sc:citation , "pubmed:31111152" ; sc:description "Computation of clock violations." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Molecular clock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ugobas/Molecular_clock" ; biotools:primaryContact "Ugo Bastolla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_0634, edam:topic_3390 ; sc:citation , "pmcid:PMC7056945", "pubmed:31701156" ; sc: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.""" ; sc:featureList edam:operation_0306, edam:operation_3196, edam:operation_3226, edam:operation_3778 ; sc:name "Monarch Initiative" ; sc:url "https://monarchinitiative.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3300 ; sc:citation , "pmcid:PMC6743332", "pubmed:31071345" ; sc:description "Software tool for behavioral control and data acquisition." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MonkeyLogic" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://monkeylogic.nimh.nih.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC6394031", "pubmed:30819107" ; sc:description "Monoallelic Gene Inference from Chromatin (MaGIC) - tool to classify genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data." ; sc:featureList edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MaGIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/gimelbrantlab/magic" ; biotools:primaryContact "Alexander Gimelbrant", "Henry Ward", "Sachit Saksena", "Svetlana Vinogradova", "Sébastien Vigneau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC6394031", "pubmed:30819107" ; sc: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." ; sc:featureList edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Monoallelic gene inference from chromatin (MaGIC)" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/gimelbrantlab/magic" ; biotools:primaryContact "Alexander Gimelbrant", "Henry Ward", "Sachit Saksena", "Svetlana Vinogradova", "Sébastien Vigneau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623 ; sc: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." ; sc:name "MoonDB" ; sc:url "http://moondb.hb.univ-amu.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_3168 ; sc:citation , "pmcid:PMC6487805", "pubmed:31086739" ; sc:description "Multiple-alignment based web tool for target selection and designing taxon-specific primers in the loop-mediated isothermal amplification method." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MorphoCatcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://morphocatcher.ru" ; biotools:primaryContact "Fedor V. Shirshikov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_0160, edam:topic_0736 ; sc:citation , "pmcid:PMC6863708", "pubmed:31599029" ; sc: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""" ; sc:featureList edam:operation_0239, edam:operation_0303, edam:operation_2492 ; sc:name "MotifAnalyzer-PDZ" ; sc:url "http://motifAnalyzerPDZ.cs.wwu.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_3304, edam:topic_3489 ; sc:citation , "pmcid:PMC6934379", "pubmed:31825307" ; sc: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\"""" ; sc:featureList edam:operation_0335, edam:operation_3196, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "MouseBytes" ; sc:url "http://mousebytes.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0654, edam:topic_3298, edam:topic_3300, edam:topic_3500 ; sc:citation , "pmcid:PMC7145612", "pubmed:31696236" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3196, edam:operation_3557 ; sc:name "Mouse Phenome Database" ; sc:softwareHelp ; sc:url "https://phenome.jax.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6805343", "pubmed:31640560" ; sc: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""" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3258, edam:operation_3800 ; sc:name "MrNV" ; sc:url "https://github.com/prawnseq/Mrosenbergii_MrNV_RNAseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC7523683", "pubmed:31397844" ; sc:description "Tool for haplotype-phased structural variant detection." ; sc:featureList edam:operation_0525, edam:operation_3227, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MsPAC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/oscarlr/MsPAC" ; biotools:primaryContact "Oscar L. Rodriguez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3168, edam:topic_3474, edam:topic_3517 ; sc:citation , "pubmed:31693090" ; sc: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""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3226 ; sc:license "MIT" ; sc:name "MtBNN" ; sc:url "https://github.com/Zoesgithub/MtBNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Multiple transformer-based language models for accurate DNA methylation prediction" ; sc:name "MuLan-Methyl" ; sc:softwareVersion "1.02" ; sc:url "http://ab.cs.uni-tuebingen.de/software/mulan-methyl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_3314 ; sc:citation , "pubmed:31663741" ; sc: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""" ; sc:featureList edam:operation_0303, edam:operation_3436, edam:operation_3891 ; sc:name "MuLiMs-MCoMPAs" ; sc:url "http://tomocomd.com/mulims-mcompas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_3474 ; sc:citation ; sc: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)""" ; sc:featureList edam:operation_0272, edam:operation_0331, edam:operation_2492 ; sc:name "MuPIPR" ; sc:url "https://github.com/guangyu-zhou/MuPIPR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2269, edam:topic_2640 ; sc:citation , "pmcid:PMC3409272", "pubmed:22759861" ; sc: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." ; sc:featureList edam:operation_0362, edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MuSiC2" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "0.2" ; sc:url "http://gmt.genome.wustl.edu/packages/genome-music/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC4576697", "pubmed:26330601" ; sc:description "Tool for finding connected clusters in multi-parametric networks." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Multi-netclust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bioinformatics.nl/netclust/" ; biotools:primaryContact "Jack A.M. Leunissen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0988 ; sc:encodingFormat edam:format_3681 ; sc:name "Peptide identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3922 ; sc: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." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Multi-omics Visualization Platform" ; sc:softwareHelp ; sc:url "https://github.com/galaxyproteomics/mvpapplication-git.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "Multi-processing tool for designing CRISPR guide RNA libraries." ; sc:featureList edam:operation_3096, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MultiGuideScan" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/bioinfomaticsCSU/MultiGuideScan" ; biotools:primaryContact "Jianxin Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3056, edam:topic_3299 ; sc:citation , "pmcid:PMC6303267", "pubmed:30206356" ; sc:description "Models discrete and continuous gene flow to reconstruct complex population admixtures." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:name "MultiWaver" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "2.0" ; sc:url "http://www.picb.ac.cn/PGG/resource.php" ; biotools:primaryContact "Shuhua Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC6358100", "pubmed:30668570" ; sc:description "Set of tools to perform integrative gene mapping studies." ; sc:featureList edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MultiXcan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hakyimlab/MetaXcan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation "pmcid:PMC6927681", "pubmed:31871433" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:name "Multilayer Extraction" ; sc:url "https://github.com/jdwilson4/MultilayerExtraction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6612862", "pubmed:31510656" ; sc: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" ; sc:featureList edam:operation_3891 ; sc:name "MultimodalPrognosis" ; sc:url "https://github.com/gevaertlab/MultimodalPrognosis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "This is the dockerized environment for the winning algorithm in the 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3." ; sc:license "GPL-3.0" ; sc:name "Multiple Myeloma survival prediction" ; sc:operatingSystem "Linux" ; sc:url "https://www.synapse.org/#!Synapse:syn11459638" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382 ; sc:citation , "pubmed:31697593" ; sc: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.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "Muscle2View" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31697593" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3308, edam:topic_3517 ; sc:citation , "pmcid:PMC6498474", "pubmed:31053169" ; sc:description "Versatile methodological aid to functional genomics in the neuromuscular field." ; sc:featureList edam:operation_0571, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Muscle Gene Sets" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.sys-myo.com/muscle_gene_sets" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC7373173", "pubmed:31588509" ; sc: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.""" ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_3223 ; sc:name "MutEx" ; sc:url "http://www.innovebioinfo.com/Databases/Mutationdb_About.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2269, edam:topic_2640 ; sc:citation , , "pmcid:PMC3919509", "pmcid:PMC4048962", "pubmed:23770567", "pubmed:24390350" ; sc: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." ; sc:featureList edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:name "MutSig2CV" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://software.broadinstitute.org/cancer/cga/mutsig" ; biotools:primaryContact "Michael S. Lawrence" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3173 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3202, edam:operation_3798 ; sc:name "MutSpot" ; sc:url "https://github.com/skandlab/MutSpot/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation , "pmcid:PMC5570203", "pubmed:28498993" ; sc:description "Variant effect prediction with interpretation at the protein structure level" ; sc:featureList edam:operation_0331, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:name "MutaFrame" ; sc:url "https://mutaframe.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0749 ; sc:citation , "pmcid:PMC6192214", "pubmed:29087464" ; sc:description "Tool for automated analysis of genomic mutations in gene regulatory networks." ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MutaNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://service.bioinformatik.uni-saarland.de/mutanet/" ; biotools:primaryContact "Volkhard Helms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0601, edam:topic_0821, edam:topic_3297 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0307, edam:operation_0331, edam:operation_0417 ; sc:license "GPL-3.0" ; sc:name "MutateX" ; sc:url "https://github.com/ELELAB/mutatex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0736, edam:topic_3068 ; sc:citation , "pmcid:PMC6519802", "pubmed:31091262" ; sc:description "Tool for plotting complex mutation data with flexibility." ; sc:featureList edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Mutplot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinformaticstools.shinyapps.io/lollipop/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0605, edam:topic_0625, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6882182", "pubmed:31775760" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_3196, edam:operation_3227, edam:operation_3283 ; sc:name "MySeq" ; sc:url "https://go.middlebury.edu/myseq-demo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC6821319", "pubmed:31095292" ; sc:description "ImageJ macro for high throughput analysis of myelinating cultures." ; sc:featureList edam:operation_3435, edam:operation_3450 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MyelinJ" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/BarnettLab/MyelinJ" ; biotools:primaryContact "Susan Barnett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0632, edam:topic_3174, edam:topic_3673 ; sc:citation , "pmcid:PMC7004237", "pubmed:32055708" ; sc: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""" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3227, edam:operation_3482 ; sc:license "MIT" ; sc:name "Mykrobe" ; sc:url "https://github.com/mykrobe-tools/mykrobe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2229, edam:topic_3375, edam:topic_3489 ; sc:citation , "pmcid:PMC6776608", "pubmed:31611808" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_3096, edam:operation_3562 ; sc:name "Myo-REG" ; sc:url "https://myoreg.uniroma2.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3510 ; sc:citation , "pmcid:PMC6731604", "pubmed:31516400" ; sc: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" ; sc:featureList edam:operation_0417, edam:operation_2929, edam:operation_3646 ; sc:name "N-GlycositeAtlas" ; sc:url "http://nglycositeatlas.biomarkercenter.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3320 ; sc:citation , "pmcid:PMC6521780", "pubmed:31143202" ; sc:description "Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes." ; sc:featureList edam:operation_0533, edam:operation_3501, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "N1PAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/grizant/n1pas/tree/master" ; biotools:primaryContact "Alfred Grant Schissler", "Yves A. Lussier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0632, edam:topic_0659 ; sc:citation , "pmcid:PMC9883715", "pubmed:31504159" ; sc: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" ; sc:featureList edam:operation_0571, edam:operation_2939, edam:operation_3218 ; sc:license "LGPL-3.0" ; sc:name "NACHO" ; sc:url "https://github.com/mcanouil/NACHO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_3474, edam:topic_3534 ; sc:citation , "pmcid:PMC6933864", "pubmed:31654438" ; sc: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""" ; sc:featureList edam:operation_0272, edam:operation_0321, edam:operation_2575 ; sc:name "NAGbinder" ; sc:url "https://webs.iiitd.edu.in/raghava/nagbinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780 ; sc:citation , "pubmed:30945190" ; sc:description "Noncoding Assessment of long RNAs in Magnoliophyta Species." ; sc:featureList edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "NAMS" ; sc:operatingSystem "Linux" ; sc:url "http://sunlab.cpy.cuhk.edu.hk/NAMS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3068, edam:topic_3071 ; sc:citation , "pmcid:PMC6301334", "pubmed:30576482" ; sc:description "Comprehensive repository for semantic data in life sciences." ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NBDC RDF Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://integbio.jp/rdf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6693229", "pubmed:31409293" ; sc: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 |" ; sc:featureList edam:operation_3200, edam:operation_3258, edam:operation_3766 ; sc:name "NBGLM-LBC" ; sc:url "https://shka.github.io/NBGLM-LBC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3369 ; sc:citation , "pmcid:PMC6524730", "pubmed:31133849" ; sc:description "Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics." ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NCATS BioPlanet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tripod.nih.gov/bioplanet/" ; biotools:primaryContact "Ruili Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "domain sequence-NES site" ; sc:name "NCBI-protein" ; sc:url "https://www.ncbi.nlm.nih.gov/protein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3335 ; sc:citation , "pubmed:31686064" ; sc: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:""" ; sc:featureList edam:operation_3435, edam:operation_3439 ; sc:license "GPL-2.0" ; sc:name "NCPHLDA" ; sc:url "https://github.com/bryanze/NCPHLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0634 ; sc:citation , "pmcid:PMC8597621", "pubmed:31730176" ; sc: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), )""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "NCutYX" ; sc:url "https://cran.r-project.org/web/packages/NCutYX/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6754439", "pubmed:31541145" ; sc: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" ; sc:featureList edam:operation_3439, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "NDD" ; sc:url "https://github.com/nrohani/NDD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0196, edam:topic_0602, edam:topic_0821, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_2476, edam:operation_3893 ; sc:license "GPL-3.0" ; sc:name "NERDSS" ; sc:url "https://github.com/mjohn218/NERDSS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3305, edam:topic_3315 ; sc:citation , "pmcid:PMC6738962", "pubmed:31511852" ; sc: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" ; sc:featureList edam:operation_3766, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "NET-EXPO" ; sc:url "https://github.com/UTH-Tuan/NET-EXPO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0625 ; sc:author "Samuele Bovo" ; sc:citation ; sc: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" ; sc:featureList edam:operation_2436, edam:operation_3083, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "NETGE-PLUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://net-ge2.biocomp.unibo.it" ; biotools:primaryContact , "ELIXIR-ITA-BOLOGNA", "Samuele Bovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0634 ; sc:citation ; sc: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)" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "NETPAGE" ; sc:url "https://github.com/maffleur/NETPAGE.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_2640 ; sc:citation , "pmcid:PMC8215919", "pubmed:31504175" ; sc: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" ; sc:featureList edam:operation_3562, edam:operation_3891 ; sc:name "NExUS" ; sc:url "https://github.com/priyamdas2/NExUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC6320579", "pubmed:30609936" ; sc:description "Next Generation-Targeted Amplicon Sequencing (NG-TAS) - an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NG-TAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cclab-brca/NGTAS_pipeline" ; biotools:primaryContact "Carlos Caldas's la" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3047, edam:topic_3382 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0321, edam:operation_0337, edam:operation_3891 ; sc:license "MIT" ; sc:name "NGL" ; sc:url "https://github.com/vbchen/ngl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_3474 ; sc:citation ; sc: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" ; sc:name "NGLY1" ; sc:url "http://ngly1graph.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation , "pmcid:PMC6547473", "pubmed:31159881" ; sc:description "NGLess is a domain-specific language for NGS (next-generation sequencing data) processing with a focus on metagenomics" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NGLess" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://ngless.embl.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3308 ; sc:citation ; sc:description "Network-augmented Gene Set Enrichment Analysis." ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NGSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.inetbio.org/ngsea" ; biotools:primaryContact "Insuk Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3810 ; sc:citation , "pmcid:PMC6853766", "pubmed:31099384" ; sc:description "NGSEP (Next Generation Sequencing Experience Platform) - accurate variant calling across species and sequencing protocols." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NGSEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ngsep.sf.net" ; biotools:primaryContact "Jorge Duitama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:31689213" ; sc: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.""" ; sc:name "NGSL" ; sc:url "https://github.com/Fjr9516/GSL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC6690869", "pubmed:31406180" ; sc: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" ; sc:featureList edam:operation_0290, edam:operation_3216, edam:operation_3564 ; sc:name "NGSReadsTreatment" ; sc:url "https://sourceforge.net/projects/ngsreadstreatment/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3056, edam:topic_3517, edam:topic_3676 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3227 ; sc:name "NIPT" ; sc:url "https://github.com/nh2tran/NIPT_WGS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3411 ; sc:citation , "pmcid:PMC6296037", "pubmed:30558531" ; sc:description "R package for fast and accurate trisomy prediction in non-invasive prenatal testing." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "NIPTeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/molgenis/NIPTeR" ; biotools:primaryContact "Lennart Johansson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3678 ; sc:citation , "pmcid:PMC6444531", "pubmed:30940082" ; sc: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." ; sc:featureList edam:operation_3565, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NITPicker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://cran.r-project.org/package=NITPicker" ; biotools:primaryContact "Daphne Ezer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC8215918", "pubmed:31593244" ; sc: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)""" ; sc:featureList edam:operation_2495, edam:operation_3629, edam:operation_3659 ; sc:name "NITUMID" ; sc:url "https://github.com/tdw1221/NITUMID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0769 ; sc:citation , "pmcid:PMC6642500", "pubmed:31360216" ; sc: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)" ; sc:featureList edam:operation_0544, edam:operation_0546, edam:operation_0548 ; sc:name "NJMerge" ; sc:url "http://github.com/ekmolloy/njmerge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3398 ; sc:citation ; sc: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/)" ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3435 ; sc:name "NLIMED" ; sc:url "https://github.com/napakalas/NLIMED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_3384, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "NLP ML" ; sc:url "http://github.com/pySRURGS/nlp_ml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2828 ; sc:citation , "pmcid:PMC6767145", "pubmed:31510014" ; sc: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" ; sc:featureList edam:operation_2476, edam:operation_2939, edam:operation_3891 ; sc:name "NMA" ; sc:url "http://apps.cbu.uib.no/webnma/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3360, edam:topic_3382 ; sc:citation , "pubmed:31593222" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3860 ; sc:name "NMF-RI" ; sc:url "https://github.com/djimenezsanchez/Blind_Unmixing_NMF_RI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0593, edam:topic_3172 ; sc:citation , "pmcid:PMC6837886", "pubmed:31363225" ; sc: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”" ; sc:featureList edam:operation_0483, edam:operation_2495, edam:operation_3799 ; sc:name "NMR" ; sc:url "http://github.com/systemsnmr/ivtnmr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_2640 ; sc:citation ; sc: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)" ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:name "NMTF" ; sc:url "https://github.com/parks-cs-ccf/BayesianSNMTF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3474 ; sc:citation , "pmcid:PMC6795129", "pubmed:31649723" ; sc: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""" ; sc:featureList edam:operation_3439, edam:operation_3625 ; sc:name "NNLDA" ; sc:url "https://github.com/gao793583308/NNLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC6777013", "pubmed:31608146" ; sc: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.""" ; sc:featureList edam:operation_2497 ; sc:name "NOCAD" ; sc:url "https://github.com/abonyilab/NOCAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3071, edam:topic_3301, edam:topic_3307, edam:topic_3332 ; sc:citation , , , , , ; sc:description "NORINE is a platform that includes a database of nonribosomal peptides together with tools for their analysis." ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "NORINE" ; sc:url "http://norine.univ-lille.fr/norine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3308 ; sc:citation , "pmcid:PMC6724309", "pubmed:31481014" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_3439, edam:operation_3660 ; sc:name "NPA" ; sc:url "https://github.com/philipmorrisintl/NPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:citation , "pubmed:31752016" ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "NPD" ; sc:url "https://github.com/hz-zhu/NPD-micro-saccade-detection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_3318, edam:topic_3520 ; sc:citation , "pubmed:31753619" ; sc:description """Quantitative Structural Interpretation of Protein Crosslinks. NRGXL: a tool to compute protein crosslinker conformations and energies""" ; sc:featureList edam:operation_0480, edam:operation_2476, edam:operation_3630 ; sc:name "NRGXL" ; sc:url "https://nrgxl.pasteur.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3176, edam:topic_3295 ; sc:citation , "pmcid:PMC6868436", "pubmed:31665434" ; sc: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).""" ; sc:featureList edam:operation_2575, edam:operation_3222, edam:operation_3659 ; sc:name "NRL" ; sc:url "https://github.com/chrisclarkson/NRLcalc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3382 ; sc:citation , "pubmed:31116382" ; sc:description "software for processing and analysis of terabyte-scale volume images locally or on a computing cluster." ; sc:featureList edam:operation_0232, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NRStitcher" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/arttumiettinen/pi2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0654 ; sc:citation , "pubmed:27153714" ; sc:description "DNA comparison tool with increased speed, sensitivity and accuracy." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NSimScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/abadona/qsimscan" ; biotools:primaryContact "Denis Kaznadzey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3697, edam:topic_3855 ; sc:citation ; sc:description "Massively Parallel Simulator for Individual-based Modelling of Microbial Communities." ; sc:featureList edam:operation_0337, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NUFEB" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/nufeb/NUFEB" ; biotools:primaryContact "Paolo Zuliani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_0769, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC6933719", "pubmed:31878873" ; sc: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.""" ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3359 ; sc:name "NUMT" ; sc:url "https://github.com/robbueck/arcnumt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC6878956", "pubmed:31424551" ; sc: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')" ; sc:featureList edam:operation_3211, edam:operation_3435, edam:operation_3472 ; sc:name "NUQA" ; sc:url "https://github.com/ACRoddy/NUQA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3343 ; sc:citation , "pmcid:PMC6688286", "pubmed:31399811" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3803 ; sc:name "NaPLeS" ; sc:url "http://naples.naturalproducts.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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." ; sc:name "NaS" ; sc:url "http://www.genoscope.cns.fr/nas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0452, edam:operation_0484, edam:operation_3196, edam:operation_3227, edam:operation_3454 ; sc:name "NanoCaller" ; sc:url "https://github.com/WGLab/NanoCaller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3295 ; sc:citation , "pmcid:PMC6509807", "pubmed:31072312" ; sc:description "Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly." ; sc:featureList edam:operation_0525, edam:operation_3185, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoDJ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/genomicsITER/NanoDJ" ; biotools:primaryContact , "Marcos Colebrook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6803960", "pubmed:31590255" ; sc: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.""" ; sc:featureList edam:operation_2428, edam:operation_3457 ; sc:license "MIT" ; sc:name "NanoDefiner" ; sc:url "https://fh.do/nanodefiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6360650", "pubmed:30712508" ; sc:description "Computational tool to detect DNA modifications using Nanopore long-read sequencing data." ; sc:featureList edam:operation_0417, edam:operation_0452, edam:operation_3185 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoMod" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/WGLab/NanoMod" ; biotools:primaryContact "Wang Genomics Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0781, edam:topic_3170 ; sc:citation , "pmcid:PMC6377397", "pubmed:30689855" ; sc:description "Web server for nanopore MinION sequencing data analysis." ; sc:featureList edam:operation_0484, edam:operation_3185, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "NanoPipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nanopipe.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pmcid:PMC6508625", "pubmed:31071140" ; sc:description "R package to analyze and compare nanopore sequencing data." ; sc:featureList edam:operation_2422, edam:operation_3185, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://github.com/davidebolo1993/NanoR" ; biotools:primaryContact "Davide Bolognini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0160, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC6857246", "pubmed:31727106" ; sc: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)""" ; sc:featureList edam:operation_0237, edam:operation_3194, edam:operation_3196, edam:operation_3227 ; sc:license "MIT" ; sc:name "NanoSatellite" ; sc:url "https://github.com/arnederoeck/NanoSatellite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0417, edam:operation_0428, edam:operation_3196, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "Nanocompore" ; sc:url "https://github.com/tleonardi/nanocompore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_0593, edam:topic_3297, edam:topic_3314 ; sc:citation , "pmcid:PMC6891855", "pubmed:31807684" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_3216, edam:operation_3431, edam:operation_3803 ; sc:name "Natural Products Atlas" ; sc:url "http://www.npatlas.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071 ; sc:author "Universität Bayreuth, Department of Mycology" ; sc:contributor "SNSB IT Center" ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "NaviKey" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "http://www.navikey.net/" ; biotools:primaryContact "Universität Bayreuth, Department of Mycology" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3056 ; sc:citation , "pubmed:30194750" ; sc:description "NeOGen (genetic Ne for Overlapping Generations analysis; pronounced Neo-gen) is point-&-click genetic effective population size (Ne) and demographic modelling software." ; sc:featureList edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeOGen" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0.6.a1" ; sc:url "http://www.molecularfisherieslaboratory.com.au/neogen-v1-3-0-6-a1-software/" ; biotools:primaryContact "J. R. Ovenden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203 ; sc:citation , "pubmed:29522153" ; sc:description "Tool for the identification of approximate DNA sequence symmetries." ; sc:featureList edam:operation_0239, edam:operation_3472, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeSSie" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.medcomp.medicina.unipd.it/main_site/doku.php?%20id=nessie" ; biotools:primaryContact "Michele Berselli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7141848", "pubmed:31755900" ; sc: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.""" ; sc:featureList edam:operation_0252, edam:operation_0310, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "NeoFuse" ; sc:url "https://icbi.i-med.ac.at/NeoFuse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0804, edam:topic_2640, edam:topic_3068, edam:topic_3400 ; sc:citation , "pmcid:PMC6901387", "pubmed:31819989" ; sc: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""" ; sc:featureList edam:operation_0252, edam:operation_2421, edam:operation_3435 ; sc:name "NeoPeptide" ; sc:url "http://www.neopeptide.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3400 ; sc:citation , "pmcid:PMC6532147", "pubmed:31117948" ; sc:description "High-throughput neoantigen prediction and recognition potential pipeline." ; sc:featureList edam:operation_0487 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeoPredPipe" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/MathOnco/NeoPredPipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625 ; sc:citation , "pubmed:31095279" ; sc:description "R Package for Risk-Gene Networks." ; sc:featureList edam:operation_2436, edam:operation_3439, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "NetDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cdal.korea.ac.kr/NetDA/" ; biotools:primaryContact "Minhyeok Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1775, edam:topic_3474 ; sc:citation , "pmcid:PMC6602452", "pubmed:31106361" ; sc:description "Web server that is able to improve improve large-scale protein function prediction with massive network information." ; sc:featureList edam:operation_0267, edam:operation_1777, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NetGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://issubmission.sjtu.edu.cn/netgo/" ; biotools:primaryContact "Shanfeng Zhu", "Shuwei Yao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation , "pubmed:31688914" ; sc: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.""" ; sc:featureList edam:operation_2426, edam:operation_3463, edam:operation_3501 ; sc:name "NetML" ; sc:url "https://github.com/compbiolabucf/NetML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6746993", "pubmed:31527713" ; sc: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:" ; sc:featureList edam:operation_3501, edam:operation_3631 ; sc:name "NeuRiPP" ; sc:url "https://github.com/emzodls/neuripp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc: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)" ; sc:featureList edam:operation_3629 ; sc:license "BSD-2-Clause" ; sc:name "Neuro-Current Response Functions" ; sc:url "https://github.com/proloyd/neuro-currentRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3304, edam:topic_3474 ; sc:citation , "pubmed:31721688" ; sc: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""" ; sc:featureList edam:operation_0422 ; sc:name "NeuroCS" ; sc:url "http://i.uestc.edu.cn/NeuroCS/dist/index.html#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc: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""" ; sc:name "NeuroChaT" ; sc:url "https://github.com/shanemomara/NeuroChaT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6499165", "pubmed:31105546" ; sc:description "Software Package for Quantification of Cortical Motor Maps Using Frameless Stereotaxic Transcranial Magnetic Stimulation." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NeuroMeasure" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/EdwardsLabNeuroSci/NeuroMeasure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0157, edam:topic_3510 ; sc:author "Prof. Jian Huang" ; sc:citation , "pubmed:29525981" ; sc:description "Tool for the prediction of neuropeptide precursors based on optimal sequence composition." ; sc:featureList edam:operation_0253, edam:operation_0418, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NeuroPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://i.uestc.edu.cn/neuropeptide/neuropp/home.html" ; biotools:primaryContact "Prof. Jian Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3334, edam:topic_3421 ; sc:citation , "pmcid:PMC6901659", "pubmed:31849818" ; sc:description """The Effect of Medication and Deep Brain Stimulation on Posture in Parkinson's Disease. NeuroPostureApp©, Klinik für 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.""" ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:name "NeuroPostureApp" ; sc:url "http://www.neuroimaging.uni-kiel.de/NeuroPostureApp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3359, edam:operation_3435, edam:operation_3454 ; sc:name "NeuroPycon" ; sc:url "https://neuropycon.github.io/ephypype/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3334 ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeuroServer" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://openeeg.sourceforge.net/neuroserver_doku/" ; biotools:primaryContact "Rudi Cilibrasi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6988999", "pubmed:31831521" ; sc:description """Genome-wide analysis of differential gene expression and splicing in excitatory neurons and interneuron subtypes. Transcriptomics of cortical excitatory and inhibitory neurons""" ; sc:featureList edam:operation_2495, edam:operation_2499, edam:operation_3223, edam:operation_3891 ; sc:name "NeuronSubtypeTranscriptomes" ; sc:url "http://research-pub.gene.com/NeuronSubtypeTranscriptomes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3474 ; sc:description "Implementation of Neutrosophic Recommender System" ; sc:isAccessibleForFree true ; sc:name "Neutrosophic Recommender System for Medical Diagnosis Based on Algebraic Neutrosophic Measures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/55239-a-neutrosophic-recommender-system-for-medical-diagnosis-based-on-algebraic-neutrosophic-measures" ; biotools:primaryContact "pham viet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3314, edam:topic_3489 ; sc:citation , "pubmed:31600445" ; sc: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""" ; sc:featureList edam:operation_2422, edam:operation_3283 ; sc:license "BSD-3-Clause" ; sc:name "New Basis Set Exchange" ; sc:softwareHelp ; sc:url "https://www.basissetexchange.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC4340097", "pubmed:25849067" ; sc: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." ; sc:featureList edam:operation_0315, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NexGenEx-Tom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://140.164.45.142/NexGenEx-Tom/expression/exp-search.aspx" ; biotools:primaryContact "Hamed Bostan", "Maria Luisa Chiusano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0780 ; sc:citation , "pubmed:31778144" ; sc: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""" ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3472 ; sc:name "NextPolish" ; sc:url "https://github.com/Nextomics/NextPolish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0621, edam:topic_0736, edam:topic_2830, edam:topic_3474 ; sc:citation , "pubmed:31577193" ; sc: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""" ; sc:featureList edam:operation_0417 ; sc:name "Nglyc" ; sc:url "https://github.com/bioinformaticsML/Ngly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3361, edam:topic_3474 ; sc:citation , "pmcid:PMC6795684", "pubmed:31649523" ; sc: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".""" ; sc:featureList edam:operation_3659 ; sc:name "NiceBot" ; sc:url "https://github.com/TNTLFreiburg/NiceBot" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2333 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308 ; sc:citation , , "pmcid:PMC6876284", "pubmed:31561945", "pubmed:31819264" ; sc: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." ; sc:featureList edam:operation_2423, edam:operation_2428, edam:operation_2497 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NicheNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/saeyslab/nichenetr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218 ; sc:citation , "pubmed:31478922" ; sc: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" ; sc:featureList edam:operation_3501 ; sc:name "NimbleMiner" ; sc:url "https://github.com/mtopaz/NimbleMiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2275 ; sc:citation ; sc:description "Predicting and Designing therapeutics against the Nipah virus." ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Nipah" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cospi.iiserpune.ac.in/Nipah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0602, edam:topic_3306, edam:topic_3336 ; sc:citation , "pmcid:PMC6831641", "pubmed:31690758" ; sc: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]""" ; sc:featureList edam:operation_0244, edam:operation_2426, edam:operation_3799 ; sc:name "NmrLineGuru" ; sc:softwareHelp ; sc:url "https://github.com/stonefonly/NmrLineGuru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3379 ; sc:citation , "pmcid:PMC6452590", "pubmed:31057324" ; sc:description "Online tool to predict the survival rate in non-small cell lung cancer patients." ; sc:featureList edam:operation_3557 ; sc:name "Nomogram Prognostic Model" ; sc:url "http://lce.biohpc.swmed.edu/lungcancer/nomogram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation , "pubmed:31106635" ; sc:description "Interactive tool for presenting cervical cancer screening indicators in the Nordic countries." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NordScreen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nordscreen.org/" ; biotools:primaryContact "Veli-Matti Partanen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6503164", "pubmed:31114611" ; sc: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." ; sc:featureList edam:operation_0571, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "NormExpression" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/NormExpression/index.html" ; biotools:primaryContact "Shan Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3305, edam:topic_3418 ; sc:citation , "pmcid:PMC6704660", "pubmed:31438883" ; sc: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" ; sc:featureList edam:operation_0308, edam:operation_3196 ; sc:name "Norovirus" ; sc:url "https://www.rivm.nl/mpf/typingtool/norovirus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2229, edam:topic_2830, edam:topic_3306 ; sc:citation , "pmcid:PMC6893490", "pubmed:31771451" ; sc: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.""" ; sc:featureList edam:operation_0321, edam:operation_2426, edam:operation_3096 ; sc:name "Notch" ; sc:url "https://github.com/asafl/NotchDelta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0621, edam:topic_0654, edam:topic_3295, edam:topic_3656 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0570, edam:operation_2476, edam:operation_3208 ; sc:name "Nucleome Data Bank" ; sc:url "https://ndb.rice.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3176, edam:topic_3308 ; sc:citation , "pmcid:PMC6765203", "pubmed:31504766" ; sc: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" ; sc:featureList edam:operation_0244, edam:operation_3454 ; sc:license "Apache-2.0" ; sc:name "Nucleosome Dynamics" ; sc:url "http://mmb.irbbarcelona.org/NucleosomeDynamics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3390, edam:topic_3518 ; sc:citation , "pmcid:PMC6821151", "pubmed:31665759" ; sc: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""" ; sc:featureList edam:operation_0315, edam:operation_0571, edam:operation_2436, edam:operation_3223 ; sc:name "NutriGenomeDB" ; sc:url "http://nutrigenomedb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:31599833" ; sc: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.""" ; sc:featureList edam:operation_2428 ; sc:name "OAB" ; sc:url "https://oabweb.herokuapp.com/app/pre/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3063, edam:topic_3335, edam:topic_3400, edam:topic_3421 ; sc:citation , , "pmcid:PMC6876873", "pubmed:31765395" ; sc: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".""" ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3435 ; sc:name "OAC" ; sc:url "https://github.com/CogStack/OAC-NLP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2828, edam:topic_3314 ; sc:citation , "pmcid:PMC6774380", "pubmed:31579260" ; sc: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:""" ; sc:featureList edam:operation_3435 ; sc:name "OAR" ; sc:url "https://github.com/usnistgov/oar-pdr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3316, edam:topic_3337 ; sc:citation , "pmcid:PMC6325911", "pubmed:30482799" ; sc: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." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OCMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "gamma 0.1" ; sc:url "https://github.com/precisionomics/OCMA" ; biotools:primaryContact "Quan Long", "Zhi Xiong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2640, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC6905554", "pubmed:31825992" ; sc: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.""" ; sc:featureList edam:operation_0315, edam:operation_2454 ; sc:name "OCSVM" ; sc:url "https://github.com/imandehzangi/OCSVM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0208, edam:topic_2640, edam:topic_3577 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3463 ; sc:name "OCTAD" ; sc:url "http://octad.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0593, edam:topic_0749 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3443 ; sc:license "MIT" ; sc:name "OCTAVVS" ; sc:url "http://pypi.org/project/octavvs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3168, edam:topic_3382 ; sc:citation , "pubmed:31658504" ; sc: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.""" ; sc:featureList edam:operation_3799 ; sc:name "OC_manager" ; sc:url "https://github.com/OfficeChromatography/OC_manager" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0209, edam:topic_3399 ; sc:citation , "pmcid:PMC6509876", "pubmed:31074377" ; sc: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." ; sc:featureList edam:operation_3280, edam:operation_3431, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ODAE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ODAE-ontology/ODAE" ; biotools:primaryContact "Oliver He" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3475 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3475 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3604 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071, edam:topic_3473, edam:topic_3678 ; sc:author ; sc:citation , "pmcid:PMC7736789", "pubmed:33319910" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ODAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "1.2" ; sc:url "https://inrae.github.io/ODAM/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC6882730", "pubmed:31781773" ; sc:description """A manually curated database of noncoding RNAs associated with orthopedics. Harbin Medical University, China""" ; sc:featureList edam:operation_2421 ; sc:name "ODNA" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/ODNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_0769 ; sc:citation , "pmcid:PMC6501302", "pubmed:31060495" ; sc:description "Consistency pipeline for hierarchies of orthologous groups (OGs) based on subsampling and tree reconciliation." ; sc:featureList edam:operation_0544, edam:operation_0555, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OG" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/meringlab/og_consistency_pipeline" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0804, edam:topic_3400 ; sc:citation , "pubmed:31566225" ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3431 ; sc:name "OGRDB" ; sc:url "https://ogrdb.airr-community.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_3293 ; sc:citation , "pmcid:PMC7145513", "pubmed:31612943" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0310 ; sc:name "OHNOLOGS v2" ; sc:url "http://ohnologs.curie.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0622, edam:topic_3293, edam:topic_3697 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0362, edam:operation_2454, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "OLGenie" ; sc:url "https://github.com/chasewnelson/OLGenie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_2269 ; sc:citation , "pubmed:31688931" ; sc: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.""" ; sc:featureList edam:operation_2436, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "OLOGRAM" ; sc:url "https://github.com/dputhier/pygtftk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC5409310", "pubmed:28172448" ; sc:description "Alignment tool for optical mapping using a seed-and-extend approach." ; sc:featureList edam:operation_0491, edam:operation_3216, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OMBlast" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/TF-Chan-Lab/OMBlast" ; biotools:primaryContact "Kevin Y. Yip", "Ting-Fung Chan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_3174 ; sc:citation , "pmcid:PMC6612865", "pubmed:31510667" ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_3096 ; sc:name "OMH" ; sc:url "http://github.com/Kingsford-Group/omhismb2019" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6444640", "pubmed:30940089" ; sc:description "Method for the statistical analysis of RNA-Seq paired design data." ; sc:featureList edam:operation_3223, edam:operation_3436, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:name "OMICfpp" ; sc:url "http://www.uv.es/ayala/software/OMICfpp_0.2.tar.gz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:15473683" ; sc: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." ; sc:name "OMSSA" ; sc:url "https://pubchem.ncbi.nlm.nih.gov/omssa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3174 ; sc:citation ; sc:description "Ontology-based, data-driven metadata tracking system." ; sc:featureList edam:operation_2422, edam:operation_3352, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OMeta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JCVenterInstitute/OMeta-Public" ; biotools:primaryContact "J. Craig Venter Institute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3334, edam:topic_3512 ; sc:citation , "pmcid:PMC6734442", "pubmed:31500643" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3431 ; sc:name "OPA1" ; sc:url "https://www.lovd.nl/OPA1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3421, edam:topic_3855 ; sc:citation ; sc: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" ; sc:name "OPETH" ; sc:url "https://github.com/hangyabalazs/opeth.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3981 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128 ; sc:author , ; sc:citation , "pubmed:19714772" ; sc: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." ; sc:featureList edam:operation_3902 ; sc:name "OPRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Barcelona Supercomputing Center" ; sc:softwareHelp , ; sc:url "https://life.bsc.es/pid/opra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3407, edam:topic_3421 ; sc:citation , "pubmed:31720757" ; sc: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.""" ; sc:featureList edam:operation_3659 ; sc:name "OPSCC" ; sc:url "https://rasmussen.shinyapps.io/OPSCCmodelFDG_PET/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6521604", "pubmed:30819774" ; sc:description "Algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis." ; sc:featureList edam:operation_0415, edam:operation_3196, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OPTIMIR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/FlorianThibord/OptimiR" ; biotools:primaryContact "Florian Thibord" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3382 ; sc:citation , "pmcid:PMC6832278", "pubmed:31623266" ; sc: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.""" ; sc:featureList edam:operation_2429, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "ORB-SLAM" ; sc:url "https://github.com/lsyads/fisheye-ORB-SLAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3293, edam:topic_3500 ; sc:citation , "pmcid:PMC6389317", "pubmed:30517749" ; sc:description "Automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa." ; sc:featureList edam:operation_0544, edam:operation_0552, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ORTHOSCOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.orthoscope.jp" ; biotools:primaryContact "Jun Inoue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3172, edam:topic_3295 ; sc:citation , "pmcid:PMC6537380", "pubmed:31138268" ; sc:description "OSCA (OmicS-data-based Complex trait Analysis) is a software tool for the analysis of complex traits using multi-omics data." ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OSCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cnsgenomics.com/software/osca/#Overview" ; biotools:primaryContact "Futao Zhang", "Jian Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0632, edam:topic_2885 ; sc:citation , "pmcid:PMC6482647", "pubmed:31040636" ; sc:description "Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer." ; sc:featureList edam:operation_0237, edam:operation_0308, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OSTRFPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/vivekmathema/OSTRFPD" ; biotools:primaryContact "Mallika Imwong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC6817837", "pubmed:31749633" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2495 ; sc:name "OSacc" ; sc:url "http://bioinfo.henu.edu.cn/ACC/ACCList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360 ; sc:citation , "pubmed:31512935" ; sc: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" ; sc:name "OScc" ; sc:url "http://bioinfo.henu.edu.cn/CESC/CESCList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3360, edam:topic_3379 ; sc:citation , "pubmed:31646691" ; sc: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.""" ; sc:featureList edam:operation_2495, edam:operation_3503 ; sc:name "OSuvm" ; sc:url "http://bioinfo.henu.edu.cn/UVM/UVMList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3292, edam:topic_3895 ; sc:citation , "pmcid:PMC6660583", "pubmed:31372451" ; sc: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" ; sc:name "OVERFRAG" ; sc:url "http://www.each.usp.br/digiampietri/overfrag" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Quercus robur annotation database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "OakMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "2.3" ; sc:url "https://urgi.versailles.inra.fr/OakMine_PM1N" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1138 ; sc:encodingFormat edam:format_2330, edam:format_3464 ; sc:name "Pfam accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:encodingFormat edam:format_1370 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929, edam:format_3464 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_3464 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3508, edam:format_3579, edam:format_3603, edam:format_3604 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2331 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1984 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_3752 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3174, edam:topic_3387, edam:topic_3941 ; sc:citation , "pmcid:PMC6030836", "pubmed:29788376" ; sc: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.""" ; sc:featureList edam:operation_0292, edam:operation_0567, edam:operation_0573, edam:operation_3478, edam:operation_3799 ; sc:funder "OCEANOMICS" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Ocean Gene Atlas" ; sc:provider "MIO" ; sc:softwareHelp , ; sc:url "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3068, edam:topic_3489, edam:topic_3500 ; sc:citation ; sc: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.""" ; sc:name "OdoBD" ; sc:url "http://www.odobd.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0625, edam:topic_0637, edam:topic_3293, edam:topic_3489 ; sc:citation , "pmcid:PMC6908694", "pubmed:31831730" ; sc: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""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3196, edam:operation_3431 ; sc:name "Odonate Phenotypic Database" ; sc:url "http://www.odonatephenotypicdatabase.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_1775, edam:topic_3063, edam:topic_3325 ; sc:author "Alexandre Renaux" ; sc:citation , "pmcid:PMC6602484", "pubmed:31147699" ; sc: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." ; sc:featureList edam:operation_0331, edam:operation_3083, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Oligogenic resource for variant analysis (ORVAL)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Interuniversity Institute of Bioinformatics in Brussels" ; sc:softwareHelp , ; sc:softwareVersion "3.0.0" ; sc:url "https://orval.ibsquare.be" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3050 ; sc:citation , "pmcid:PMC6783963", "pubmed:31443503" ; sc: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" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "OliveR" ; sc:url "https://github.com/nicocriscuolo/OliveR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3172 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0417 ; sc:license "Apache-2.0" ; sc:name "Omic-Sig" ; sc:url "https://github.com/hzhangjhu/Omic-Sig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC6842565", "pubmed:31720124" ; sc: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。.""" ; sc:featureList edam:operation_2495, edam:operation_3083, edam:operation_3799 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "OmicShare" ; sc:url "http://www.omicshare.com/tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3170, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC6839229", "pubmed:31703610" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_2495 ; sc:name "OmicsARules" ; sc:url "https://github.com/BioinformaticsSTU/OmicsARules" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_3172 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2939, edam:operation_3501, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "OmicsOne" ; sc:url "https://github.com/huizhanglab-jhu/OmicsOne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3174 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2436, edam:operation_3891 ; sc:name "OmicsX" ; sc:url "http://bioinfo.wilmer.jhu.edu/OmicsX/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation , "pubmed:27898060" ; sc: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." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "OmniPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://omnipathdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc: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/""" ; sc:featureList edam:operation_2495, edam:operation_3223 ; sc:name "OnClass" ; sc:url "https://onclass.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_3169, edam:topic_3170 ; sc:citation , "pmcid:PMC6918570", "pubmed:31847870" ; sc: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 [-penalty ] [-maxsz ] [-minsz ] [-ldiff ] [-lsize ] [-bedout ] [-log2] [-o output_file]""" ; sc:featureList edam:operation_0337, edam:operation_0481, edam:operation_3435 ; sc:license "MIT" ; sc:name "OnTAD" ; sc:url "https://github.com/anlin00007/OnTAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC6881748", "pubmed:31828101" ; sc: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.""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3659 ; sc:name "OncoLnc" ; sc:url "http://www.oncolnc.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0128, edam:topic_0202, edam:topic_2640 ; sc:citation , "pubmed:31583637" ; sc: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.""" ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_3083, edam:operation_3439 ; sc:name "OncoPPi" ; sc:url "http://oncoppi.emory.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3421, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC6836658", "pubmed:31699073" ; sc: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.""" ; sc:featureList edam:operation_3216, edam:operation_3283, edam:operation_3907 ; sc:name "OncoWiki" ; sc:url "https://www.oncowiki.co.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation , "pmcid:PMC6954649", "pubmed:31369060" ; sc:description "A sequence-based clustering method to identify cancer drivers" ; sc:license "GPL-3.0" ; sc:name "OncodriveCLUSTL" ; sc:url "https://bitbucket.org/bbglab/oncodriveclustl/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0821, edam:topic_3068, edam:topic_3314 ; sc:citation , "pubmed:31846323" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_3280, edam:operation_3454 ; sc:name "OntoKin" ; sc:url "http://www.theworldavatar.com/kb/ontokin/ontokin.owl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3500 ; sc:citation ; sc: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++.""" ; sc:featureList edam:operation_2426 ; sc:name "Open-Sim Moco" ; sc:url "https://simtk.org/projects/opensim-moco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6398228", "pubmed:30832730" ; sc:description "Tool for assessing taxonomic metagenome profilers. Implements commonly used performance metrics together with convenient visualizations." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Open-community Profiling Assessment tooL (OPAL)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/CAMI-challenge/OPAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC6355034", "pubmed:30657753" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OpenCASA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/calquezar/OpenCASA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0634, edam:topic_0769, edam:topic_2640 ; sc:citation ; sc: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`.""" ; sc:featureList edam:operation_0331, edam:operation_3226, edam:operation_3227 ; sc:license "BSD-3-Clause" ; sc:name "OpenCRAVAT" ; sc:url "https://opencravat.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0634, edam:topic_3382 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:name "OpenFlexure" ; sc:url "https://gitlab.com/openflexure/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6860425", "pubmed:31738777" ; sc: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.""" ; sc:featureList edam:operation_3435, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "OpenFmriAnalysis" ; sc:url "https://github.com/TimVanMourik/OpenFmriAnalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3474 ; sc:description "A PyTorch framework for tertiary protein structure prediction." ; sc:featureList edam:operation_0474, edam:operation_0477 ; sc:license "MIT" ; sc:name "OpenProtein" ; sc:softwareVersion "0.0.1" ; sc:url "https://openprotein.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3246, edam:format_3475 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3245, edam:format_3710 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3621, edam:format_3654 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3621, edam:format_3654 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3475, edam:format_3621, edam:format_3833 ; sc:name "Peptide mass fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:24727770" ; sc:description "OpenSWATH is a proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) and implemented as part of OpenMS." ; sc:featureList edam:operation_0335, edam:operation_3203, edam:operation_3215, edam:operation_3628, edam:operation_3649 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "OpenSWATH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "OpenMS 2.4.0" ; sc:url "http://www.openswath.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:27153681" ; sc:description "3D automatic quantitative analysis tool for Single Plane Illumination Microscopy data." ; sc:featureList edam:operation_3629, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "OpenSegSPIM" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://opensegspim.weebly.com/" ; biotools:primaryContact "Laurent Gole", "Sohail Ahmed", "Weimiao Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3067, edam:topic_3068, edam:topic_3300, edam:topic_3304 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_2426, edam:operation_2428 ; sc:license "MIT" ; sc:name "OpenWorm" ; sc:url "http://www.openworm.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3325 ; sc:citation , "pubmed:28289778" ; sc: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." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "OSSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.4" ; sc:url "https://www.osse-register.de/en/" ; biotools:primaryContact "Holger Storf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3336, edam:topic_3391 ; sc: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.""" ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "Open Targets" ; sc:softwareHelp ; sc:url "https://www.opentargets.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0208, edam:topic_2259, edam:topic_3336, edam:topic_3342, edam:topic_3391, edam:topic_3574 ; sc:citation , , , , "pmcid:PMC5210543", "pmcid:PMC6324073", "pmcid:PMC7779013", "pmcid:PMC9825572", "pubmed:27899665", "pubmed:30462303", "pubmed:33196847", "pubmed:36399499" ; sc: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.""" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Open Targets Platform" ; sc:softwareHelp , , , , ; sc:url "https://platform.opentargets.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_3385, edam:topic_3452, edam:topic_3794 ; sc:citation , "pmcid:PMC6821862", "pubmed:31666606" ; sc: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.""" ; sc:featureList edam:operation_0337 ; sc:name "OptiJ" ; sc:url "https://lag-opt.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3436, edam:operation_3443, edam:operation_3799 ; sc:name "Orbit" ; sc:softwareHelp ; sc:url "http://www.orbit.bio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3068 ; sc:citation ; sc:description "Visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples." ; sc:featureList edam:operation_1812, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "Ordino" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ordino.caleydoapp.org/" ; biotools:primaryContact "Caleydo Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0194, edam:topic_0797, edam:topic_3293 ; sc:citation , , "pmcid:PMC4531804", "pubmed:26243257" ; sc: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." ; sc:featureList edam:operation_0324, edam:operation_0540, edam:operation_3182, edam:operation_3209 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OrthoFinder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/davidemms/OrthoFinder" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , , "pmcid:PMC3196566", "pmcid:PMC403725", "pubmed:12952885", "pubmed:21901743" ; sc: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." ; sc:featureList edam:operation_0553, edam:operation_3942 ; sc:name "OrthoMCL" ; sc:url "https://github.com/stajichlab/OrthoMCL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC6602458", "pubmed:31053848" ; sc:description "Web server for whole-genome comparison and annotation of orthologous clusters across multiple species." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "OrthoVenn2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://orthovenn2.bioinfotoolkits.net" ; biotools:primaryContact "Yi Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3360, edam:topic_3399 ; sc:citation , "pmcid:PMC6487800", "pubmed:31086734" ; sc:description "Human osteoporosis-related gene database." ; sc:featureList edam:operation_2495, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "OsteoporosAtlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biokb.ncpsb.org/osteoporosis/" ; biotools:primaryContact "Dong Li", "Yang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0736, edam:topic_0820, edam:topic_3510 ; sc:citation , "pmcid:PMC6923414", "pubmed:31857603" ; sc: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""" ; sc:featureList edam:operation_0269, edam:operation_0418, edam:operation_3767 ; sc:name "OutCyte" ; sc:url "http://www.outcyte.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3293, edam:topic_3305 ; sc:citation , "pmcid:PMC6717506", "pubmed:31523522" ; sc: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" ; sc:featureList edam:operation_0323, edam:operation_0552, edam:operation_0557 ; sc:name "OutbreakFinder" ; sc:url "https://github.com/skypes/Newton-method-MDS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:28172520" ; sc:description "Parallel processing pipeline software for automatic analysis of bisulfite sequencing data." ; sc:featureList edam:operation_3186, edam:operation_3192, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "P3BSseq" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/p/p3bsseq/wiki/Home/" ; biotools:primaryContact "Marcos J. Araúzo-Bravo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0130, edam:topic_0154, edam:topic_0623, edam:topic_0736 ; sc:citation , "pubmed:31584628" ; sc:description """Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation. Predicting Protein Folding Routes.""" ; sc:featureList edam:operation_0244, edam:operation_0303, edam:operation_0474, edam:operation_2415, edam:operation_3439 ; sc:name "P3Fold" ; sc:url "http://csb.cs.mcgill.ca/P3Fold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6668381", "pubmed:31366994" ; sc: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)" ; sc:featureList edam:operation_0417, edam:operation_2495, edam:operation_3431 ; sc:name "PACES" ; sc:url "http://www.rnanut.net/paces/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0209, edam:topic_0821 ; sc:citation , "pmcid:PMC7029793", "pubmed:31786268" ; sc:description """Characterizing and Predicting Protein Hinges for Mechanistic Insight. PACKMAN: PACKing and Motion ANalysis""" ; sc:featureList edam:operation_0244, edam:operation_1843, edam:operation_2476 ; sc:name "PACKMAN" ; sc:url "https://PACKMAN.bb.iastate.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_0820 ; sc:citation , "pubmed:31120747" ; sc:description "Generalized workflow for automated building of membrane-protein-lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PACKMOL-Memgen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ambermd.org/AmberTools.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_1637, edam:format_2585 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:author "Méziane Aite" ; sc:citation , , , "pmcid:PMC5988327", "pmcid:PMC6912245", "pubmed:29791443", "pubmed:31744163" ; sc: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." ; sc:featureList edam:operation_2409, edam:operation_3927, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PADMet" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/AuReMe/padmet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_0654, edam:topic_3292, edam:topic_3489 ; sc:citation , "pmcid:PMC7145686", "pubmed:31620779" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_0435, edam:operation_2422 ; sc:name "PADS Arsenal" ; sc:url "https://bigd.big.ac.cn/padsarsenal" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:citation ; sc: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." ; sc:featureList edam:operation_0523 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PAFScaff" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "v0.2.1" ; sc:url "https://github.com/slimsuite/pafscaff/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3382, edam:topic_3474 ; sc:citation "pubmed:31797610" ; sc: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""" ; sc:featureList edam:operation_3436 ; sc:name "PAGE-Net" ; sc:url "https://github.com/DataX-JieHao/PAGE-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3047 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3432, edam:operation_3436, edam:operation_3454 ; sc:name "PAMOGK" ; sc:url "https://pypi.org/project/pamogk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2269 ; sc:citation , "pmcid:PMC6184437", "pubmed:29790911" ; sc:description "Tool for statistical analysis and visualization of quantitative proteomics data" ; sc:featureList edam:operation_2939, edam:operation_3557, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "PANDA-view" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/panda-view/" ; biotools:primaryContact "Cheng Chang", "Yunping Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3305, edam:topic_3321, edam:topic_3324, edam:topic_3673 ; sc:citation , "pmcid:PMC6922483", "pubmed:31815935" ; sc: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""" ; sc:featureList edam:operation_0484, edam:operation_3198, edam:operation_3227, edam:operation_3432 ; sc:name "PANPASCO" ; sc:url "https://gitlab.com/rki_bioinformatics/panpasco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3306 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "PARC" ; sc:url "https://github.com/ShobiStassen/PARC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:name "Alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621 ; sc: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." ; sc:featureList edam:operation_0232, edam:operation_0310 ; sc:name "PASA" ; sc:url "https://sourceforge.net/projects/pasa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6343338", "pubmed:30669970" ; sc: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." ; sc:featureList edam:operation_0313, edam:operation_2495, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PASCCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/BMILAB/PASCCA" ; biotools:primaryContact "Wenbin Ye", "Yuqi Long" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "PASER" ; sc:url "http://github.com/DepartmentofNeurophysiology/Paser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3360, edam:topic_3407 ; sc:citation , "pmcid:PMC6296065", "pubmed:30558539" ; sc:description "Pathway-associated sparse deep neural network for prognosis prediction from high-throughput data." ; sc:featureList edam:operation_0277, edam:operation_3439, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PASNet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/DataX-JieHao/PASNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:author "URGI" ; sc:citation , "pmcid:PMC4008368", "pubmed:24786468" ; sc:contributor "URGI" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "CECILL-2.0" ; sc:name "PASTEClassifier" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "URGI" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/PASTEClassifier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0769, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC6913009", "pubmed:31842968" ; sc: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""" ; sc:featureList edam:operation_0321, edam:operation_1812, edam:operation_2429, edam:operation_3096, edam:operation_3767 ; sc:name "PASTMUS" ; sc:url "https://figshare.com/articles/PASTMUS_mapping_functional_elements_at_single_amino_acid_resolution_in_human_cells/10435370" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0781 ; sc:citation "pmcid:PMC6736041" ; sc: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" ; sc:name "PASeq" ; sc:url "https://www.paseq.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC6606892", "pubmed:31101593" ; sc:description "R package for crosstalk correction in Pathway Deregulation Score (PDS) inferred by Pathifier algorithm." ; sc:featureList edam:operation_0487 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PATHcrosstalk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fabotao/PATHcrosstalk" ; biotools:primaryContact "Botao Fa", "Zhangsheng Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2269, edam:topic_2640, edam:topic_3676 ; sc:citation , "pmcid:PMC6889196", "pubmed:31791231" ; sc: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 a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC7141844", "pubmed:31790154" ; sc: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:.""" ; sc:featureList edam:operation_0524, edam:operation_3227, edam:operation_3258 ; sc:name "PAVFinder" ; sc:url "https://github.com/bcgsc/pavfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3337 ; sc:citation , "pmcid:PMC6612857", "pubmed:31510689" ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_2421, edam:operation_3211 ; sc:name "PBWT-Query" ; sc:url "http://genome.ucf.edu/pbwt-query" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC6538748", "pubmed:31138829" ; sc: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." ; sc:featureList edam:operation_2939, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PCA-PAM50" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "ftp://ftp.wriwindber.org/" ; biotools:primaryContact "Praveen K. Raj Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0602, edam:topic_2828 ; sc:citation , "pmcid:PMC6849643", "pubmed:31580061" ; sc: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""" ; sc:featureList edam:operation_1812, edam:operation_2476, edam:operation_2939, edam:operation_3890, edam:operation_3891 ; sc:name "PCAViz" ; sc:url "http://durrantlab.com/pcaviz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_3170, edam:topic_3179, edam:topic_3315 ; sc:citation , "pmcid:PMC6933681", "pubmed:31881819" ; sc:description """Topological structure analysis of chromatin interaction networks. Analysis and visualisation tools for PCHi-C interaction networks""" ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_3083 ; sc:license "GPL-3.0" ; sc:name "PCHi-C" ; sc:url "https://github.com/IMCS-Bioinformatics/PCHiCNetworkExplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3293, edam:topic_3360, edam:topic_3810 ; sc:citation , "pmcid:PMC6835207", "pubmed:31696928" ; sc: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""" ; sc:featureList edam:operation_0282, edam:operation_0337, edam:operation_2421 ; sc:name "PCIR" ; sc:url "http://biodb.sdau.edu.cn/pcir/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_2269, edam:topic_3293 ; sc:citation , "pubmed:31805292" ; sc: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.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567, edam:operation_3891 ; sc:name "PCMBase" ; sc:url "https://github.com/venelin/PCMBase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0219, edam:topic_0602, edam:topic_0634 ; sc:citation , "pubmed:31725861" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3439 ; sc:name "PCOSBase" ; sc:url "http://pcosbase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , "pmcid:PMC6337464", "pubmed:30621295" ; sc:description "Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment." ; sc:featureList edam:operation_0224, edam:operation_0279, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PDBUSQLExtractor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zti.polsl.pl/w3/dmrozek/science/pdbusqlext.htm" ; biotools:primaryContact "D. Mrozek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation ; sc:description "Parameter fitting toolbox for partial differential equations in Python." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PDEparams" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/systemsmedicine/PDE_params" ; biotools:primaryContact "Esteban A. Hernandez-Vargas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3056, edam:topic_3336 ; sc:citation ; sc: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.""" ; sc:name "PDGA" ; sc:url "https://github.com/reymond-group/PeptideDesignGA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3382, edam:topic_3518 ; sc:citation , "pubmed:31714620" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0315, edam:operation_0571 ; sc:name "PEATmoss" ; sc:softwareHelp ; sc:url "https://peatmoss.online.uni-marburg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , , "pmcid:PMC6642660", "pubmed:31081335" ; sc: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." ; sc:featureList edam:operation_0335, edam:operation_0417, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PEFF" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.psidev.info/peff" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_3315, edam:topic_3375 ; sc:citation , "pubmed:31589430" ; sc: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.""" ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3896 ; sc:name "PELE-MSM" ; sc:softwareHelp ; sc:url "https://github.com/miniaoshi/MSM_PELE.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1931 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:name "Biodiversity data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3050 ; sc:description "a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes" ; sc:featureList edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PEMA" ; sc:softwareHelp ; sc:url "https://github.com/hariszaf/pema" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0623, edam:topic_0634 ; sc:citation ; sc:description "Identification of pathogenic variant enriched regions across genes and gene families." ; sc:featureList edam:operation_3225, edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PER viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://per.broadinstitute.org" ; biotools:primaryContact "Dennis Lal", "Eduardo Pérez-Palma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0623, edam:topic_0634, edam:topic_3120, edam:topic_3168 ; sc:citation , "pmcid:PMC6961572", "pubmed:31871067" ; sc:description "PERs is a tool for Identification of pathogenic variant enriched regions across genes and gene families." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:license "MIT" ; sc:name "PERs" ; sc:url "https://github.com/edoper/PERs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3325 ; sc:citation , "pmcid:PMC3742411", "pubmed:23920006" ; sc: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." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "PFOND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pfond.cmmt.ubc.ca/index.html" ; biotools:primaryContact "Wasserman Lab" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681, edam:format_3684, edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681, edam:format_3684, edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3684 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3681 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3004 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681, edam:format_3684, edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681, edam:format_3684, edam:format_3827 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071, edam:topic_3520 ; sc: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." ; sc:featureList edam:operation_0335, edam:operation_0336, edam:operation_1812, edam:operation_2409, edam:operation_2422, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PGConverter" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.8.5" ; sc:url "https://github.com/PRIDE-Toolsuite/PGConverter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3517, edam:topic_3673 ; sc:citation , "pmcid:PMC6943055", "pubmed:31584086" ; sc: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.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3454, edam:operation_3557, edam:operation_3791 ; sc:name "PGG Han" ; sc:url "http://www.pgghan.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2815, edam:topic_3056, edam:topic_3796 ; sc:citation , "pmcid:PMC6805450", "pubmed:31640808" ; sc: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.""" ; sc:featureList edam:operation_0488, edam:operation_2421, edam:operation_3196, edam:operation_3211, edam:operation_3227 ; sc:name "PGG SNV" ; sc:url "https://www.pggsnv.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3173, edam:topic_3308, edam:topic_3518, edam:topic_3577 ; sc:citation , "pmcid:PMC6823446", "pubmed:31672996" ; sc:description "PGP-UK is an open access resource of human multi-omics data." ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3227 ; sc:name "PGP-UK" ; sc:url "http://opendata.lifebit.ai/table/pgp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Manipulation,filter and sort NGS data." ; sc:name "PGP_tools" ; sc:url "https://bioweb.pasteur.fr/packages/pack@PGP_tools@0.0.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_3068 ; sc: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." ; sc:name "PGxLOD" ; sc:url "https://pgxlod.loria.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0218, edam:topic_3375, edam:topic_3474, edam:topic_3577 ; sc:citation "pmcid:PMC6917032", "pubmed:31797632" ; sc: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." ; sc:featureList edam:operation_0306, edam:operation_1812, edam:operation_3675 ; sc:license "MIT" ; sc:name "PGxMine" ; sc:url "https://pgxmine.pharmgkb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:30561651" ; sc: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." ; sc:featureList edam:operation_3196, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PHAT" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.10.1-beta.1" ; sc:url "https://github.com/chgibb/PHAT" ; biotools:primaryContact "Chris Gibb" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_3749 ; sc:name "Genotype/phenotype report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation , "pmcid:PMC6792114", "pubmed:30903186" ; sc: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.""" ; sc:featureList edam:operation_2429 ; sc:isAccessibleForFree true ; sc:name "PHENO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "https://brapi.biodata.pt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_2259, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6898514", "pubmed:31811131" ; sc: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." ; sc:featureList edam:operation_2429, edam:operation_3802, edam:operation_3891 ; sc:name "PHENOSTAMP" ; sc:url "https://github.com/anchangben/PHENOSTAMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3810 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3211, edam:operation_3557 ; sc:name "PHG" ; sc:url "https://bitbucket.org/bucklerlab/p_sorghumphg/src/master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0621, edam:topic_0625, edam:topic_0659, edam:topic_0780 ; sc:citation , "pmcid:PMC6908471", "pubmed:31866958" ; sc:description "PHI-Nets is a network resource for Ascomycete fungal pathogens to annotate and identify putative virulence interacting proteins and siRNAs." ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_3439, edam:operation_3461 ; sc:license "MIT" ; sc:name "PHI-Nets" ; sc:url "https://github.com/PHI-base/phi-nets/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_0605, edam:topic_3306 ; sc:citation ; sc:description "PHOSforUS is a fully biophysical parameter-based protein phosphorylation site predictor." ; sc:featureList edam:operation_0303, edam:operation_0417, edam:operation_3891 ; sc:license "MIT" ; sc:name "PHOSforUS" ; sc:url "https://github.com/bxlab/PHOSforUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation , "pmcid:PMC5815242", "pubmed:29467814" ; sc:description "Scalable data integration and visualization for multiple phylogenetic inference methods." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PHYLOViZ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.phyloviz.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_3308 ; sc:citation , "pmcid:PMC6694207", "pubmed:31414118" ; sc:description "PICEAdatabase is a web database for Picea omics and phenotypic information." ; sc:featureList edam:operation_3639 ; sc:name "PICEAdatabase" ; sc:url "http://www.piceadb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3518 ; sc:citation , "pubmed:30649727" ; sc:description "Pipeline for Integrated Microarray Expression Normalization Tool kit (PIMENTo) for tumor microarray profiling experiments." ; sc:featureList edam:operation_2428, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PIMENTo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/MUSC-CGM/PIMENTo/" ; biotools:primaryContact "Thomas Nash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3063, edam:topic_3068 ; sc:citation ; sc:description "PINOT is a Protein Interaction Network Online Tool." ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_3083 ; sc:name "PINOT" ; sc:softwareVersion "1.1" ; sc:url "http://www.reading.ac.uk/bioinf/PINOT/PINOT_form.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3295, edam:topic_3384 ; sc:citation , "pubmed:30590381" ; sc:description "Tool for tumor subtype discovery in integrated genomic data." ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PINSPlus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0.0" ; sc:url "https://bioinformatics.cse.unr.edu/software/PINSPlus/" ; biotools:primaryContact "Hung Nguyen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3360, edam:topic_3518, edam:topic_3519 ; sc:citation , "pmcid:PMC6879478", "pubmed:31772190" ; sc: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. 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It provides a pipeline for functional classification of non-coding RNAs associated with distinct histone modifications" ; sc:featureList edam:operation_2436, edam:operation_2441, edam:operation_3222 ; sc:name "PIRCh-seq" ; sc:url "https://github.com/QuKunLab/PIRCh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_3400 ; sc:citation , "pubmed:31373607" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3431 ; sc:name "PIRD" ; sc:url "https://db.cngb.org/pird" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_2275 ; sc:citation , "pmcid:PMC6602501", "pubmed:31114890" ; sc:description "Protein Interaction Z-Score Assessment." ; sc:featureList edam:operation_0272, edam:operation_0321, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PIZSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cospi.iiserpune.ac.in/pizsa" ; biotools:primaryContact "M. S. Madhusudhan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2840, edam:topic_3375, edam:topic_3379 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3196, edam:operation_3435 ; sc:name "PK-DB" ; sc:url "https://pk-db.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196 ; sc:citation , "pubmed:29036591" ; sc:description "Web-based tool for plasmid reconstruction from bacterial genomes." ; sc:featureList edam:operation_3195, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PLACNETw" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://castillo.dicom.unican.es/upload/" ; biotools:primaryContact "Fernando de la Cruz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0749, edam:topic_3314 ; sc:citation , "pubmed:31363226" ; sc: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" ; sc:featureList edam:operation_0244, edam:operation_2476 ; sc:name "PLUMED" ; sc:url "https://www.plumed-nest.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0821, edam:topic_3297, edam:topic_3489, edam:topic_3697 ; sc:citation , "pmcid:PMC6859810", "pubmed:31738435" ; sc:description "PMBD is a Comprehensive Plastics Microbial Biodegradation Database." ; sc:featureList edam:operation_0305 ; sc:name "PMBD" ; sc:url "http://pmbd.genome-mining.cn/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3512, edam:topic_3520 ; sc:citation ; sc:description "PMD-FDR is a Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits." ; sc:featureList edam:operation_2929, edam:operation_3216, edam:operation_3644, edam:operation_3645, edam:operation_3649 ; sc:name "PMD-FDR" ; sc:url "https://github.com/slhubler/PMD-FDR-for-paper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2830 ; sc:citation ; sc:description "High-dimensional Bayesian phenotype classification and model selection using genomic predictors." ; sc:featureList edam:operation_3659 ; sc:name "PMMLogit" ; sc:url "https://github.com/v-panchal/PMML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2640, edam:topic_3421 ; sc:citation , "pmcid:PMC6954125", "pubmed:31073852" ; sc:description "Patient Navigation Barriers and Outcomes Tool™ (PN-BOT™), a new information management and reporting tool for oncology PN programs." ; sc:featureList edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PN-BOTTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bit.ly/AboutPNBOT" ; biotools:primaryContact "Mandi Pratt-Chapman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0625, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC6901264", "pubmed:31765387" ; sc:description "The PNC package is to identify personalized driver genes of an individual patient by using network control principle ." ; sc:featureList edam:operation_0277, edam:operation_2454, edam:operation_3223, edam:operation_3439, edam:operation_3463 ; sc:name "PNC" ; sc:url "https://github.com/NWPU-903PR/PNC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3050, edam:topic_3306, edam:topic_3474 ; sc:citation ; sc:description "PNV is an assessment of Machine Learning algorithms for estimating land potential." ; sc:featureList edam:operation_2429, edam:operation_3431, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "PNV" ; sc:url "https://github.com/envirometrix/PNVmaps" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3292, edam:topic_3855 ; sc:citation , "pubmed:30945242" ; sc:description "Interactive visual environment for rule-based modelling of biochemical systems." ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PORGY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://porgy.labri.fr/" ; biotools:primaryContact "Bruno Pinaud", "Guy Melancon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_2275 ; sc:citation , "pubmed:31535472" ; sc: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." ; sc:featureList edam:operation_0394, edam:operation_2492, edam:operation_3899 ; sc:name "PPCheck" ; sc:url "http://caps.ncbs.res.in/ppcheck/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0602, edam:topic_2640, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC6842548", "pubmed:31706268" ; sc:description "Genome-wide prediction and prioritization of human aging genes by data fusion." ; sc:featureList edam:operation_2454, edam:operation_3439, edam:operation_3501 ; sc:name "PPHAGE" ; sc:url "https://cbb.ut.ac.ir/pphage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0218 ; sc:citation , "pubmed:30521143" ; sc:description "Tool for extracting comprehensive protein-protein interaction information." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PPICurator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ppicurator.hupo.org.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0769, edam:topic_3810 ; sc:citation , "pubmed:31529041" ; sc:description "PPNID: a manually curated reference database and identification tool for plant-parasitic nematode." ; sc:license "GPL-3.0" ; sc:name "PPNID" ; sc:softwareHelp ; sc:url "https://github.com/xueqing4083/PPNID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3796 ; sc:citation ; sc:description """A Software Platform for Facilitating Population Genomic Analyses. Installation — PPP 0.1.1 documentation. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_0335, edam:operation_3435 ; sc:name "PPP" ; sc:url "https://ppp.readthedocs.io/en/latest/PPP_pages/install.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_3382, edam:topic_3473 ; sc:citation , "pmcid:PMC6819326", "pubmed:31664891" ; sc: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""" ; sc:featureList edam:operation_3096, edam:operation_3280, edam:operation_3625, edam:operation_3778 ; sc:name "PPR-SSM" ; sc:url "https://github.com/lasigeBioTM/PPRSSM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0601, edam:topic_3474 ; sc:citation , "pubmed:31412138" ; sc: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" ; sc:featureList edam:operation_0417 ; sc:name "PPSBoost" ; sc:url "http://cse.iitkgp.ac.in/~pralay/resources/PPSBoost/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3360 ; sc:citation , "pmcid:PMC6460848", "pubmed:31093546" ; sc:description "Novel method for interrogating receiver operating characteristic curves for assessing prognostic tests." ; sc:featureList edam:operation_0337, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PPV NPV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://d4ta.link/ppvnpv/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0623, edam:topic_3174, edam:topic_3305 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3797, edam:operation_3891 ; sc:name "PPanGGOLiN" ; sc:url "https://github.com/labgem/PPanGGOLiN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3305 ; sc:citation , "pubmed:31724381" ; sc:description "PQStat is an application which enables users to carry out a statistical data analysis in a simple and accurate way." ; sc:featureList edam:operation_3432, edam:operation_3658, edam:operation_3891 ; sc:name "PQStat" ; sc:url "http://www.pqstat.pl/en" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0868 ; sc:encodingFormat edam:format_1929 ; sc:name "Profile-profile alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:author ; sc: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." ; sc:featureList edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PRALINE 2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.0.0", "1.1.0" ; sc:url "https://github.com/ibivu/PRALINE" ; biotools:primaryContact "Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "Pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments." ; sc:featureList edam:operation_0264, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PRAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://bioconductor.org/packages/pram" ; biotools:primaryContact "Peng Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC6716675", "pubmed:31425505" ; sc: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" ; sc:featureList edam:operation_3222, edam:operation_3901, edam:operation_3902 ; sc:name "PRAS" ; sc:url "https://github.com/ouyang-lab/PRAS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2331 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC6602504", "pubmed:31143927" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2423, edam:operation_2990 ; sc:name "PRECOG: Predicting coupling probabilities of G-protein coupled receptors" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.1" ; sc:url "http://precog.russelllab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0623, edam:topic_0749, edam:topic_0820, edam:topic_2814 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_0303, edam:operation_0476, edam:operation_3214 ; sc:name "PRIGSA2" ; sc:url "http://bioinf.iiit.ac.in/PRIGSA2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3518, edam:topic_3519, edam:topic_3673 ; sc:citation , "pmcid:PMC6917790", "pubmed:31848453" ; sc:description "PRIMEval is a tool for optimization and screening of multiplex oligonucleotide assays." ; sc:featureList edam:operation_2419, edam:operation_2428, edam:operation_3198 ; sc:license "MIT" ; sc:name "PRIMEval" ; sc:url "https://primeval.ait.ac.at" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3263, edam:topic_3325 ; sc:citation , "pmcid:PMC5860394", "pubmed:28065902" ; sc:description "Privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PRINCESS" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/achenfengb/PRINCESS_opensource" ; biotools:primaryContact "Feng Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6612819", "pubmed:31510697" ; sc: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" ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3629 ; sc:license "MIT" ; sc:name "PRISM" ; sc:url "https://github.com/dohlee/prism" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:author ; sc:citation , "pubmed:31051038" ; sc:description "Large-scale prediction of binding affinity in protein-small ligand complexes." ; sc:featureList edam:operation_0272, edam:operation_0482, edam:operation_2492 ; sc:funder "European H2020 e-Infrastructure grant, BioExcel, grant no. 675728", "European H2020 e-Infrastructure grant, BioExcel, grant no. 823830", "European H2020 e-Infrastructure grant, EOSC-Hub, grant no.777536" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PRODIGY-LIG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider , "University of Utrecht" ; sc:softwareHelp , ; sc:url "http://milou.science.uu.nl/services/PRODIGY-LIG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0196, edam:topic_1317, edam:topic_2828 ; sc:citation , "pmcid:PMC9186318", "pubmed:31141126" ; sc: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." ; sc:featureList edam:operation_0321 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PRODIGY-CRYSTAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bianca.science.uu.nl/prodigy/cryst" ; biotools:primaryContact , "Anna Vangone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3360 ; sc:citation ; sc:description "PROMO (Profiler of Multi-Omics data) - interactive tool for analyzing clinically-labeled multi-omic cancer datasets." ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PROMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://acgt.cs.tau.ac.il/promo/" ; biotools:primaryContact "Dvir Netanely", "Ron Shamir" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_0780, edam:topic_3295 ; sc:citation , "pmcid:PMC6891001", "pubmed:31796964" ; sc: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.""" ; sc:featureList edam:operation_1781, edam:operation_3083, edam:operation_3207, edam:operation_3792 ; sc:name "PRP" ; sc:url "https://scbb.ihbt.res.in/PRP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3400, edam:topic_3473, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0267, edam:operation_0416, edam:operation_2489 ; sc:name "PRRpred" ; sc:url "http://webs.iiitd.edu.in/raghava/prrpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3298, edam:topic_3416, edam:topic_3517 ; sc:citation ; sc:description "Atlas of polygenic burden associations across the human phenome." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mrcieu.mrsoftware.org/PRS_atlas" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3710, edam:format_3712 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:encodingFormat edam:format_3752 ; sc:name "Quality control report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc: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.""" ; sc:featureList edam:operation_3635 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "PReMiS" ; sc:operatingSystem "Windows" ; sc:url "https://promega.com/resources/software-firmware/other/6x5-premis-software-download/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6534809", "pubmed:31127811" ; sc:description "Photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PS-Plant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/g2-bernotas/PS-Plant-Framework" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3534 ; sc:citation ; sc:description "Protein Structural Class Prediction." ; sc:featureList edam:operation_0474, edam:operation_0482, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PSCP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://brl.uiu.ac.bd/PL/" ; biotools:primaryContact "Swakkhar Shatabda​" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6901072", "pubmed:31135034" ; sc:description "Splicing-detection method for short-read and long-read RNA-seq analysis." ; sc:featureList edam:operation_3680, edam:operation_3798, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PSI-Sigma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wososa/PSI-Sigma" ; biotools:primaryContact "Kuan-Ting Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC6612829", "pubmed:31510650" ; sc:description "Fully-sensitive seed finding in sequence graphs using a hybrid index | Graph REad Mapper (C++ implementation) | Google protocol buffer >= v3.0.0" ; sc:featureList edam:operation_0249, edam:operation_0524, edam:operation_3211 ; sc:license "MIT" ; sc:name "PSI" ; sc:url "https://github.com/cartoonist/psi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2640, edam:topic_2885, edam:topic_3489, edam:topic_3810 ; sc:citation , "pubmed:31599098" ; sc: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""" ; sc:featureList edam:operation_0237, edam:operation_0308, edam:operation_2421, edam:operation_3196 ; sc:license "MIT" ; sc:name "PSMD" ; sc:url "http://big.cdu.edu.cn/psmd/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_3464 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:30994888" ; sc:description "Prediction of FUS-like phase separation proteins" ; sc:featureList edam:operation_3092 ; sc:name "PSPer" ; sc:url "http://bio2byte.com/psp/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3170 ; sc:citation , "pmcid:PMC6307140", "pubmed:30587128" ; sc:description "Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PSRN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://syslab5.nchu.edu.tw/" ; biotools:primaryContact "Systems Biology Lab, National Chung Hsing University" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6895799", "pubmed:31717904" ; sc:description "PSSRdt is a novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data." ; sc:featureList edam:operation_0237, edam:operation_0308, edam:operation_0524, edam:operation_3196, edam:operation_3258 ; sc:name "PSSRdt" ; sc:url "https://github.com/PSSRdt/program" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0601, edam:topic_3295, edam:topic_3520 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_3755, edam:operation_3799 ; sc:name "PTM-CrossTalkMapper" ; sc:url "https://github.com/veitveit/CrossTalkMapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC6555389", "pubmed:31198645" ; sc:description "R package for PTM site localization and motif extraction from proteomic datasets." ; sc:featureList edam:operation_0335, edam:operation_0417, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PTMphinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/jmwozniak/PTMphinder" ; biotools:primaryContact "Jacob M. Wozniak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0203, edam:topic_0659, edam:topic_2640 ; sc:citation "pubmed:31797620" ; sc:description "PTR is an approach to identify and explore Post Transcriptional Regulatory mechanisms using proteogenomics." ; sc:featureList edam:operation_3431 ; sc:name "PTR" ; sc:url "https://github.com/arunima2/PTRE_PSB_2020" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3403, edam:topic_3421, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "PTRBC" ; sc:url "https://github.com/niu-lab/PTRBC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3170, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc: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]""" ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3659, edam:operation_3664, edam:operation_3891 ; sc:name "PTWAS" ; sc:url "https://github.com/xqwen/ptwas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3314 ; sc:citation , "pmcid:PMC6688265", "pubmed:31399858" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3431 ; sc:name "PUG-View" ; sc:url "https://pubchemdocs.ncbi.nlm.nih.gov/pug-view" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0780, edam:topic_2259, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC6812194", "pubmed:31667383" ; sc: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""" ; sc:featureList edam:operation_3359, edam:operation_3432 ; sc:name "PVCTools" ; sc:url "https://github.com/CNaibon/PVCTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3337, edam:topic_3577 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:name "PXS" ; sc:url "http://apps.chiragjpgroup.org/pxs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2269, edam:topic_3056 ; sc:citation ; sc: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:""" ; sc:featureList edam:operation_3658, edam:operation_3659, edam:operation_3664 ; sc:name "PYLFIRE" ; sc:url "https://github.com/elfi-dev/zoo/tree/master/pylfire" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC6899669", "pubmed:31389023" ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_3660, edam:operation_3745 ; sc:license "Apache-2.0" ; sc:name "PYRO-NN" ; sc:url "https://github.com/csyben/PYRO-NN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC6933905", "pubmed:31878881" ; sc:description """Fast and scalable processing of whole exome and targeted sequencing data. PaCBAM_Performance_analysis – Google Drev""" ; sc:featureList edam:operation_2422, edam:operation_3227, edam:operation_3695 ; sc:name "PaCBAM" ; sc:url "http://bcglab.cibio.unitn.it/PaCBAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3315, edam:topic_3512 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0495, edam:operation_3196, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PaSGAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://alurulab.cc.gatech.edu/PaSGAL" ; biotools:primaryContact "Haowen Zhang", "Srinivas Aluru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3474 ; sc:citation , "pmcid:PMC6746931", "pubmed:31551749" ; sc: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" ; sc:name "PaWFE" ; sc:url "http://ninapro.hevs.ch/node/229" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3168 ; sc:citation , "pmcid:PMC6588853", "pubmed:31226925" ; sc:description "Sequencing simulator for PacBio sequencing with a high fidelity." ; sc:featureList edam:operation_0524, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PaSS" ; sc:operatingSystem "Linux" ; sc:url "http://cgm.sjtu.edu.cn/PaSS/" ; biotools:primaryContact "Wenmin Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3407 ; sc:citation ; sc: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." ; sc:isAccessibleForFree true ; sc:name "PanGeneHome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pangenehome.lmge.uca.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_0621, edam:topic_0780, edam:topic_3174 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0524, edam:operation_3182, edam:operation_3198, edam:operation_3472 ; sc:name "PanTools" ; sc:url "https://git.wur.nl/bioinformatics/pantools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3292, edam:topic_3315, edam:topic_3474 ; sc:citation ; sc: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).""" ; sc:featureList edam:operation_0335, edam:operation_3431, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "Pandoc Scholar" ; sc:softwareHelp ; sc:url "https://github.com/pandoc-scholar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6742414", "pubmed:31469823" ; sc: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)" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:license "MIT" ; sc:name "PanoView" ; sc:url "https://github.com/mhu10/scPanoView" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3444 ; sc:citation , "pmcid:PMC6267067", "pubmed:30497372" ; sc:description "Time-course network medicine platform integrating molecular assays and pathophenotypic data." ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PanoromiX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinfo-abcc.ncifcrf.gov/panoromics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3303, edam:topic_3304 ; sc:citation , "pmcid:PMC6345070", "pubmed:30678631" ; sc:description "Open-source web-based search and metadata organization of scientific literature." ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "PaperBot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://paperbot.ai/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3068 ; sc:citation , "pmcid:PMC6513153", "pubmed:30321303" ; sc:description "Tool for massively parallel model selection and phylogenetic tree inference on thousands of genes." ; sc:featureList edam:operation_0325, edam:operation_0552, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ParGenes" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/BenoitMorel/ParGenes" ; biotools:primaryContact "Benoit Morel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC6923905", "pubmed:31856721" ; sc: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.""" ; sc:featureList edam:operation_0524, edam:operation_3195, edam:operation_3472 ; sc:name "ParLECH" ; sc:url "https://github.com/arghyakusumdas/GenomicErrorCorrection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation ; sc:description "Graph realignment tools for structural variants." ; sc:featureList edam:operation_3196, edam:operation_3228, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Paragraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Illumina/paragraph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Paraload is an original utility which ensures job distribution between thousands of processors, according to the type of the data to be analysed." ; sc:name "Paraload" ; sc:url "ftp://doua.prabi.fr/pub/logiciel/paraload" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation , "pmcid:PMC6735705", "pubmed:31127303" ; sc: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." ; sc:featureList edam:operation_0567, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PastML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pastml.pasteur.fr/" ; biotools:primaryContact "Anna Zhukova", "Olivier Gascuel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3293, edam:topic_3305 ; sc:citation ; sc:description "User-friendly interface to explore evolutionary scenarios." ; sc:featureList edam:operation_0545, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PastView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.pastview.org" ; biotools:primaryContact "Francois Chevenet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Catalogue of public databases for molecular typing and microbial genome diversity." ; sc:featureList edam:operation_3840 ; sc:name "Pasteur MLST" ; sc:url "https://pubmlst.org/databases.shtml" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein complex" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1957 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1401 ; sc:encodingFormat edam:format_3752 ; sc:name "Match reward score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_3534 ; sc:citation , , "pmcid:PMC6602448", "pubmed:28282119", "pubmed:31131411" ; sc:description "Identify structurally conserved regions at the protein surfaces." ; sc:featureList edam:operation_3666 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "PatchSearch" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PatchSearch" ; biotools:primaryContact "Frédéric Guyon", "Gautier Moroy", "Julien Rey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC8551608", "pubmed:34721010" ; sc: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." ; sc:featureList edam:operation_2423 ; sc:name "Path4Drug" ; sc:url "https://www.ebi.ac.uk/transqst/transqstWeb/DRUG_PATHWAY_RESOURCE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2229, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC6943071", "pubmed:31602464" ; sc: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""" ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_3083, edam:operation_3799 ; sc:name "PathBank" ; sc:url "http://www.pathbank.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "Efficient pan-cancer whole-slide image classification and outlier detection using convolutional neural networks." ; sc:featureList edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PathCNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sedab/PathCNN" ; biotools:primaryContact "Seda Bilaloglu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2640 ; sc:citation , "pubmed:31583640" ; sc: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).""" ; sc:featureList edam:operation_2495, edam:operation_3282, edam:operation_3439 ; sc:name "PathClass" ; sc:url "https://pathclass.compbio.sdu.dk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3377 ; sc:citation , "pmcid:PMC6821302", "pubmed:31114840" ; sc: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." ; sc:featureList edam:operation_3436, edam:operation_3439, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PathFXweb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.pathfxweb.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3474 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3891 ; sc:license "MIT" ; sc:name "PathFlowAI" ; sc:url "https://github.com/jlevy44/PathFlowAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6521546", "pubmed:31092193" ; sc: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." ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PathMe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://pathme.scai.fraunhofer.de/" ; biotools:primaryContact "Daniel Domingo-Fernández" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634 ; sc:citation ; sc: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" ; sc:license "GPL-3.0" ; sc:name "Pathfinder" ; sc:url "http://github.com/MatthewBCooke/Pathfinder" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:encodingFormat edam:format_3790 ; sc:name "Query script" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2331, edam:format_2376, edam:format_3261, edam:format_3464, edam:format_3752 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "SPARQL endpoint" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3307 ; sc:citation , "pmcid:PMC3013659", "pubmed:21071392" ; sc: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." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "PathwayCommons SPARQL endpoint" ; sc:softwareHelp ; sc:softwareVersion "11" ; sc:url "http://rdf.pathwaycommons.org/sparql/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:encodingFormat edam:format_2330 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1047 ; sc:encodingFormat edam:format_2330 ; sc:name "URI" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3261 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web service" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3307 ; sc:citation , "pmcid:PMC3013659", "pubmed:21071392" ; sc: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." ; sc:featureList edam:operation_2497 ; sc:isAccessibleForFree true ; sc:name "PathwayCommons web service API" ; sc:softwareHelp ; sc:softwareVersion "11" ; sc:url "https://www.pathwaycommons.org/pc2/home" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0602 ; sc:citation , "pmcid:PMC6667378", "pubmed:31363752" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_0417, edam:operation_0533 ; sc:name "PathwayMatcher" ; sc:softwareHelp , , ; sc:url "http://github.com/PathwayAnalysisPlatform/PathwayMatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407, edam:topic_3895 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3501, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Pathways Analyzer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://gitlab.com/lvasquezcr/pathways-analyzer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC6724669", "pubmed:31439692" ; sc: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" ; sc:featureList edam:operation_3208, edam:operation_3225, edam:operation_3227 ; sc:name "PeCanPIE" ; sc:url "https://pecan.stjude.cloud/variant/67664" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3510, edam:topic_3512 ; sc:citation , "pubmed:31393553" ; sc: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""" ; sc:featureList edam:operation_0267, edam:operation_0480 ; sc:name "PeNGaRoo" ; sc:url "http://pengaroo.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3295 ; sc:citation ; sc: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)." ; sc:featureList edam:operation_0238, edam:operation_3631, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "PeSA" ; sc:url "http://www.github.com/EmineTopcu/PeSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3314, edam:topic_3474 ; sc:citation , "pmcid:PMC6677017", "pubmed:31373570" ; sc: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" ; sc:featureList edam:operation_0417, edam:operation_0480, edam:operation_3891 ; sc:name "PeakProbe" ; sc:url "https://github.com/paulsmith638/PeakProbe.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "A mine with peanut data from Legume Information Systems (LIS) PeanutBase" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "PeanutMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/peanutmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3318, edam:topic_3518 ; sc:citation , "pmcid:PMC6944377", "pubmed:31860654" ; sc: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 -m -o --intf . 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""" ; sc:featureList edam:operation_0282, edam:operation_2944, edam:operation_3196, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "Ped-sim" ; sc:url "https://github.com/williamslab/ped-sim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3322, edam:topic_3407, edam:topic_3418 ; sc:citation , "pmcid:PMC6883068", "pubmed:31780760" ; sc: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)""" ; sc:featureList edam:operation_2429, edam:operation_3432, edam:operation_3659 ; sc:name "PedMap" ; sc:url "http://pedmap.nbscn.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31132275" ; sc:description "Software package for semi-automated processing of protein footprinting data." ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PepFoot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jbellamycarter/pepfoot" ; biotools:primaryContact "Jedd Bellamy-Carter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0820, edam:topic_2275, edam:topic_3542 ; sc:citation , "pmcid:PMC7447090", "pubmed:31793016" ; sc:description "PepPro is a Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking." ; sc:featureList edam:operation_0480, edam:operation_0482, edam:operation_2488, edam:operation_3899 ; sc:name "PepPro" ; sc:url "http://zoulab.dalton.missouri.edu/PepPro_benchmark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6396417", "pubmed:30610011" ; sc:description "Peptide-centric search engine for novel peptide identification and validation." ; sc:featureList edam:operation_3647, edam:operation_3649, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "PepQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pepquery.org/" ; biotools:primaryContact "Gitter", "PepQuery Google Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_2275 ; sc:citation , "pubmed:31441995" ; sc: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.""" ; sc:featureList edam:operation_0418, edam:operation_0482, edam:operation_3899 ; sc:license "GPL-3.0" ; sc:name "PepVis" ; sc:url "https://github.com/inpacdb/PepVis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3512, edam:topic_3520 ; sc:citation , "pmcid:PMC6337836", "pubmed:30654742" ; sc:description "Proteogenomics workflow for the expert annotation of eukaryotic genomes." ; sc:featureList edam:operation_2929, edam:operation_3643, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Peptimapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://hub.docker.com/r/dockerprotim/peptimapper/" ; biotools:primaryContact "L. Guillot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0621, edam:topic_0736, edam:topic_0820, edam:topic_3068 ; sc:citation , "pubmed:31629694" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0303, edam:operation_2492, edam:operation_3431 ; sc:name "PerMemDB" ; sc:softwareHelp ; sc:url "http://bioinformatics.biol.uoa.gr/db=permemdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation , "pmcid:PMC6602478", "pubmed:31106365" ; sc:description "Web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Pergola-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pergola.crg.eu/" ; biotools:primaryContact "Cedric Notredame", "Julia Ponomarenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0420, edam:operation_1812, edam:operation_3501 ; sc:name "PertInInt" ; sc:url "http://github.com/Singh-Lab/PertInInt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199 ; sc:citation , "pmcid:PMC6836735", "pubmed:31628256" ; sc: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)." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3233 ; sc:name "PhISCS" ; sc:url "https://github.com/sfu-compbio/PhISCS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0659, edam:topic_0736, edam:topic_2229, edam:topic_3512 ; sc:citation , "pubmed:31612960" ; sc: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." ; sc:featureList edam:operation_0361, edam:operation_2422, edam:operation_3216, edam:operation_3454 ; sc:name "PhaSePro" ; sc:url "https://phasepro.elte.hu" ; biotools:primaryContact "Rita Pancsa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0121, edam:topic_2229, edam:topic_3068 ; sc:citation , "pmcid:PMC6943039", "pubmed:31584089" ; sc: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.""" ; sc:featureList edam:operation_2421, edam:operation_3454, edam:operation_3767 ; sc:name "PhaSepDB" ; sc:url "http://db.phasep.pro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:31359029" ; sc:description "PhagePromoter is a python tool that predicts promoter sequences in phage genomes, using machine learning models." ; sc:isAccessibleForFree true ; sc:name "PhagePromoter" ; sc:url "https://www.bit.do/phagepromoter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2830, edam:topic_3047, edam:topic_3168, edam:topic_3957 ; sc:citation , "pubmed:31712799" ; sc:description "PhageXress us a Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing." ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3795 ; sc:name "PhageXpress" ; sc:url "https://github.com/mdcao/phagexpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3375, edam:topic_3377, edam:topic_3379 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0277, edam:operation_3223, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "PharmOmics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mergeomics.research.idre.ucla.edu/PharmOmics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0632, edam:topic_3047, edam:topic_3336 ; sc:citation , "pmcid:PMC6933858", "pubmed:31576621" ; sc:description "Pharmacophore is a tool for modeling and hit identification based on druggability simulations." ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3891 ; sc:name "Pharmmaker" ; sc:softwareHelp ; sc:url "http://prody.csb.pitt.edu/pharmmaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0153, edam:topic_2885, edam:topic_3298, edam:topic_3517 ; sc:citation , "pubmed:31860083" ; sc:description "PheGWAS is a three-dimensional approach to dynamically visualize GWAS across multiple phenotypes. It does interactive 3D visualization on many variants many phenotypes" ; sc:featureList edam:operation_0337 ; sc:name "PheGWAS" ; sc:url "https://github.com/georgeg0/PheGWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3422 ; sc:citation , , "pmcid:PMC7736922", "pubmed:31369862", "pubmed:35995107" ; sc:description "PheValuator is a phenotype algorithm evaluator." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PheValuator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/OHDSI/PheValuator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3325 ; sc:citation , "pubmed:25086502" ; sc:description "Combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "Phen-Gen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://phen-gen.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_3325, edam:topic_3512 ; sc:citation ; sc: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." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3226 ; sc:license "MIT" ; sc:name "Phen2Gene" ; sc:url "https://phen2gene.wglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3517 ; sc:citation , "pmcid:PMC5507752", "pubmed:28079902" ; sc:description "Web catalog of high-priority measures for consideration and inclusion in biomedical and epidemiologic research." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "PhenX Toolkit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.phenxtoolkit.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_0780, edam:topic_3382, edam:topic_3810 ; sc:citation , "pmcid:PMC6805894", "pubmed:31641140" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3435 ; sc:license "AGPL-3.0" ; sc:name "PhenoCam" ; sc:softwareHelp ; sc:url "https://phenocam.sr.unh.edu/webcam/gallery/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3325, edam:topic_3335, edam:topic_3577 ; sc:citation , "pmcid:PMC5785853", "pubmed:29370821" ; sc:description "Database for phenotypic characterization of rare cardiac diseases." ; sc:featureList edam:operation_2422, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "PhenoDis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mips.helmholtz-muenchen.de/phenodis/" ; biotools:primaryContact "Dr. Andreas Ruepp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6426163", "pubmed:30937222" ; sc:description "Software package for the prediction of flowering phenology." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhenoForecaster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/isaacWpark/PhenoForecaster" ; biotools:primaryContact "Isaac W Park" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3050, edam:topic_3697 ; sc:citation ; sc:description "Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity." ; sc:featureList edam:operation_3431, edam:operation_3557, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhenoGMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/prubbens/PhenoGMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3517 ; sc:citation ; sc:description "Gene/disease prioritization tool that utilizes heterogeneous gene disease network." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PhenoGeneRanker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bozdaglab/PhenoGeneRanker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3298 ; sc:citation , "pmcid:PMC6377398", "pubmed:30535405" ; sc: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." ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhenoMeNal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://portal.phenomenal-h2020.eu/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0621, edam:topic_0625, edam:topic_3295, edam:topic_3574 ; sc:citation , "pmcid:PMC7145690", "pubmed:31642469" ; sc:description "PhenoModifier is a genetic modifier database for elucidating the genetic basis of human phenotypic variation." ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3799 ; sc:name "PhenoModifier" ; sc:url "https://www.biosino.org/PhenoModifier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3295, edam:topic_3298 ; sc:citation , "pmcid:PMC6853652", "pubmed:31233103" ; sc:description "Database of human genotype-phenotype associations." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhenoScanner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://www.phenoscanner.medschl.cam.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3298, edam:topic_3308, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description "PhenomeXcan is a tool for mapping the genome to the phenome through the transcriptome." ; sc:featureList edam:operation_2429 ; sc:license "MIT" ; sc:name "PhenomeXcan" ; sc:url "http://apps.hakyimlab.org/phenomexcan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3325 ; sc:citation , "pubmed:28334266" ; sc:description "Open platform for harmonization and analysis of genetic and phenotypic data." ; sc:featureList edam:operation_3226, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Phenopolis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://phenopolis.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0089, edam:topic_0625, edam:topic_2275, edam:topic_3067 ; sc:citation , "pmcid:PMC7672696", "pubmed:31596473" ; sc:description "Phenoscape is a Logical Model of Homology for Comparative Biology." ; sc:featureList edam:operation_0310, edam:operation_0477, edam:operation_2421 ; sc:license "MIT" ; sc:name "Phenoscape" ; sc:softwareHelp ; sc:url "http://phenoscape.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0621, edam:topic_0749, edam:topic_3170 ; sc:citation ; sc:description "PhiMRF is an R package for Poisson Hierarchical Markov Random Field model for analysis of spatial dependency on count data." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3800 ; sc:license "GPL-2.0" ; sc:name "PhiMRF" ; sc:url "https://github.com/ashleyzhou972/PhiMRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3489 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2422 ; sc:name "PhilDB" ; sc:softwareHelp ; sc:url "http://github.com/amacd31/phildb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC6753174", "pubmed:31572139" ; sc: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." ; sc:featureList edam:operation_2428, edam:operation_3659, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "Phobos" ; sc:url "https://github.com/Felippe-espinelli/Phobos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3473, edam:topic_3520 ; sc:citation ; sc:description "Phoenix Enhancer is an online service/tool for proteomics data mining using clustered spectra." ; sc:featureList edam:operation_3432, edam:operation_3631, edam:operation_3767 ; sc:name "Phoenix Enhancer" ; sc:url "http://enhancer.ncpsb.org.cn/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC7868059", "pubmed:31410451" ; sc: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." ; sc:featureList edam:operation_0417, edam:operation_2492, edam:operation_3639 ; sc:name "Phosphoproteome Prediction" ; sc:url "https://github.com/GuanLab/phosphoproteome_prediction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0194, edam:topic_0196, edam:topic_0621, edam:topic_3293 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0546, edam:operation_3359, edam:operation_3478, edam:operation_3745 ; sc:license "BSD-3-Clause" ; sc:name "PhyChro" ; sc:url "http://www.lcqb.upmc.fr/phychro2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "PhyDL (Phylogenetics by Deep Learning) is a deep learning predictor for phylogenetic reconstruction." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0551, edam:operation_0567 ; sc:name "PhyDL" ; sc:url "https://gitlab.com/ztzou/phydl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3293 ; sc:citation , "pmcid:PMC5850602", "pubmed:28472384" ; sc:description "Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SMS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.8.4" ; sc:url "http://www.atgc-montpellier.fr/sms/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0602, edam:topic_3676 ; sc:citation "pubmed:31797599" ; sc: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).""" ; sc:featureList edam:operation_0323, edam:operation_3435 ; sc:name "PhySigs" ; sc:url "https://github.com/elkebir-group/PhySigs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0659, edam:topic_0769, edam:topic_3293 ; sc:citation , "pmcid:PMC6889546", "pubmed:31791235" ; sc:description "PhySpeTree is an automated pipeline for reconstructing phylogenetic species trees." ; sc:featureList edam:operation_0325, edam:operation_0326, edam:operation_0327, edam:operation_0544, edam:operation_3478 ; sc:name "PhySpeTree" ; sc:url "https://pypi.org/project/PhySpeTree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC6785678", "pubmed:31616568" ; sc: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" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3196, edam:operation_3432 ; sc:license "LGPL-3.0" ; sc:name "Phydelity" ; sc:url "https://github.com/alvinxhan/Phydelity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3305 ; sc:citation , "pmcid:PMC6859488", "pubmed:31512371" ; sc:description "This tool is a gene database for Phyllosticta citricarpa and sister species." ; sc:featureList edam:operation_3216 ; sc:name "Phyllosticta citricarpa" ; sc:url "https://genome.jgi.doe.gov/Phyllosticta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3512, edam:topic_3517 ; sc:citation , "pmcid:PMC6886504", "pubmed:31537640" ; sc: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." ; sc:featureList edam:operation_0436, edam:operation_3192, edam:operation_3216 ; sc:license "AGPL-3.0" ; sc:name "PhyloCSF" ; sc:url "https://github.com/mlin/PhyloCSF/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3293, edam:topic_3308, edam:topic_3837 ; sc:citation , "pmcid:PMC7703773", "pubmed:31647547" ; sc: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" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_3258, edam:operation_3460, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "PhyloMagnet" ; sc:softwareHelp ; sc:url "http://github.com/maxemil/PhyloMagnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0602, edam:topic_3293 ; sc:citation , "pmcid:PMC6612858", "pubmed:31510688" ; sc:description "PhyloNet is a tool that applies a divide-and-conquer method for scalable phylogenetic network inference from multilocus data." ; sc:featureList edam:operation_0547, edam:operation_3501, edam:operation_3562 ; sc:name "PhyloNet" ; sc:url "https://bioinfocs.rice.edu/PhyloNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3500 ; sc:citation , "pmcid:PMC6657734", "pubmed:31062861" ; sc:description "A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes." ; sc:featureList edam:operation_3478, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhyloToL" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Katzlab/PhyloTOL" ; biotools:primaryContact "L. A. Katz", "Mario Cerón-Romero" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_3120 ; sc:citation , "pmcid:PMC6597944", "pubmed:31075275" ; sc:description "Dynamic web application that enables the exploration and mapping of genetic variants onto experimental and predicted structures of proteins and protein complexes." ; sc:featureList edam:operation_0302, edam:operation_0331, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhyreRisk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://phyrerisk.bc.ic.ac.uk" ; biotools:primaryContact "Alessia David" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0749, edam:topic_3318, edam:topic_3512 ; 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For example, it can be used to classify the contigs in a (metagenomic) assembly." ; sc:featureList edam:operation_0310, edam:operation_2995, edam:operation_3472 ; sc:license "MIT" ; sc:name "PlasClass" ; sc:url "https://github.com/Shamir-Lab/PlasClass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0632, edam:topic_3673 ; sc:citation , "pubmed:31584170" ; sc:description "PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS)." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3840 ; sc:name "PlasmidFinder" ; sc:url "https://cge.cbs.dtu.dk/services/PlasmidFinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0780, edam:topic_3474 ; sc:citation , "pubmed:31120045" ; sc:description "Automatised pharmacophoric deconvolution of plant extracts." ; sc:featureList edam:operation_0337, edam:operation_3501, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "CECILL-1.0" ; sc:name "Plasmodesma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://plasmodesma.igbmc.science" ; biotools:primaryContact "Marc-André Delsuc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3308 ; sc:author , ; sc:citation , , "pubmed:31235882" ; sc:description "Protein-Level ASSembler (PLASS): sensitive and precise protein assembler" ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Plass" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1-2e0ef", "2-c7e35", "3-764a3", "4-687d7" ; sc:url "https://plass.mmseqs.com" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3293, edam:topic_3512 ; sc:citation , "pmcid:PMC6528300", "pubmed:31139240" ; sc:description "Software package for rapid, accurate, and flexible batch annotation of plastomes." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Plastid Genome Annotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/quxiaojian/PGA" ; biotools:primaryContact "Xiao-Jian Qu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0798 ; sc:author ; sc:citation , "pmcid:PMC7660248", "pubmed:32579097" ; sc:description "Identification and characterization of bacterial plasmid contigs from short-read draft assemblies." ; sc:featureList edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Platon" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.6" ; sc:url "https://github.com/oschwengers/platon" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634 ; sc:citation , "pmcid:PMC6792104", "pubmed:30865284" ; sc:description "Web-based visualization tool for exploring pleiotropy across complex traits." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PleioNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pleionet.com/" ; biotools:primaryContact "X. R. Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3304, edam:topic_3382 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3798 ; sc:name "PlotTwist" ; sc:url "https://huygens.science.uva.nl/PlotTwist" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3474, edam:topic_3500, edam:topic_3520 ; sc:citation , "pubmed:31735706" ; sc:description "MHC-I epitope presentation prediction based on transfer learning." ; sc:featureList edam:operation_0252, edam:operation_0416 ; sc:name "Pluto" ; sc:url "https://github.com/weipenegHU/Pluto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0780, edam:topic_3293, edam:topic_3512 ; sc:citation , "pmcid:PMC6943064", "pubmed:31602478" ; sc:description "PmiREN is a comprehensive encyclopedia of plant miRNAs." ; sc:featureList edam:operation_0463, edam:operation_2422, edam:operation_3192, edam:operation_3792 ; sc:name "PmiREN" ; sc:url "http://www.pmiren.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0218, edam:topic_3474 ; sc:author "Shubham Vishnoi" ; sc:citation , "pubmed:31483930" ; sc: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." ; sc:featureList edam:operation_2423, edam:operation_2426, edam:operation_2930 ; sc:name "PnGT" ; sc:softwareHelp ; sc:url "http://14.139.57.41/pngt/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3174, edam:topic_3519, edam:topic_3577, edam:topic_3837 ; sc:citation , "pubmed:31758176" ; sc:description "Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens." ; sc:featureList edam:operation_0337, edam:operation_3200, edam:operation_3431 ; sc:license "MIT" ; sc:name "Pneumocystis" ; sc:url "https://github.com/Yiheng323/clinical_diagnosis_of_pneumocystis.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_0654, edam:topic_3517, edam:topic_3673 ; sc:citation , "pmcid:PMC6834686", "pubmed:31736907" ; sc: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." ; sc:featureList edam:operation_3202, edam:operation_3482, edam:operation_3695 ; sc:name "PointFinder" ; sc:url "http://bitbucket.org/genomicepidemiology/pointfinder_db" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0166, edam:topic_0209, edam:topic_3534 ; sc:citation ; sc:description "PointSite is a point cloud segmentation tool for identification of protein ligand binding atoms." ; sc:featureList edam:operation_0482, edam:operation_2575, edam:operation_3767 ; sc:name "PointSite" ; sc:url "https://github.com/PointSite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC7145510", "pubmed:31617559" ; sc: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.""" ; sc:featureList edam:operation_0363, edam:operation_0428, edam:operation_3208 ; sc:name "PolyASite" ; sc:url "https://polyasite.unibas.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3377 ; sc:citation , "pmcid:PMC5319934", "pubmed:28270862" ; sc:description "PolyPharmacology Browser (PPB) - Web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data" ; sc:featureList edam:operation_2489, edam:operation_2929, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "PPB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gdbtools.unibe.ch:8080/PPB/" ; biotools:primaryContact "Mahendra Awale", "Prof. Jean Louis Reymond" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3751, edam:format_3752 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3905 ; sc:encodingFormat edam:format_3604 ; sc:name "Histogram" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3932 ; sc:encodingFormat edam:format_3752 ; sc:name "Q-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3604 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3752 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation , "pmcid:PMC8015005", "pubmed:32424025" ; sc: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." ; sc:featureList edam:operation_3664, edam:operation_3741 ; sc:license "GPL-2.0" ; sc:name "PolySTest" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://computproteomics.bmb.sdu.dk/Apps/PolySTest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3325 ; sc:author "Sebastian Roskosch" ; sc:description "A tool for population level deletion calling from short paired-end sequence reads." ; sc:featureList edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PopDel" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.1.1" ; sc:url "https://github.com/kehrlab/PopDel" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_0769, edam:topic_2640 ; sc:citation ; sc: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\"""" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:name "PopInf" ; sc:url "https://github.com/SexChrLab/PopInf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:30321304" ; sc:description "Tool for linkage disequilibrium decay analysis based on variant call format files." ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PopLDdecay" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/BGI-shenzhen/PopLDdecay" ; biotools:primaryContact "Wei-Ming He" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3796, edam:topic_3810 ; sc:citation , "pmcid:PMC6668580", "pubmed:31095319" ; sc:description "Network-Based Web Resource for Exploring Population Structure." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PopNetD3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compsysbio.org/popnetd3" ; biotools:primaryContact "John Parkinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0659, edam:topic_2885, edam:topic_3056, edam:topic_3170 ; sc:citation , "pmcid:PMC6790967", "pubmed:31608947" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_0463, edam:operation_2421 ; sc:license "MIT" ; sc:name "PopTargs" ; sc:url "https://poptargs.essex.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3305, edam:topic_3517 ; sc:citation , "pmcid:PMC6973052", "pubmed:31659794" ; sc:description """The Parkinson's Disease Mendelian Randomization Research Portal. iPDGC PD MR Research Portal""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3659 ; sc:name "Portal" ; sc:url "https://pdgenetics.shinyapps.io/MRportal/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3542 ; sc:citation , , "pmcid:PMC6710256", "pubmed:31451723" ; sc:description "Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes" ; sc:featureList edam:operation_0267, edam:operation_0468, edam:operation_0469, edam:operation_0470 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Porter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "5" ; sc:url "http://distilldeep.ucd.ie/porter/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3542 ; sc:citation , , , "pmcid:PMC6710256", "pubmed:31451723" ; sc:description "Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes" ; sc:featureList edam:operation_0267, edam:operation_0468, edam:operation_0469, edam:operation_0470 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Porter5" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "5" ; sc:url "http://distilldeep.ucd.ie/porter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_2885, edam:topic_3517, edam:topic_3676 ; sc:citation , , "pubmed:33275856" ; sc: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.""" ; sc:featureList edam:operation_0484, edam:operation_2238, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "Potpourri" ; sc:url "https://github.com/gizemcaylak/Potpourri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31552639" ; sc: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" ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_3631 ; sc:name "PowerShell" ; sc:url "https://cpm.lumc.nl/yassene/powershell/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3304, edam:topic_3401 ; sc:citation , "pmcid:PMC6827337", "pubmed:31449248" ; sc: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)" ; sc:featureList edam:operation_3799 ; sc:name "PrAnCER" ; sc:url "https://github.com/hayleybounds/PrAnCER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3534 ; sc:citation , , "pmcid:PMC6091426", "pmcid:PMC6602436", "pubmed:30109435", "pubmed:31114880" ; sc:description "Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application." ; sc:featureList edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PrankWeb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://prankweb.cz/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:31710075" ; sc:description """Prediction of S-nitrosylation sites by integrating support vector machines and random forest. PreSNO is only available to academic users""" ; sc:featureList edam:operation_0417 ; sc:name "PreSNO" ; sc:url "http://kurata14.bio.kyutech.ac.jp/PreSNO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3912 ; sc:citation , "pubmed:31526842" ; sc: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" ; sc:name "Pred-BVP-Unb" ; sc:url "https://github.com/Muhammad-Arif-NUST/BVP_Pred_Unb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_0736, edam:topic_0820, edam:topic_3474 ; sc:citation , "pubmed:31821684" ; sc: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""" ; sc:featureList edam:operation_0269, edam:operation_0331, edam:operation_2241 ; sc:name "Pred-MutHTP" ; sc:url "https://www.iitm.ac.in/bioinfo/PredMutHTP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:citation , "pmcid:PMC6688581", "pubmed:31428122" ; sc: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" ; sc:featureList edam:operation_3659, edam:operation_3901, edam:operation_3902 ; sc:name "PredPRBA" ; sc:url "http://PredPRBA.denglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6744342", "pubmed:31070294" ; sc:description "Predicting the change of percent spliced in (delta-PSI or ) caused by genetic variants." ; sc:featureList edam:operation_0433, edam:operation_0446, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PredPSI-SVR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/chenkenbio/PredPSI-SVR" ; biotools:primaryContact "Huiying Zhao", "Yuedong Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0632, edam:topic_3050, edam:topic_3168, edam:topic_3500 ; sc:citation ; sc:description "PrimerMiner is an R package for the development and validation of DNA metabarcoding COI primers for aquatic invertebrates." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3200, edam:operation_3237 ; sc:name "PrimerMiner" ; sc:url "https://github.com/VascoElbrecht/PrimerMiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3375, edam:topic_3379 ; sc:citation , "pmcid:PMC6763777", "pubmed:31408580" ; sc: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" ; sc:featureList edam:operation_2436, edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "PriorCD" ; sc:url "https://cran.r-project.org/web/packages/PriorCD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0128, edam:topic_0154, edam:topic_0199 ; sc:citation , "pubmed:31713585" ; sc: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)""" ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3431 ; sc:name "ProAffiMuSeq" ; sc:url "https://web.iitm.ac.in/bioinfo2/proaffimuseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0152, edam:topic_0154, edam:topic_0199 ; sc:citation , "pmcid:PMC6943041", "pubmed:31598690" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_0570, edam:operation_3092 ; sc:name "ProCarbDB" ; sc:url "http://www.procarbdb.science/procarb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0252, edam:operation_3211 ; sc:name "ProGeo-neo" ; sc:url "https://github.com/kbvstmd/ProGeo-neo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_2640, edam:topic_3325 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0306, edam:operation_3778 ; sc:name "ProPheno" ; sc:url "http://propheno.cs.montana.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0602 ; sc:citation , "pmcid:PMC6602423", "pubmed:31114881" ; sc:description "Web-based application for exploration and analysis of protein structures using network formalism." ; sc:featureList edam:operation_0244, edam:operation_0272, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ProSNEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prosnex-tool.com" ; biotools:primaryContact , "Onur Sercinoglu", "Rasim Murat Aydinkal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6853706", "pubmed:31070745" ; sc:description "Ultra-fast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery." ; sc:featureList edam:operation_0238, edam:operation_0239 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ProSampler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zhengchangsulab/prosampler" ; biotools:primaryContact "Yang Li", "Zhengchang Su" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3336, edam:topic_3520 ; sc:citation , "pmcid:PMC6915695", "pubmed:31844049" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3629, edam:operation_3767 ; sc:name "ProTargetMiner" ; sc:url "http://protargetminer.genexplain.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0130, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC6830000", "pubmed:31684883" ; sc: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.""" ; sc:featureList edam:operation_0267, edam:operation_0331, edam:operation_2489, edam:operation_3659 ; sc:name "ProTstab" ; sc:url "http://structure.bmc.lu.se/ProTstab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3047 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3891 ; sc:name "ProcMod" ; sc:url "https://git.metabarcoding.org/lecasofts/ProcMod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3047 ; sc:citation , "pubmed:31678214" ; sc: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""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3461 ; sc:name "PromPDD" ; sc:url "http://www.immunoinformatics.net/PromPDD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0749, edam:topic_3398, edam:topic_3474 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0321, edam:operation_0440, edam:operation_3659 ; sc:name "PromoterPredict" ; sc:url "https://github.com/PromoterPredict" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3474, edam:topic_3557 ; sc:citation , "pmcid:PMC6602508", "pubmed:31114893" ; sc: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." ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Prophage Hunter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pro-hunter.bgi.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31133760" ; sc:description "Proteome-wide prediction of peptide tandem mass spectra by deep learning." ; sc:featureList edam:operation_3627, edam:operation_3649, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Prosit" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.proteomicsdb.org/prosit/" ; biotools:primaryContact "Prof. Dr. Bernhard Küster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_0194 ; sc:citation , "pmcid:PMC6436989", "pubmed:30535314" ; sc:description "Alignment-free phylogeny reconstruction based on whole-proteome sequences." ; sc:featureList edam:operation_0289, edam:operation_0557, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Prot-SpaM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jschellh/ProtSpaM" ; biotools:primaryContact "Jendrik Schellhorn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0218, edam:topic_3512 ; sc:citation , "pmcid:PMC6705771", "pubmed:31437145" ; sc: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" ; sc:featureList edam:operation_0306, edam:operation_2492 ; sc:name "ProtFus" ; sc:url "http://protfus.md.biu.ac.il/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0218, edam:topic_0601, edam:topic_0602 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0306, edam:operation_0310, edam:operation_0417, edam:operation_3436, edam:operation_3755 ; sc:license "BSD-2-Clause" ; sc:name "ProtMapper" ; sc:url "https://github.com/indralab/protmapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3068, edam:topic_3489, edam:topic_3534 ; sc:citation , "pmcid:PMC6813136", "pubmed:31650170" ; sc: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.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3896 ; sc:name "ProtMiscuity" ; sc:url "http://ufq.unq.edu.ar/protmiscuity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0203, edam:topic_3520 ; sc:citation , "pmcid:PMC6842221", "pubmed:31706265" ; sc:description """bypassing the imputation of missing values in differential expression analysis of proteomic data. Python package for differential abundance analysis of proteomics data""" ; sc:featureList edam:operation_2495, edam:operation_3557, edam:operation_3741 ; sc:license "GPL-3.0" ; sc:name "ProtRank" ; sc:url "https://github.com/8medom/ProtRank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3306, edam:topic_3474 ; sc:citation ; sc:description "Solubility from protein sequence prediction." ; sc:featureList edam:operation_0409, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Protein-sol" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://protein-sol.manchester.ac.uk/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0736 ; sc:citation , "pmcid:PMC9883681", "pubmed:31392322" ; sc: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" ; sc:featureList edam:operation_2428, edam:operation_3501 ; sc:name "Protein Homeostasis Database" ; sc:url "http://PHDB.switchlab.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1957 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1957 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1957 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2628 ; sc:encodingFormat edam:format_1957 ; sc:name "BioGRID interaction ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3464 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3510 ; sc:description "Integration of structural information with interactomics data." ; sc:featureList edam:operation_0276, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Proteo3Dnet" ; sc:softwareHelp ; sc:softwareVersion "1.02" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Proteo3Dnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3512, edam:topic_3520 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3644, edam:operation_3767, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "ProteoClade" ; sc:softwareHelp ; sc:url "http://github.com/HeldLab/ProteoClade" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_1775, edam:topic_2259, edam:topic_3360 ; sc:citation , , "pubmed:30852829", "pubmed:34236662" ; sc: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." ; sc:name "ProteoRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.2" ; sc:url "https://proteore.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3655 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_3520, edam:topic_3557 ; sc: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""" ; sc:featureList edam:operation_3631, edam:operation_3694, edam:operation_3695, edam:operation_3767, edam:operation_3802 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "ProteoWorker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.proteoworker.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2229, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC6901355", "pubmed:31690884" ; sc:description "ProteomeHD is an R script for creating a co-regulation map of the human proteome enables identification of protein functions." ; sc:featureList edam:operation_2495, edam:operation_3216, edam:operation_3638, edam:operation_3766, edam:operation_3767 ; sc:name "ProteomeHD" ; sc:url "http://www.proteomeHD.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "Web portal dedicated to the diatom Pseudo-nitzschia multistriata. A genome browser, a BLAST service and a download section are available." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Pseudo-nitzschia multistriata genome portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.szn.it/pmultistriata/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pmcid:PMC6797663", "pubmed:31432329" ; sc: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" ; sc:license "Apache-2.0" ; sc:name "PsiZ" ; sc:url "https://github.com/roads/psiz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0199, edam:topic_0749, edam:topic_3320 ; sc:citation , "pmcid:PMC6943783", "pubmed:31809863" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3227 ; sc:name "PsyMuKB" ; sc:url "http://psymukb.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3303, edam:topic_3473 ; sc:citation , "pmcid:PMC6602571", "pubmed:31114887" ; sc:description "Web-based application that provides computer-annotated biomedical concepts, such as genes and mutations, in PubMed citations and PMC full-text articles." ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PubTator Central" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.ncbi.nlm.nih.gov/research/pubtator/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0621, edam:topic_0634 ; sc:citation , "pmcid:PMC6323318", "pubmed:30624653" ; sc:description "Web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records." ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "PubTerm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioinformatica.mty.itesm.mx:8080/Biomatec/pubterm.html" ; biotools:primaryContact "Victor Trevino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0634, edam:topic_3308 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0224, edam:operation_2495, edam:operation_3258 ; sc:name "PulmonDB" ; sc:url "http://pulmondb.liigh.unam.mx/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0736, edam:topic_2830, edam:topic_3293 ; sc:citation ; sc:description "Punchline is a tool for identifying and comparing significant Pfam protein domain differences across draft whole genome sequences." ; sc:featureList edam:operation_0303, edam:operation_0310, edam:operation_2454 ; sc:name "Punchline" ; sc:url "https://github.com/LCrossman/punchline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0736 ; sc:citation ; sc:description "Efficient and accurate prediction of transmembrane topology from amino acid sequence only." ; sc:featureList edam:operation_0269, edam:operation_0468, edam:operation_2241 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PureseqTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pureseqtm.predmp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3385, edam:topic_3452 ; sc:citation , "pubmed:31086343" ; sc:description "Software tools for automated transmission electron microscopy." ; sc:featureList edam:operation_1812, edam:operation_3457, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Py-EM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://git.embl.de/schorb/pyem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_3047, edam:topic_3314 ; sc:citation , "pmcid:PMC6776882", "pubmed:31612127" ; sc:description """A Global Optimizer for Nanoclusters. Python program for aggregation and reaction. PyAR stands for "Python program for aggregation and reaction\"""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3436 ; sc:name "PyAR" ; sc:url "https://github.com/anooplab/pyar" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation ; sc:description "A command-line tool for analysis of big biological data sets for distributed HPC clusters." ; sc:featureList edam:operation_2939, edam:operation_2945, edam:operation_3432, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PyBDA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://pybda.readthedocs.io/en/latest/#" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "Algorithm for BSA-Seq data analysis." ; sc:featureList edam:operation_0484, edam:operation_3211, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PyBSASeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dblhlx/PyBSASeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2269 ; sc:citation , , "pmcid:PMC10060707", "pmcid:PMC6744527", "pubmed:31522114", "pubmed:34986226" ; sc: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)." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PyBioNetFit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bionetfit.nau.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pmcid:PMC6438028", "pubmed:30922213" ; sc:description "Python package for easy retrieval of biological data from heterogeneous sources." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Apache-1.0" ; sc:name "PyCellBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.7.1" ; sc:url "https://pypi.org/project/pycellbase/" ; biotools:primaryContact "Daniel Perez-Gil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc: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.""" ; sc:name "PyDFN3D" ; sc:url "https://github.com/BinWang0213/PyDFN3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0749, edam:topic_3512 ; sc:citation , "pmcid:PMC6761934", "pubmed:30850831" ; sc:description "Python-based effective feature generation tool for DNA, RNA and protein sequences." ; sc:featureList edam:operation_0440, edam:operation_3092, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PyFeat" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/mrzResearchArena/PyFeat/" ; biotools:primaryContact "Rafsanjani Muhammod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3489 ; sc:citation , "pmcid:PMC6842186", "pubmed:31703553" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3791 ; sc:license "Apache-2.0" ; sc:name "PyGMQL" ; sc:url "https://github.com/DEIB-GECO/PyGMQL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3372 ; sc:citation , "pmcid:PMC6894873", "pubmed:31805157" ; sc: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...)""" ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "PyLandStats" ; sc:softwareHelp ; sc:url "https://anaconda.org/conda-forge/pylandstats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3343, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6698780", "pubmed:31456680" ; sc: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" ; sc:featureList edam:operation_1816 ; sc:license "MIT" ; sc:name "PyParadigm" ; sc:softwareHelp ; sc:url "https://github.com/KnorrFG/pyparadigm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3325, edam:topic_3332 ; sc:citation , "pubmed:31742744" ; sc: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 .""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3799 ; sc:name "PyRETIS 2" ; sc:url "http://www.pyretis.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0769, edam:topic_2640, edam:topic_3384 ; sc:citation , "pmcid:PMC6916323", "pubmed:31580484" ; sc:description "PyRadiomics is an ontology-guided radiomics analysis workflow (O-RAW)." ; sc:featureList edam:operation_1812, edam:operation_3435, edam:operation_3443 ; sc:name "PyRadiomics" ; sc:url "https://github.com/Radiomics/pyradiomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , "pubmed:31373614" ; sc: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" ; sc:featureList edam:operation_3802 ; sc:license "MIT" ; sc:name "PyRanges" ; sc:url "https://pyranges.readthedocs.io/en/master/autoapi/pyranges/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC6913930", "pubmed:31841550" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2497, edam:operation_3562, edam:operation_3907 ; sc:license "GPL-3.0" ; sc:name "PyRates" ; sc:softwareHelp ; sc:url "https://www.cbs.mpg.de/departments/neurophysics/software/pyrates" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2275 ; sc:citation , "pubmed:31117512" ; sc: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." ; sc:featureList edam:operation_0244, edam:operation_0482, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PyRod" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/schallerdavid/pyrod" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3546 ; sc:encodingFormat edam:format_3752 ; sc:name "Image metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3508, edam:format_3752 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3579, edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:31872957" ; sc: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.""" ; sc:featureList edam:operation_2238, edam:operation_3435, edam:operation_3443, edam:operation_3552, edam:operation_3799, edam:operation_3891 ; sc:name "PySpacell" ; sc:url "https://pypi.org/project/pySpacell/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_3047 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0387, edam:operation_2575 ; sc:license "MIT" ; sc:name "PyVOL" ; sc:url "https://github.com/schlessingerlab/pyvol/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_0601 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0331, edam:operation_0417, edam:operation_3755 ; sc:license "MIT" ; sc:name "Pyntheon" ; sc:url "https://github.com/AhmedArslan/pyntheon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "PypeAmplicon" ; sc:url "https://github.com/vitorpavinato/PypeAmplicon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31743789" ; sc: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.""" ; sc:name "Pypreclin" ; sc:url "https://github.com/neurospin/pypreclin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092 ; sc: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." ; sc:featureList edam:operation_0226, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Python Video Annotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.306" ; sc:url "https://pythonvideoannotator.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0634 ; sc:citation , "pubmed:30661589" ; sc: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." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Q-HIU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/LobanovaEG-LobanovSV/Q-HIU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3393, edam:topic_3810 ; sc:citation , "pmcid:PMC6749258", "pubmed:31443603" ; sc: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" ; sc:name "QA4ECV FAPAR" ; sc:url "http://www.qa4ecv.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6602471", "pubmed:31114870" ; sc:description "Quantitative predictions of transcription factor binding changes due to sequence variants." ; sc:featureList edam:operation_0331, edam:operation_0445, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "QBiC-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://qbic.genome.duke.edu" ; biotools:primaryContact "Raluca Gordân" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:encodingFormat edam:format_2330 ; sc:name "Quality control report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A tool for real-time quality control assessment of mass spectrometry-based proteomics data." ; sc:featureList edam:operation_2238, edam:operation_2940 ; sc:name "QC-ART" ; sc:url "https://ascm.shinyapps.io/bas_QCART/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31099962" ; sc:description "Web-Tool for Performance Diagnosis and Prediction of liquid chromatography-mass spectrometry (LC-MS) Systems." ; sc:featureList edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "QCMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://shiny.maths.usyd.edu.au/QCMAP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3382, edam:topic_3489 ; sc:citation , , ; sc:description "QGIS is a free and open source Geographic Information System." ; sc:featureList edam:operation_0387, edam:operation_3454, edam:operation_3565 ; sc:name "QGIS" ; sc:url "http://qgis.osgeo.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC6385979", "pubmed:30541929" ; sc:description "Statistical procedure for genome-wide detection of QTL hotspots using public databases." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:name "QHOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.stat.sinica.edu.tw/chkao/RQTL/download.htm" ; biotools:primaryContact "Chen-Hung Kao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2275, edam:topic_3474 ; sc:citation , "pmcid:PMC7075525", "pubmed:31697312" ; sc: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:""" ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3435 ; sc:name "QMEANDisCo" ; sc:url "https://swissmodel.expasy.org/qmean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_0625, edam:topic_0749, edam:topic_3519 ; sc:citation , "pubmed:31683036" ; sc:description "The roles of Qishen granules recipes, Qingre Jiedu, Wenyang Yiqi and Huo Xue, in the treatment of heart failure." ; sc:featureList edam:operation_2497, edam:operation_3223, edam:operation_3799 ; sc:name "QPA" ; sc:url "https://github.com/github-gs/QPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3337, edam:topic_3384, edam:topic_3399 ; sc:citation , "pmcid:PMC7029361", "pubmed:31868683" ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:name "QPN" ; sc:url "http://rpq-qpn.ca/en/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3335, edam:topic_3422, edam:topic_3577 ; sc:citation ; sc: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 . 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""" ; sc:featureList edam:operation_2428, edam:operation_3283 ; sc:license "GPL-3.0" ; sc:name "QRISK3" ; sc:url "https://cran.r-project.org/web/packages/QRISK3/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3335, edam:topic_3399 ; sc:citation , "pubmed:15140353" ; sc:description "General practice database for research." ; sc:featureList edam:operation_3283, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "QResearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.qresearch.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0637, edam:topic_3293 ; sc:citation , "pmcid:PMC6667645", "pubmed:31396256" ; sc: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" ; sc:featureList edam:operation_0548, edam:operation_3478, edam:operation_3660 ; sc:license "MIT" ; sc:name "QS-Net" ; sc:url "https://github.com/Tmyiri/QS-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC6815455", "pubmed:31655545" ; sc: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.""" ; sc:featureList edam:operation_3436, edam:operation_3659, edam:operation_3799 ; sc:name "QSAR" ; sc:url "http://data.snu.ac.kr/QSAR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3343 ; sc:citation , "pubmed:31083984" ; sc:description "Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "QSAR-Co" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/view/qsar-co" ; biotools:primaryContact "Pravin Ambure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3400, edam:topic_3444 ; sc:citation , "pmcid:PMC6814493", "pubmed:31379055" ; sc: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" ; sc:featureList edam:operation_3454, edam:operation_3629, edam:operation_3799 ; sc:name "QSM" ; sc:url "http://pre.weill.cornell.edu/mri/pages/qsm.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3673 ; sc:citation , "pubmed:31388943" ; sc: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" ; sc:featureList edam:operation_0282, edam:operation_0484, edam:operation_3232 ; sc:name "QTL-BSA" ; sc:url "https://github.com/sanlengjing/QTL-BSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3173, edam:topic_3517, edam:topic_3518 ; sc:citation , "pmcid:PMC6943073", "pubmed:31598699" ; sc: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""" ; sc:featureList edam:operation_0282, edam:operation_0337, edam:operation_2422, edam:operation_3232, edam:operation_3799 ; sc:name "QTLbase" ; sc:url "http://mulinlab.org/qtlbase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3810 ; sc:citation ; sc:description "R package for random-effect multiple quantitative trait loci (QTL) mapping in autopolyploids." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "QTLpoly" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/guilherme-pereira/qtlpoly" ; biotools:primaryContact "Guilherme da Silva Pereira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0209, edam:topic_3047 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2476, edam:operation_3893 ; sc:name "QUBEKit" ; sc:url "https://github.com/cole-group/QuBeKit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC8215922", "pubmed:31503285" ; sc: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" ; sc:featureList edam:operation_3501 ; sc:name "QUBIC2" ; sc:url "https://github.com/OSU-BMBL/QUBIC2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199 ; sc:citation , "pubmed:31436990" ; sc: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" ; sc:featureList edam:operation_0480, edam:operation_0482 ; sc:name "QresFEP" ; sc:url "https://github.com/qusers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3237 ; sc:license "BSD-3-Clause" ; sc:name "QuAdTrim" ; sc:url "https://bitbucket.org/arobinson/quadtrim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6895564", "pubmed:31849692" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:name "QuantiMus" ; sc:url "https://quantimus.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC6853675", "pubmed:31070704" ; sc:description "Decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery." ; sc:featureList edam:operation_3216, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "QuantileBootstrap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/owatson/QuantileBootstrap" ; biotools:primaryContact "James A. Watson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3570 ; sc:citation , "pmcid:PMC6287823", "pubmed:30532140" ; sc:description "Modern general-purpose multi-threaded quantum computing library." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Quantum++" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/vsoftco/qpp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3315, edam:topic_3318 ; sc:citation , "pubmed:31470430" ; sc: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" ; sc:featureList edam:operation_3216, edam:operation_3891 ; sc:name "QuantumATK" ; sc:url "https://docs.quantumatk.com/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293 ; sc:citation , "pubmed:31504977" ; sc: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" ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0552 ; sc:license "GPL-3.0" ; sc:name "QuartetScores" ; sc:url "https://github.com/lutteropp/QuartetScores" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_3475 ; sc:name "Text" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_3475 ; sc:name "Text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769 ; sc:author "James E. Johnson" ; sc:citation , "pmcid:PMC6248266", "pubmed:30519459" ; sc: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. 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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. 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It uses an alignment-free approach for phylogenetic placement, thus removing the hurdle of query sequence alignment." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:name "RAPPAS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://www.atgc-montpellier.fr/RAPPAS/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0610, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc: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.""" ; sc:featureList edam:operation_0227, edam:operation_2421, edam:operation_3625, edam:operation_3908 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "RARe" ; sc:softwareHelp , , , ; sc:url "https://urgi.versailles.inrae.fr/rare/" ; biotools:primaryContact "Support service" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0203, edam:topic_0769, edam:topic_3170 ; sc:citation ; sc:description """An RNA-Seq Analysis Workflow with Snakemake. 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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""" ; sc:featureList edam:operation_2428, edam:operation_3226, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "RBV" ; sc:url "https://github.com/whitneywhitford/RBV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_0749 ; sc:citation , "pmcid:PMC6929455", "pubmed:31874608" ; sc:description "RCMF is a robust collaborative matrix factorization method to predict miRNA-disease associations." ; sc:featureList edam:operation_3435 ; sc:name "RCMF" ; sc:url "https://github.com/cuizhensdws/L21-GRMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0203, edam:topic_3295, edam:topic_3336, edam:topic_3518 ; sc:citation , "pubmed:31774912" ; sc:description "RCSM(Recommended Connectivity-map Scoring Methods) is a comprehensive evaluation of connectivity methods for L1000 data." ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3799 ; sc:name "RCSM" ; sc:url "https://github.com/Jasonlinchina/RCSM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "SPARQL endpoint" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3172, edam:topic_3325 ; sc:citation , "pmcid:PMC5584330", "pubmed:28870259" ; sc:description "Extends the RDF import and export functionality in Semantic MediaWiki (SMW) to enable using SMW as a collaborative platform for editing semantic data." ; sc:featureList edam:operation_0337, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:name "RDFIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://pharmb.io/project/rdfio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_3047 ; sc:citation ; sc:description "RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel." ; sc:featureList edam:operation_0475, edam:operation_1844, edam:operation_2476 ; sc:name "RDKit" ; sc:url "http://www.rdkit.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3673 ; sc:citation , , "pmcid:PMC2752127", "pmcid:PMC6555534", "pubmed:19657104", "pubmed:31136576" ; sc: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)""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3230 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RDXplorer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/rdxplorer/" ; biotools:primaryContact "Makarov V." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3384, edam:topic_3417, edam:topic_3474 ; sc:citation , "pubmed:31630011" ; sc: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.""" ; sc:featureList edam:operation_3283, edam:operation_3443, edam:operation_3553 ; sc:name "REFUGE Challenge" ; sc:url "https://refuge.grand-challenge.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3295, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_3208, edam:operation_3222 ; sc:name "REPIC" ; sc:url "https://repicmod.uchicago.edu/repic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625 ; sc:author "Amanda Kowalczyk", "Maria Chikina", "Nathan Clark", "Raghavendran Partha", "Weiguang (Wayne) Mao", "Wynn Meyer" ; sc:citation , "pmcid:PMC6853647", "pubmed:31192356" ; sc:description "R package for associating evolutionary rates with convergent traits." ; sc:featureList edam:operation_0547, edam:operation_0554, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RERconverge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/nclark-lab/RERconverge" ; biotools:primaryContact "Maria Chikina", "Nathan Clark", "Raghavendran Partha", "Weiguang (Wayne) Mao", "Wynn Meyer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2830, edam:topic_3360, edam:topic_3382, edam:topic_3518 ; sc:citation ; sc:description "Robust intEnSiTy nORmalization mEthod for Multiplexed Imaging." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:name "RESTORE" ; sc:url "https://gitlab.com/Chang_Lab/cycif_int_norm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736 ; sc:citation , "pmcid:PMC6802825", "pubmed:31634369" ; sc:description "Random Forest Quality Assessment to identify a predicted protein structure in the correct fold." ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0321, edam:operation_0474 ; sc:name "RFQAmodel" ; sc:url "https://github.com/clarewest/RFQAmodel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6697926", "pubmed:31419933" ; sc: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" ; sc:featureList edam:operation_0430, edam:operation_3233, edam:operation_3659 ; sc:name "RF_Purify" ; sc:url "https://github.com/mwsill/RFpurify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC6364042", "pubmed:30583062" ; sc:description "Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes." ; sc:featureList edam:operation_0525, edam:operation_3209, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RGAAT" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/wushyer/RGAAT_v2" ; biotools:primaryContact "Qiang Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6836459", "pubmed:31694536" ; sc:description "RGADE is a tool with genomic features and differential expression of the innate immune system from a smut-resistant genotype." ; sc:featureList edam:operation_0303, edam:operation_0524, edam:operation_3196, edam:operation_3432 ; sc:name "RGADE" ; sc:url "http://github.com/hugorody/rga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0654, edam:topic_3293 ; sc:citation , "pmcid:PMC6828935", "pubmed:31737036" ; sc: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.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567, edam:operation_3745 ; sc:name "RGRPT" ; sc:url "https://github.com/wangjuanimu/data-of-genome-rearrangement" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3173, edam:topic_3512 ; sc:citation , "pmcid:PMC6917511", "pubmed:31848596" ; sc: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""" ; sc:featureList edam:operation_0239, edam:operation_2495, edam:operation_3083, edam:operation_3439 ; sc:name "RHPCG" ; sc:url "http://www.medsysbio.org/RHPCG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0780, edam:topic_3474 ; sc:citation , "pmcid:PMC6806664", "pubmed:31640541" ; sc: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.""" ; sc:featureList edam:operation_3435 ; sc:name "RICE-GUARD" ; sc:url "http://multisite.iris.cat/riceguard/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3316, edam:topic_3517 ; sc:citation , "pmcid:PMC7868045", "pubmed:31393554" ; sc: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" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:name "RICOPILI" ; sc:url "https://sites.google.com/a/broadinstitute.org/RICOPILI/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC6646456", "pubmed:31089974" ; sc:description "Medical Imaging Dataset Annotation Tool for and with Deep Learning." ; sc:featureList edam:operation_2422, edam:operation_3553, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "RIL-Contour" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.com/Philbrick/rilcontour" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0736 ; sc:citation , , "pmcid:PMC5860209", "pmcid:PMC5998007", "pubmed:29028877", "pubmed:29946443" ; sc:description "Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions." ; sc:featureList edam:operation_0248, edam:operation_2406 ; sc:isAccessibleForFree true ; sc:name "RINspector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0" ; sc:url "http://apps.cytoscape.org/apps/rinspector" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308, edam:topic_3407 ; sc:citation ; sc:description "Transcriptomic analyses of bacteria have become instrumental to our understanding of their responses to changes in their environment." ; sc:featureList edam:operation_3629, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RIPTiDe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mjenior/riptide" ; biotools:primaryContact "Matthew L. Jenior" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_3794 ; sc:citation , "pmcid:PMC6714961", "pubmed:31523495" ; sc: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" ; sc:featureList edam:operation_3216, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "RIPper" ; sc:url "http://theripper.hawk.rocks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3295 ; sc:citation , "pmcid:PMC7924719", "pubmed:33816903" ; sc: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)" ; sc:featureList edam:operation_0575, edam:operation_2429 ; sc:license "Artistic-2.0" ; sc:name "RIdeogram" ; sc:url "https://cran.r-project.org/web/packages/RIdeogram/" ; biotools:primaryContact "Guangchuang Yu", "Jinhui Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0659, edam:topic_3512 ; sc:description "Tool for RNA–RNA interaction extraction from the literature." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RIscoper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rna-society.org/riscoper/" ; biotools:primaryContact "Wang Dong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC5753293", "pubmed:29040692" ; sc: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)." ; sc:featureList edam:operation_0417, edam:operation_2495, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RMBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://rna.sysu.edu.cn/rmbase/index.php" ; biotools:primaryContact "Jian-Hua Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6694479", "pubmed:31416413" ; sc: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) . These methods identify the convex combination of candidate kernels to construct an optimal hyperplane" ; sc:featureList edam:operation_0306, edam:operation_0463, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "RMKL" ; sc:url "https://CRAN.R-project.org/package=RMKL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_3336 ; sc:citation , "pmcid:PMC6424452", "pubmed:30889216" ; sc:description "R package for a Boolean sensitivity analysis against various types of mutations." ; sc:featureList edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "RMut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/csclab/RMut" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0203, edam:topic_0634, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3563, edam:operation_3565, edam:operation_3800 ; sc:name "RNA-seq" ; sc:url "http://rna-seq-browser.herokuapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC7523641", "pubmed:31593214" ; sc: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""" ; sc:featureList edam:operation_0226, edam:operation_0452, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "RNAIndel" ; sc:softwareHelp ; sc:softwareVersion "2.2.2" ; sc:url "https://github.com/stjude/RNAIndel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0154 ; sc:citation , "pmcid:PMC6482512", "pubmed:31023239" ; sc:description "Fixed-parameter tractable sampling for RNA design with multiple target structures." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNARedPrint" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/yannponty/RNARedPrint" ; biotools:primaryContact "Yann Ponty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3382 ; sc:citation , "pubmed:31769800" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "RNASeq_similarity_matrix" ; sc:url "http://www.github.com/nicokist/RNASeq_similarity_matrix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6612824", "pubmed:31510698" ; sc: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" ; sc:featureList edam:operation_0441, edam:operation_0443, edam:operation_2489 ; sc:license "GPL-3.0" ; sc:name "RNATracker" ; sc:url "https://www.github.com/HarveyYan/RNATracker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0659, edam:topic_0749, edam:topic_3047, edam:topic_3512 ; sc:citation , "pubmed:31799597" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_3792 ; sc:name "RNAactDrug" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/RNAactDrug" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2725 ; sc:name "Ensembl transcript ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3752 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0602 ; sc:author ; sc:citation , "pmcid:PMC6324028", "pubmed:30445601" ; sc:contributor ; sc: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.""" ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "RNAct" ; sc:softwareHelp ; sc:url "https://rnact.tartaglialab.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pubmed:31751879" ; sc:description "RNAdemocracy is an ensemble method for RNA secondary structure prediction using consensus scoring." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441 ; sc:name "RNAdemocracy" ; sc:url "https://github.com/beskidmore/RNAdemocracy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0632, edam:topic_3168, edam:topic_3308 ; sc:citation , "pubmed:31669269" ; sc: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""" ; sc:featureList edam:operation_0295, edam:operation_0502, edam:operation_2441 ; sc:name "RNAdt" ; sc:url "http://www.zhounan.org/rnadt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0659, edam:topic_3372 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0278, edam:operation_0295, edam:operation_0502 ; sc:name "RNAfamProb Plus NeoFold" ; sc:url "https://github.com/heartsh/rnafamprob" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6859278", "pubmed:31726390" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_0526 ; sc:name "RNAm5CPred" ; sc:url "http://zhulab.ahu.edu.cn/RNAm5CPred/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1254 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0659, edam:topic_3308, edam:topic_3391, edam:topic_3474 ; sc:citation , "pmcid:PMC7671399", "pubmed:33575571" ; sc: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." ; sc:featureList edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNAsamba" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.4" ; sc:url "https://rnasamba.lge.ibi.unicamp.br/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0820, edam:topic_3474 ; sc:citation , "pubmed:31472418" ; sc: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" ; sc:featureList edam:operation_2474, edam:operation_2475, edam:operation_3439 ; sc:name "RNN" ; sc:url "https://github.com/YellowcardD/RNN-for-membrane-protein-types-prediction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3421 ; sc:citation , "pmcid:PMC6708148", "pubmed:31462928" ; sc: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" ; sc:name "RNSCLC-PRSP software" ; sc:url "http://www.rnsclcpps.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3173 ; sc:citation , "pmcid:PMC4530010", "pubmed:25693563" ; sc: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." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ROADMAP epigenomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://egg2.wustl.edu/roadmap/web_portal/index.html" ; biotools:primaryContact "Jin Wook Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3855 ; sc:citation , "pubmed:31410449" ; sc: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" ; sc:featureList edam:operation_0224 ; sc:license "MIT" ; sc:name "ROBOKOP" ; sc:url "http://robokop.renci.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382 ; sc:citation , "pubmed:31769676" ; sc:description "ROBOKOP KG is an Integrated Knowledge Graphs from Federated Sources." ; sc:featureList edam:operation_0224 ; sc:name "ROBOKOP KG" ; sc:url "http://robokopkg.renci.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3372 ; sc:citation , "pmcid:PMC6664714", "pubmed:31357927" ; sc: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. 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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""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3435 ; sc:license "MIT" ; sc:name "ROMOP" ; sc:url "http://romop.ucsf.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0625, edam:topic_3293 ; sc:citation , "pubmed:31682272" ; sc: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." ; sc:featureList edam:operation_0399, edam:operation_3745 ; sc:name "RPANDA" ; sc:url "https://github.com/hmorlon/PANDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2229, edam:topic_3518 ; sc:citation , "pmcid:PMC6846243", "pubmed:31712826" ; sc:description "RPGeNet v2.0 - Retinitis Pigmentosa Gene Network: interacting with the network of genes related to retinitis pigmentosa genes." ; sc:featureList edam:operation_0224, edam:operation_3083, edam:operation_3439 ; sc:name "RPGeNet" ; sc:softwareVersion "2.0" ; sc:url "https://compgen.bio.ub.edu/RPGeNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6429152", "pubmed:30832218" ; sc:description "Hierarchical deep learning model for predicting ncRNA-protein interaction." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RPITER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Pengeace/RPITER" ; biotools:primaryContact "C. Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation , "pubmed:31648100" ; sc: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""" ; sc:featureList edam:operation_3096, edam:operation_3799 ; sc:name "RR-APET" ; sc:url "https://gitlab.com/MegMcC/rr-apet-hrv-analysis-software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:29579198" ; sc:description "Reduced representation bisulfite sequencing simulator for next-generation sequencing." ; sc:featureList edam:operation_0430, edam:operation_3186, edam:operation_3206 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RRBSsim" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/xwBio/RRBSsim" ; biotools:primaryContact "Xiwei Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0176 ; sc:citation , "pmcid:PMC4410660", "pubmed:25540183" ; sc:description "UCSF Chimera tool for viewing and comparing protein distance maps." ; sc:featureList edam:operation_2937, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RRDistMaps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html" ; biotools:primaryContact "Conrad C. Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0623, edam:topic_0736 ; sc:citation , "pmcid:PMC6334006", "pubmed:30649297" ; sc:description "Evolutionary-oriented database of RNA recognition motif sequences." ; sc:featureList edam:operation_0239, edam:operation_0246, edam:operation_0303 ; sc:isAccessibleForFree true ; sc:name "RRMdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://iimcb.genesilico.pl/rrm/" ; biotools:primaryContact "S. Dunin-Horkawicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_3500 ; sc:citation , "pmcid:PMC6934287", "pubmed:31881075" ; sc: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.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0551 ; sc:name "RRphylo" ; sc:url "https://github.com/pasraia/RRphylo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3511 ; sc:author ; sc:citation , "pmcid:PMC102588", "pubmed:10648794" ; sc:description "Detect oligomers (k-mers) whose positional distribution significantly discard from a homogeneous distribution." ; sc:featureList edam:operation_0238, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "RSAT position-analysis" ; sc:operatingSystem "Linux", "Mac" ; sc:provider ; sc:softwareHelp , , , , ; sc:url "http://teaching.rsat.eu/position-analysis_form.cgi" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1942, edam:format_1957 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204 ; sc:author ; sc:citation , "pmcid:PMC6030903", "pubmed:10641039", "pubmed:29722874" ; sc:description "Starting from a list of genes, returns upstream or downstream sequences." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "RSAT - Retrieve Sequence" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://pedagogix-tagc.univ-mrs.fr/rsat/retrieve-seq_form.cgi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3500, edam:topic_3517 ; sc:citation ; sc:description "Accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding." ; sc:featureList edam:operation_0239, edam:operation_0438, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RSAT Var-tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rsat.eu" ; biotools:primaryContact "Alejandra Medina-Rivera", "Jacques van Helden" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3511 ; sc:author ; sc:citation , "pmcid:PMC102821", "pubmed:10734201" ; sc:description "Detect over- or under-represented dyads (spaced pairs of k-mers) in sequences." ; sc:featureList edam:operation_0238, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "RSAT dyad-analysis" ; sc:operatingSystem "Linux", "Mac" ; sc:provider ; sc:softwareHelp , , , , ; sc:url "http://teaching.rsat.eu/dyad-analysis_form.cgi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3398 ; sc:citation , "pmcid:PMC6698671", "pubmed:31114928" ; sc:description "Regulostat Inferelator (RSI) - network biology platform to uncover molecular devices that predetermine cellular response phenotypes." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rsi.hulilab.org/" ; biotools:primaryContact "Hu Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3047, edam:topic_3382 ; sc:citation , "pmcid:PMC7162425", "pubmed:31626286" ; sc:description "Topological data analysis quantifies biological nano-structure from single molecule localization microscopy." ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "RSMLM" ; sc:softwareHelp ; sc:url "https://github.com/JeremyPike/RSMLM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC6732981", "pubmed:31516576" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3659 ; sc:license "LGPL-2.0" ; sc:name "RSQLite" ; sc:url "http://CRAN.R-project.org/package=RSQLite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3173 ; sc:citation , "pmcid:PMC6724675", "pubmed:31434679" ; sc: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" ; sc:featureList edam:operation_0277, edam:operation_0443, edam:operation_3439 ; sc:name "RT networks" ; sc:url "https://github.com/sebkim/RTNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0749, edam:topic_0798, edam:topic_3673 ; sc:citation , "pmcid:PMC6771411", "pubmed:31575651" ; sc:description "RUFUS is a Pedigree-based estimation of human mobile element retrotransposition rates." ; sc:name "RUFUS" ; sc:url "https://github.com/jandrewrfarrell/RUFUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6614807", "pubmed:31114909" ; sc:description "Removing Unwanted Variation-III (RUV-III) - normalization for Nanostring nCounter gene expression data." ; sc:featureList edam:operation_2939, edam:operation_2940, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "RUV-III" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=ruv" ; biotools:primaryContact , "Johann Gagnon-Bartsch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2258, edam:topic_3314, edam:topic_3474 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_3439, edam:operation_3454 ; sc:name "RXN" ; sc:url "https://rxn.res.ibm.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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." ; sc:name "R plus" ; sc:softwareHelp ; sc:url "https://github.com/Incpink-Liu/DNA-storage-R_plus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC6366910", "pubmed:30591514" ; sc:description "Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Rqtl2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://kbroman.org/qtl2/" ; biotools:primaryContact "Karl Broman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_2229, edam:topic_3168 ; sc:citation , "pmcid:PMC6816165", "pubmed:31661016" ; sc: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:""" ; sc:featureList edam:operation_0525, edam:operation_3182, edam:operation_3192, edam:operation_3216 ; sc:license "MIT" ; sc:name "RaGOO" ; sc:url "https://github.com/malonge/RaGOO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0769, edam:topic_3170 ; sc:citation , "pubmed:31730197" ; sc: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." ; sc:featureList edam:operation_2436, edam:operation_3680, edam:operation_3800 ; sc:name "RaNA-Seq" ; sc:url "https://ranaseq.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3673 ; sc:citation , "pmcid:PMC6724115", "pubmed:31390788" ; sc: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.""" ; sc:featureList edam:operation_0523, edam:operation_0525 ; sc:license "MIT" ; sc:name "Racon" ; sc:url "https://github.com/isovic/racon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_3500 ; sc:citation , "pmcid:PMC6585820", "pubmed:30019526" ; sc:description "Identification of radical amino acid changes in multiple sequence alignments." ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RadAA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sciseim/RadAA" ; biotools:primaryContact "Inge Seim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3474, edam:topic_3510 ; sc:citation , "pubmed:31508799" ; sc: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" ; sc:featureList edam:operation_0417, edam:operation_0418, edam:operation_3501 ; sc:license "MIT" ; sc:name "Ragp" ; sc:url "https://github.com/missuse/ragp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269, edam:topic_3056 ; sc:citation , "pubmed:31180862" ; sc: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.""" ; sc:featureList edam:operation_3209, edam:operation_3744 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "RainBio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lesfleursdunormal.fr/static/appliweb/rainbio/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3407 ; sc:citation "pubmed:12542423" ; sc:description "Rare Metabolic Diseases Database: platform independent, web-based information system for rare metabolic diseases based on filed case reports." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "Ramedis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ramedis.de" ; biotools:primaryContact "Thoralf Töpel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3360, edam:topic_3422 ; sc:citation , "pmcid:PMC6764656", "pubmed:31560690" ; sc: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" ; sc:featureList edam:operation_2939, edam:operation_3891 ; sc:name "RametrixTM" ; sc:url "https://github.com/SengerLab/RametrixLITEToolbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_2269 ; sc:citation , "pmcid:PMC6777641", "pubmed:31611898" ; sc: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:""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:name "Ramf" ; sc:url "https://github.com/mchiapello/Ramf" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3650 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3955 ; sc:citation , "pubmed:31893378" ; sc: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." ; sc:featureList edam:operation_2409 ; sc:license "Freeware" ; sc:name "Ramid" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.0.1.0" ; sc:url "https://github.com/seliv55/ramidcor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2830, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6929103", "pubmed:31816915" ; sc: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""" ; sc:featureList edam:operation_0315, edam:operation_0571, edam:operation_2436, edam:operation_3223, edam:operation_3802 ; sc:name "RankerGUI" ; sc:url "http://watson.na.icar.cnr.it/rankergui/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2269, edam:topic_3298 ; sc:citation , "pmcid:PMC6823239", "pubmed:31708940" ; sc: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”)""" ; sc:featureList edam:operation_3196, edam:operation_3435 ; sc:name "RapidACi" ; sc:url "https://github.com/ManuelLamothe/RapidACi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0128, edam:topic_2275, edam:topic_3474 ; sc:citation , "pubmed:31583631" ; sc:description "A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning." ; sc:featureList edam:operation_0272, edam:operation_2492, edam:operation_3439, edam:operation_3899 ; sc:name "RaptorX-ComplexContact" ; sc:url "http://raptorx.uchicago.edu/ComplexContact/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2885, edam:topic_3172, edam:topic_3325 ; sc:citation , "pmcid:PMC6830269", "pubmed:31688938" ; sc: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""" ; sc:featureList edam:operation_0495, edam:operation_2421, edam:operation_2422 ; sc:name "RareLSD" ; sc:url "https://webs.iiitd.edu.in/raghava/rarelsd/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "RatMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "http://ratmine.mcw.edu/ratmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC6797704", "pubmed:31062192" ; sc:description "3D graphics python package for cognitive psychology experiments." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Ratcave" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ratcave/ratcave" ; biotools:primaryContact "Del Grosso NA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3676 ; sc:citation , "pubmed:31087445" ; sc:description "Rare variant association testing for multicategory phenotype." ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Ravages" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/genostats/Ravages" ; biotools:primaryContact "Hervé Perdry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3293 ; sc:citation ; sc: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." ; sc:name "RaxmlGUI" ; sc:softwareVersion "2.0" ; sc:url "http://antonellilab.github.io/raxmlGUI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3168, edam:topic_3382, edam:topic_3577 ; sc:citation , "pmcid:PMC6797086", "pubmed:31622330" ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3196, edam:operation_3501, edam:operation_3802 ; sc:name "Rbbt" ; sc:url "https://github.com/Rbbt-Workflows" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3421, edam:topic_3520 ; sc:citation , "pubmed:31605803" ; sc:description "An R Package for Automated Chimerism Data Analysis." ; sc:featureList edam:operation_3799 ; sc:name "Rchimerism" ; sc:url "https://github.com/BioHPC/Rchimerism" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:30916068" ; sc:description "Prediction of circRNA expression and function through probe reannotation of non-circRNA microarrays." ; sc:featureList edam:operation_0308, edam:operation_0309, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ReCirc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://licpathway.net:8080/ReCirc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2939, edam:operation_3501, edam:operation_3801 ; sc:license "MIT" ; sc:name "ReDU" ; sc:softwareHelp ; sc:url "https://redu.ucsd.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495 ; sc:name "ReFDash" ; sc:url "https://web.rniapps.net/iVikodak/refdash/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6384294", "pubmed:30828503" ; sc:description "R package for annotating RNA editing in plastid genomes." ; sc:featureList edam:operation_0310, edam:operation_3096, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ReFernment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.2" ; sc:url "https://github.com/TARobison/ReFernment" ; biotools:primaryContact "Tanner Robison" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3174, edam:topic_3518 ; sc:citation , "pmcid:PMC6333964", "pubmed:30649296" ; sc:description "Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database" ; sc:featureList edam:operation_0306, edam:operation_2422, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:name "ReGEO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.regeo.org/" ; biotools:primaryContact "Canglin Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3169, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC7145625", "pubmed:31665499" ; sc:description "THIS PAGE IS DEPRECATED, GO TO : https://bio.tools/inserm-remap" ; sc:featureList edam:operation_2421, edam:operation_3192, edam:operation_3208, edam:operation_3222 ; sc:name "ReMap" ; sc:url "http://remap.univ-amu.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0204, edam:topic_0602 ; sc:citation ; sc: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:" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "ReProMin" ; sc:url "https://github.com/utrillalab/repromin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_0659, edam:topic_3170 ; sc:citation , "pmcid:PMC7058180", "pubmed:31589315" ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3463, edam:operation_3799 ; sc:name "ReQTL" ; sc:url "https://github.com/HorvathLab/ReQTL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:31116384" ; sc:description "Drug response similarity prediction using Siamese neural networks." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ReSimNet" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/dmis-lab/ReSimNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0160, edam:topic_2830, edam:topic_3474 ; sc:citation , "pmcid:PMC6916091", "pubmed:31842745" ; sc: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""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2489 ; sc:name "ReVac" ; sc:url "https://github.com/admelloGithub/ReVac-package" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0602, edam:topic_3314 ; sc:citation , "pmcid:PMC6413953", "pubmed:30818351" ; sc:description "Reaction Diffusion Dynamics (ReaDDy) - software framework for interacting-particle reaction dynamics." ; sc:featureList edam:operation_0334, edam:operation_2476, edam:operation_3457 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ReaDDy" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://readdy.github.io/" ; biotools:primaryContact "ReaDDy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3292 ; sc:citation , "pubmed:27485447" ; sc:description "Tool to predict and analyze biochemical reactions." ; sc:featureList edam:operation_2497, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ReactPRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/reactpred/" ; biotools:primaryContact "Anirban Bhaduri", "Tae Yong Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_0194, edam:topic_0196 ; sc:citation , "pmcid:PMC6916211", "pubmed:31842735" ; sc: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""" ; sc:featureList edam:operation_0289, edam:operation_0557, edam:operation_3472, edam:operation_3478, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "Read-SpaM" ; sc:url "https://github.com/burkhard-morgenstern/Read-SpaM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3300, edam:topic_3390, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC6848197", "pubmed:31728416" ; sc:description "Real-time is a health monitoring through urine metabolomics." ; sc:featureList edam:operation_2939, edam:operation_3799, edam:operation_3803 ; sc:name "Real-time" ; sc:url "https://github.com/ijmiller2/RealTimeUrineMetabolomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Tool for preparing 3D models of biochemical structures for augmented and virtual reality." ; sc:name "RealityConvert" ; sc:url "http://www.realityconvert.com/" ; biotools:primaryContact "Denis Fourches" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6472834", "pubmed:30958827" ; sc:description "Robust comparative analysis and contamination removal for metagenomics." ; sc:featureList edam:operation_2495, edam:operation_3460, edam:operation_3730 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Recentrifuge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.28.10" ; sc:url "https://sites.google.com/view/recentrifuge" ; biotools:primaryContact "Jose Manuel Martí" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0194, edam:topic_0797, edam:topic_3293 ; sc:citation , , "pmcid:PMC15866", "pmcid:PMC4094424", "pubmed:10077608", "pubmed:25013894" ; sc: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." ; sc:featureList edam:operation_0292, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Reciprocal Best Hits - Best Bidirectional Hits" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://www.protocols.io/view/reciprocal-best-hit-blast-q3rdym6" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3293 ; sc:author ; sc:citation ; sc:description "Rapid determination of appropriate reference genomes." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ReferenceSeeker" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "v1.7.3" ; sc:url "https://github.com/oschwengers/referenceseeker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3305, edam:topic_3517 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Reference Panel Reconstruction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Abyss-bai/reference-panel-reconstruction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc: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." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "refgenie" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://refgenie.databio.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3855 ; sc:citation , "pmcid:PMC6612893", "pubmed:31510694" ; sc: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!" ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:license "GPL-3.0" ; sc:name "RegLinker" ; sc:url "https://github.com/Murali-group/RegLinker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0634, edam:topic_2885, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6883696", "pubmed:31779641" ; sc: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""" ; sc:featureList edam:operation_0417, edam:operation_2499, edam:operation_3461 ; sc:license "MIT" ; sc:name "RegSNPs-intron" ; sc:url "https://regsnps-intron.ccbb.iupui.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3172, edam:topic_3517 ; sc:citation , "pmcid:PMC4293375", "pubmed:24008273" ; sc:description "Performance of fast association analysis between allele frequencies and continuous traits. Uses linear regression to estimate marker effects on continuous traits." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RegScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.5" ; sc:url "https://www.geenivaramu.ee/en/tools/regscan" ; biotools:primaryContact "T. Haller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3325 ; sc:citation , "pmcid:PMC6602480", "pubmed:31106382" ; sc: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.""" ; sc:featureList edam:operation_3225 ; sc:isAccessibleForFree true ; sc:name "RegulationSpotter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.regulationspotter.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0780, edam:topic_0798, edam:topic_3168 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0452, edam:operation_3192, edam:operation_3196 ; sc:license "MIT" ; sc:name "RelocaTE2" ; sc:url "https://github.com/stajichlab/RelocaTE2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0821, edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:31800321" ; sc: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""" ; sc:featureList edam:operation_0417, edam:operation_2421 ; sc:name "RemeDB" ; sc:url "https://www.niot.res.in/Remedb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6883653", "pubmed:31783882" ; sc: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""" ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3472 ; sc:license "MIT" ; sc:name "ReorientExpress" ; sc:url "https://github.com/comprna/reorientexpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157, edam:topic_2885, edam:topic_3399 ; sc:citation , "pubmed:30598392" ; sc:description "Web server to extract sequence repeats from protein and DNA sequences." ; sc:featureList edam:operation_0237 ; sc:isAccessibleForFree true ; sc:name "RepEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioserver2.physics.iisc.ac.in/RepEx/" ; biotools:primaryContact "Professor K. Sekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0749, edam:topic_0798 ; sc:citation , "pmcid:PMC6862929", "pubmed:31742600" ; sc: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." ; sc:featureList edam:operation_0491, edam:operation_0495, edam:operation_3182 ; sc:name "RepeatFiller" ; sc:url "https://github.com/hillerlab/GenomeAlignmentTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0196, edam:topic_0621, edam:topic_0798, edam:topic_3673 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0362, edam:operation_0525, edam:operation_3644 ; sc:name "RepeatModeler" ; sc:url "https://github.com/Dfam-consortium/RepeatModeler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , "pubmed:15961478" ; sc:description "RepeatScout is a tool to discover repetitive substrings in DNA." ; sc:featureList edam:operation_3472 ; sc:name "RepeatScout" ; sc:url "http://bix.ucsd.edu/repeatscout/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Repeats intermine database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "RepetDB" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://urgi.versailles.inra.fr/repetdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31484108" ; sc: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" ; sc:featureList edam:operation_0479, edam:operation_3436 ; sc:name "Res2Net" ; sc:url "https://mmcheng.net/res2net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3053 ; sc:citation , "pubmed:31845517" ; sc: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""" ; sc:featureList edam:operation_0282, edam:operation_2950 ; sc:name "ResDisMapper" ; sc:url "https://github.com/takfung/ResDisMapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6853658", "pubmed:31070716" ; sc:description "Algorithm for protein residue-residue contact-map prediction." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0303 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ResPRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zhanglab.ccmb.med.umich.edu/ResPRE" ; biotools:primaryContact "Yang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0736, edam:topic_3538 ; sc:citation , "pmcid:PMC6748046", "pubmed:31411026" ; sc: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" ; sc:featureList edam:operation_0244, edam:operation_0303, edam:operation_3904 ; sc:name "ResidueDisorder" ; sc:url "https://www.rosettacommons.org/docs/latest/ResidueDisorder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0081 ; sc:citation , "pmcid:PMC6954431", "pubmed:31799624" ; sc: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." ; sc:featureList edam:operation_0249, edam:operation_1844, edam:operation_2518 ; sc:name "RestraintLib" ; sc:url "http://achesym.ibch.poznan.pl/restraintlib/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3398, edam:topic_3407 ; sc:citation , "pmcid:PMC6734243", "pubmed:31500573" ; sc: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" ; sc:featureList edam:operation_3083, edam:operation_3439, edam:operation_3660 ; sc:license "BSD-2-Clause" ; sc:name "RetSynth" ; sc:url "https://github.com/sandialabs/RetSynth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0749 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0331, edam:operation_0477, edam:operation_3461 ; sc:name "Rhapsody" ; sc:url "http://rhapsody.csb.pitt.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0196, edam:topic_0203, edam:topic_0659, edam:topic_2229 ; sc:citation ; sc:description "RiboFlow is an ecosystem for analyzing ribosome profiling data at read length resolution." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3436 ; sc:name "RiboFlow" ; sc:url "https://github.com/ribosomeprofiling/riboflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0196, edam:topic_0203, edam:topic_0659, edam:topic_2229 ; sc:citation ; sc:description "RiboPy is an ecosystem for analyzing ribosome profiling data at read length resolution." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3436 ; sc:name "RiboPy" ; sc:url "https://ribopy.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_0769, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3436 ; sc:name "RiboR" ; sc:url "https://ribosomeprofiling.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_0749, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC6954398", "pubmed:31777932" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_2495, edam:operation_3192, edam:operation_3891 ; sc:name "RiboVIEW" ; sc:url "https://github.com/carinelegrand/RiboVIEW" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:29659702" ; sc:description "Web tool for bacterial classification through m/z data from ribosomal proteins." ; sc:featureList edam:operation_2929, edam:operation_3460, edam:operation_3627 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Ribopeaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ribopeaks.com." ; biotools:primaryContact "Rafael Mazer Etto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0623, edam:topic_3293 ; sc:citation , "pmcid:PMC6764101", "pubmed:31560050" ; sc: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" ; sc:featureList edam:operation_0553, edam:operation_3431, edam:operation_3501 ; sc:name "RiceRelativesGD" ; sc:url "http://ibi.zju.edu.cn/ricerelativesgd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6527052", "pubmed:31107941" ; sc:description "Open resource for plant science." ; sc:featureList edam:operation_0308, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "Rice Galaxy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://13.250.174.27:8080/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3321, edam:topic_3366 ; sc:description "An open source database(s) for genetics, genomics and functional research in rice species" ; sc:featureList edam:operation_0292, edam:operation_0337 ; sc:funder "CRP Rice" ; sc:isAccessibleForFree true ; sc:name "Rice Genome Hub" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://rice-genome-hub.southgreen.fr/" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3454, edam:operation_3557, edam:operation_3639 ; sc:name "RobNorm" ; sc:url "https://github.com/mwgrassgreen/RobNorm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0736, edam:topic_0749 ; sc:citation , "pubmed:31800008" ; sc: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""" ; sc:featureList edam:operation_3658, edam:operation_3767 ; sc:license "MIT" ; sc:name "RocaSec" ; sc:url "https://github.com/ahmedaq/RocaSec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31634130" ; sc:description "RBM ( Restricted Boltzmann Machine ) is an unsupervised Rotation Factorization in Restricted Boltzmann Machines." ; sc:name "RBM" ; sc:url "https://bitbucket.org/tuttoweb/rotinvrbm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3512, edam:topic_3519 ; sc:citation , "pmcid:PMC6814140", "pubmed:31651257" ; sc:description "Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish." ; sc:featureList edam:operation_0239, edam:operation_2421, edam:operation_3216, edam:operation_3799 ; sc:name "RsHSF" ; sc:url "http://www.cibiv.at/services/hsf/info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2939, edam:operation_3800, edam:operation_3891 ; sc:name "RsQTL" ; sc:url "https://github.com/HorvathLab/RsQTL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3315 ; sc:citation , "pubmed:30945241" ; sc: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." ; sc:featureList edam:operation_2426, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RuleBuilder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/RuleWorld/RuleBuilder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0821, edam:topic_2258, edam:topic_3314 ; sc:citation , "pubmed:26187943" ; sc:description "Tool computes reaction similarity based on the molecular signatures of participating molecules." ; sc:featureList edam:operation_2929, edam:operation_3502 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RxnSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=RxnSim" ; biotools:primaryContact "Anirban Bhaduri", "Tae Yong Kim", "Varun Giri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3314 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0491, edam:operation_3198, edam:operation_3211 ; sc:license "GPL-3.0" ; sc:name "S-conLSH" ; sc:url "https://github.com/anganachakraborty/S-conLSH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pmcid:PMC6448907", "pubmed:30908487" ; sc: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." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:name "S4TE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://sate.cirad.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0202, edam:topic_3520 ; sc:citation , "pubmed:31612721" ; sc: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""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3226, edam:operation_3436 ; sc:license "Apache-2.0" ; sc:name "SAAVpedia" ; sc:softwareHelp ; sc:url "https://www.SAAVpedia.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_3370 ; sc:citation , "pubmed:31462040" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3431 ; sc:name "SACMES" ; sc:url "https://github.com/netzlab/SACMES.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3277 ; sc:citation ; sc:description "SAD contains efficient algorithms for sampling feasible sets of abundance distributions." ; sc:name "SAD" ; sc:url "https://github.com/klocey/partitions" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382 ; sc:citation , "pmcid:PMC6704125", "pubmed:31434941" ; sc: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" ; sc:name "SAIM" ; sc:url "https://github.com/mjc449/SAIMscannerV3.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3125 ; sc:citation , "pmcid:PMC6719893", "pubmed:31433799" ; sc: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" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:license "MIT" ; sc:name "SALSA" ; sc:url "https://github.com/machinegun/SALSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3063, edam:topic_3335, edam:topic_3379, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_1812, edam:operation_3432, edam:operation_3625 ; sc:license "MIT" ; sc:name "SALTClass" ; sc:url "https://pypi.org/project/saltclass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC6803637", "pubmed:31636330" ; sc: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""" ; sc:featureList edam:operation_3182, edam:operation_3198, edam:operation_3227, edam:operation_3675, edam:operation_3802 ; sc:name "SAMDUDE" ; sc:url "https://github.com/ihwang/SAMDUDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6943136", "pubmed:31777938" ; sc: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""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3436 ; sc:name "SAME-clustering" ; sc:url "https://github.com/yycunc/SAMEclustering" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3452 ; sc:citation , "pmcid:PMC6886563", "pubmed:31824393" ; sc: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." ; sc:featureList edam:operation_3435 ; sc:license "MIT" ; sc:name "SAMIRIX" ; sc:url "https://github.com/neurodial/am_SAMIRIX.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0602, edam:topic_3068, edam:topic_3407 ; sc:citation , "pubmed:31851289" ; sc: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""" ; sc:featureList edam:operation_0573, edam:operation_1812, edam:operation_3083, edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "SAMMI" ; sc:url "http://www.SammiTool.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_3534 ; sc:citation ; sc:description "Web server for predicting SAM binding residues of a protein from its amino acid sequence." ; sc:featureList edam:operation_0272, edam:operation_0417, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SAMbinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://webs.iiitd.edu.in/raghava/sambinder/" ; biotools:primaryContact "G.P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3474 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0417, edam:operation_0480, edam:operation_3755 ; sc:name "SAPH-ire TFx" ; sc:url "https://saphire.biosci.gatech.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6954655", "pubmed:31095298" ; sc: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." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SASM-VGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Meiyan88/SASM-VGWAS" ; biotools:primaryContact "Meiyan Huang", "Qianjin Feng" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3752 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3752 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474 ; sc:citation , "pmcid:PMC10164410", "pubmed:31591579" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3557, edam:operation_3664 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SAUCIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KrishnaswamyLab/SAUCIE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC7781045", "pubmed:31471617" ; sc: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" ; sc:featureList edam:operation_3501, edam:operation_3557 ; sc:name "SAVER-X" ; sc:url "http://singlecell.wharton.upenn.edu/saver-x/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0196, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC7230021", "pubmed:31860156" ; sc: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""" ; sc:featureList edam:operation_0303, edam:operation_0310, edam:operation_0321, edam:operation_0476, edam:operation_0477 ; sc:name "SAXSDom" ; sc:url "https://github.com/jianlin-cheng/SAXSDom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3474 ; sc:citation , , , "pubmed:31452098", "pubmed:31452104", "pubmed:31452110" ; sc: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" ; sc:featureList edam:operation_0482, edam:operation_3659, edam:operation_3899 ; sc:license "GPL-3.0" ; sc:name "SAnDReS" ; sc:url "https://github.com/azevedolab/sandres" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31081037" ; sc:description "Coordinate Descent Approach for Sparse Bayesian Learning in High Dimensional QTL Mapping and Genome-wide Association Studies." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SBL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MeiyueComputBio/sbl/tree/master/R%20packge" ; biotools:primaryContact "Meiyue Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3512 ; sc:citation , "pmcid:PMC6743255", "pubmed:31559017" ; sc:description "Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models | SBM-for-correlation-based-networks" ; sc:featureList edam:operation_3439, edam:operation_3463, edam:operation_3766 ; sc:license "GPL-3.0" ; sc:name "SBM" ; sc:url "https://gitlab.com/biomodlih/sbm-for-correlation-based-networks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_3314, edam:topic_3379, edam:topic_3407 ; sc:citation , "pubmed:31738386" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_3562 ; sc:name "SBML2Modelica" ; sc:url "https://bitbucket.org/mclab/sbml2modelica" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_2259, edam:topic_3292, edam:topic_3306 ; sc:citation ; sc: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)." ; sc:featureList edam:operation_3096, edam:operation_3660 ; sc:license "MIT" ; sc:name "SBMLLint" ; sc:url "https://github.com/ModelEngineering/SBMLLint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3223, edam:operation_3230, edam:operation_3800 ; sc:name "SBP_2019" ; sc:url "https://github.com/pachterlab/SBP_2019/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3173, edam:topic_3474 ; sc:citation , "pmcid:PMC6783552", "pubmed:31594952" ; sc: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).""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "SCALE" ; sc:url "https://github.com/jsxlei/SCALE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6853764", "pubmed:31197308" ; sc:description "Set of tools for SCoring, ANnotating and VISualizing splice junctions using annotation details (gencode or other)." ; sc:featureList edam:operation_2939 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SCANVIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.99.15" ; sc:url "https://github.com/nygenome/SCANVIS" ; biotools:primaryContact "Phaedra Agius" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3474 ; sc:citation ; sc:description "An Open Source Physical Layer for the DARPA Spectrum Collaboration Challenge." ; sc:featureList edam:operation_3215 ; sc:name "SCATTER PHY" ; sc:url "https://github.com/zz4fap/scatter-phy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3474 ; sc:citation , "pmcid:PMC6878945", "pubmed:31769834" ; sc: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." ; sc:featureList edam:operation_3096, edam:operation_3435 ; sc:name "SCDO" ; sc:url "http://scdontology.h3abionet.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6775478", "pubmed:31611909" ; sc:description """A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database""" ; sc:featureList edam:operation_2495, edam:operation_3096, edam:operation_3223 ; sc:name "SCDevDB" ; sc:url "https://scdevdb.deepomics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2814, edam:topic_2830, edam:topic_3489 ; sc:citation , "pmcid:PMC6785892", "pubmed:31601176" ; sc: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." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3432 ; sc:name "SCEptRe" ; sc:url "http://tools.iedb.org/sceptre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621, edam:topic_3174 ; sc:citation , "pubmed:31764940" ; sc: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""" ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3216, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "SCGid" ; sc:url "http://www.github.com/amsesk/SCGid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2830, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "Schema is a general algorithm for integrating heterogeneous data modalities, with application to multi-modal single-cell biological datasets." ; sc:featureList edam:operation_3435, edam:operation_3561, edam:operation_3891 ; sc:name "SCHEMA" ; sc:url "http://schema.csail.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC6612866", "pubmed:31510696" ; sc: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=;m=;gv_file='';output='';method='';nRep=;theta=;SCIFIL\"" ; sc:featureList edam:operation_0487, edam:operation_3478, edam:operation_3799 ; sc:license "MIT" ; sc:name "SCIFIL" ; sc:url "https://github.com/compbel/SCIFIL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3810, edam:topic_3855 ; sc:citation , "pubmed:31494409" ; sc: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" ; sc:featureList edam:operation_2429, edam:operation_3501 ; sc:name "SCIMAP" ; sc:url "http://www.scimap.org.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31770586" ; sc:description "Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach." ; sc:featureList edam:operation_0524, edam:operation_1781, edam:operation_3258 ; sc:name "SCMVTDb" ; sc:url "http://webtom.cabgrid.res.in/scmvtdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6837541", "pubmed:31658262" ; sc: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""" ; sc:featureList edam:operation_0313, edam:operation_3501 ; sc:name "SCMarker" ; sc:url "https://github.com/KChen-lab/SCMarker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0780, edam:topic_2885, edam:topic_3170 ; sc:citation , "pmcid:PMC6853641", "pubmed:31680133" ; sc:description """a genomics portal for the soybean cyst nematode (Heterodera glycines). All supporting analyses required for SCNBase data""" ; sc:featureList edam:operation_0362, edam:operation_0433, edam:operation_2421 ; sc:name "SCNBase" ; sc:url "http://SCNBase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3068, edam:topic_3387, edam:topic_3489 ; sc:citation , "pmcid:PMC6820755", "pubmed:31664032" ; sc:description "SCOC database is a large, open, and global database with sediment community oxygen consumption rates." ; sc:featureList edam:operation_2421, edam:operation_3431 ; sc:name "SCOC database" ; sc:url "http://data.eol.ucar.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_3307 ; sc: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." ; sc:featureList edam:operation_0313, edam:operation_2437, edam:operation_2495, edam:operation_3463, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SCOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/zhangjunpeng411/SCOM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0820, edam:topic_3517 ; sc:citation , "pmcid:PMC5225593", "pubmed:28077070" ; sc:description "Software for COrrelated Phenotype Analysis." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SCOPA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.14" ; sc:url "https://www.geenivaramu.ee/en/tools/scopa" ; biotools:primaryContact "Andrew P Morris", "Reedik Magi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:citation , "pmcid:PMC6852764", "pubmed:31718533" ; sc:description "Tool for sample size calculations for single-cell sequencing experiments." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SCOPIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://alexdavisscs.shinyapps.io/scs_power_multinomial/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_3542 ; sc:citation , "pubmed:31742326" ; sc:description "SCOT is a tool for secondary structure Classification on Turns." ; sc:featureList edam:operation_0249, edam:operation_0267, edam:operation_0319, edam:operation_2488, edam:operation_2996 ; sc:name "SCOT" ; sc:url "https://this-group.rocks/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6501316", "pubmed:31060596" ; sc:description "Single-cell RNA-seq imputation constrained by bulk RNA-seq data." ; sc:featureList edam:operation_3436, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SCRABBLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://rdrr.io/cran/SCRABBLE/" ; biotools:primaryContact "Tao Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc: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]""" ; sc:featureList edam:operation_2495, edam:operation_3557 ; sc:name "SCRIBE" ; sc:url "https://github.com/YiliangTracyZhang/SCRIBE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_2275 ; sc:citation , "pmcid:PMC6612887", "pubmed:31510679" ; sc:description "accurate and partner type-specific prediction of protein-binding residues from proteins sequences | SCRIBER - web server from Biomine lab" ; sc:featureList edam:operation_0272, edam:operation_2492, edam:operation_3899 ; sc:name "SCRIBER" ; sc:url "http://biomine.cs.vcu.edu/servers/SCRIBER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC7703785", "pubmed:31584615" ; sc: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”." ; sc:featureList edam:operation_0296, edam:operation_3198 ; sc:license "BSD-3-Clause" ; sc:name "SCSsim" ; sc:url "https://github.com/qasimyu/scssim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pubmed:31116393" ; sc:description "Statistical test of structured continuous trees based on discordance matrix." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SCTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/XQBai/SCTree-test" ; biotools:primaryContact "Liang Ma", "Lin Wan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3304, edam:topic_3308 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3891 ; sc:name "SCeNGEA" ; sc:url "https://cengen.shinyapps.io/SCeNGEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_2828, edam:topic_3318 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3454 ; sc:name "SCryPTA" ; sc:url "http://www.if.usp.br/scrypta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3399 ; sc:citation ; sc:description "Adding noise to Markov cohort state-transition models." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rowaniskandar/SDE" ; biotools:primaryContact "Rowan Iskandar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:27522083" ; sc:description "Splice graph based differential transcript expression analysis tool for population data." ; sc:featureList edam:operation_2495, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SDEAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ewyang089/SDEAP/wiki" ; biotools:primaryContact "Ei-Wen Yang", "Tao Jian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3489 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:license "MIT" ; sc:name "SDG" ; sc:softwareHelp ; sc:url "https://github.com/bioinfologics/sdg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC6796762", "pubmed:31542696" ; sc: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" ; sc:featureList edam:operation_3501 ; sc:name "SDM6A" ; sc:softwareHelp ; sc:url "http://thegleelab.org/SDM6A" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2429 ; sc:name "SDR" ; sc:url "https://github.com/pierluigiderosa/r.sdr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3305, edam:topic_3322, edam:topic_3519 ; sc:citation , "pmcid:PMC6795434", "pubmed:31618236" ; sc: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." ; sc:featureList edam:operation_3196, edam:operation_3283, edam:operation_3436 ; sc:name "SDRS" ; sc:url "http://www.fieldepi.org/SDRS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749 ; sc:citation , "pmcid:PMC6686515", "pubmed:31390979" ; sc: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" ; sc:featureList edam:operation_2492, edam:operation_3501 ; sc:name "SE-DMTG" ; sc:url "https://github.com/RongquanWang/SE-DMTG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3489, edam:topic_3678 ; sc:citation , "pmcid:PMC6817659", "pubmed:31673594" ; sc:description "Relative sea-level data from the SEAMIS database compared to ICE-5G model predictions of glacial isostatic adjustment." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "SEAMIS" ; sc:url "https://github.com/Alerovere/SEAMIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0659, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC6943056", "pubmed:31598718" ; sc: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""" ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:name "SEAweb" ; sc:url "http://sea.ims.bio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3168, edam:topic_3293, edam:topic_3512 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3198, edam:operation_3454 ; sc:license "MIT" ; sc:name "SECAPR" ; sc:softwareHelp ; sc:url "http://www.github.com/AntonelliLab/seqcap_processor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0623 ; sc:citation , "pubmed:29490010" ; sc:description "Webserver and deep neural network design tool for hierarchical biological sequence classification." ; sc:featureList edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SECLAF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pitgroup.org/seclaf/" ; biotools:primaryContact "Balázs Szalkai", "Vince Grolmusz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3315, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3227, edam:operation_3228 ; sc:license "MIT" ; sc:name "SECNVs" ; sc:url "https://github.com/YJulyXing/SECNVs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3474 ; sc:citation , "pmcid:PMC6612825", "pubmed:31510691" ; sc: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" ; sc:featureList edam:operation_0482 ; sc:name "SED" ; sc:url "https://zhanglab.ccmb.med.umich.edu/SED/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474, edam:topic_3810 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3443 ; sc:name "SEGAN" ; sc:url "https://github.com/vivitsai/SEGAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199 ; sc:citation ; sc:description "SELVa (Simulator of Evolution with Landscape Variation) - simulator of sequence evolution that allows the fitness landscape to vary according to user-specified rules." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SELVa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bazykinlab/SELVa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2640, edam:topic_3473 ; sc:citation , "pmcid:PMC6821276", "pubmed:31070723" ; sc: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" ; sc:featureList edam:operation_0306, edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SEMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sema.research.cchmc.org/" ; biotools:primaryContact "Kakajan Komurov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3169 ; sc:citation , "pmcid:PMC7999143", "pubmed:31373606" ; sc: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" ; sc:featureList edam:operation_0420, edam:operation_0445, edam:operation_3661 ; sc:name "SEMpl" ; sc:url "https://github.com/Boyle-Lab/SEM_CPP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1755 ; sc:encodingFormat edam:format_1475 ; sc:name "Protein atom" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_2814, edam:topic_3306 ; sc:citation , , "pubmed:31476974", "pubmed:31795635" ; sc: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." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "SEPAS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "SEPAS_V1, Dec 2019" ; sc:url "http://biophysics.ir/affinity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_2640, edam:topic_3174, edam:topic_3316 ; sc:citation , "pmcid:PMC6805339", "pubmed:31639030" ; sc: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""" ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_0337, edam:operation_3192, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "SEPATH" ; sc:url "https://github.com/UEA-Cancer-Genetics-Lab/sepath_tool_UEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2269, edam:topic_3168, edam:topic_3489 ; sc:citation , "pmcid:PMC6857306", "pubmed:31807141" ; sc:description "SEQdata-BEACON is a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3659 ; sc:name "SEQdata-BEACON" ; sc:url "http://seqbeacon.genomics.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3512, edam:topic_3794 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2499 ; sc:license "MIT" ; sc:name "SEQing" ; sc:url "https://github.com/malewins/SEQing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC6383233", "pubmed:30786880" ; sc:description "Modularized and customizable pipeline framework for NGS processing in R package." ; sc:featureList edam:operation_3192, edam:operation_3211, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SEQprocess" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://github.com/omicsCore/SEQprocess" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3308 ; sc:citation , "pmcid:PMC6075182", "pubmed:28172632" ; sc:description "SEQualyzer (Structure-profiling Experiment Quality Analyzer ) - interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data." ; sc:featureList edam:operation_2428, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SEQualyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bme.ucdavis.edu/aviranlab/SEQualyzer" ; biotools:primaryContact "Sharon Aviran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_0798, edam:topic_3301, edam:topic_3895 ; sc:citation , "pubmed:31740968" ; sc: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." ; sc:featureList edam:operation_0310, edam:operation_0578, edam:operation_3431, edam:operation_3435 ; sc:name "SEVA" ; sc:softwareVersion "3.0" ; sc:url "http://seva-plasmids.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3172, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:31605112" ; sc:description "SF-Matching(SubFragment-Matching) is a machine-learning based approach to predict compounds from tandem mass spectra." ; sc:featureList edam:operation_3431, edam:operation_3797, edam:operation_3803, edam:operation_3860 ; sc:name "SF-Matching" ; sc:url "http://www.bork.embl.de/Docu/sf_matching" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6901457", "pubmed:31819106" ; sc:description "SFLA IWSSr is an Efficient hybrid filter-wrapper metaheuristic-based gene selection method for high dimensional datasets." ; sc:featureList edam:operation_3454, edam:operation_3695, edam:operation_3891 ; sc:name "SFLA IWSSr" ; sc:url "https://github.com/jimy2020/SFLA_IWSSr-Feature-Selection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3173, edam:topic_3308 ; sc:citation ; sc: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  Browse 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" ; sc:featureList edam:operation_0313, edam:operation_0533, edam:operation_3501 ; sc:name "SGID" ; sc:url "http://sgid.popgenetics.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3303, edam:topic_3518 ; sc:citation , "pubmed:31786183" ; sc: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""" ; sc:featureList edam:operation_3435 ; sc:name "SGL-SVM" ; sc:url "https://github.com/QUST-AIBBDRC/SGL-SVM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0749, edam:topic_3304 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "SHYBRID" ; sc:url "https://github.com/jwouters91/shybrid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3375 ; sc:citation , "pubmed:30601937" ; sc:description "Software for Structural Identifiability ANalysis of ODE models." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SIAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/pogudingleb/SIAN" ; biotools:primaryContact "Gleb Pogudin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC7165230", "pubmed:31713070" ; sc: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.""" ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:name "SIIM" ; sc:url "https://siim.org/general/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC6868744", "pubmed:31752668" ; sc: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""" ; sc:featureList edam:operation_0253, edam:operation_0267, edam:operation_0417 ; sc:name "SIMLIN" ; sc:url "http://simlin.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2640, edam:topic_3320 ; sc:citation ; sc:description "Survival-significant Isoform Networks By Altered Domain-inclusion." ; sc:featureList edam:operation_2499, edam:operation_3359, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SINBAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/scwest/SINBAD" ; biotools:primaryContact "Sean West" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC5408816", "pubmed:28062442" ; sc:description "Tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SINE_scan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/maohlzj/SINE_Scan" ; biotools:primaryContact "Hao Wang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2546, edam:format_2572 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0860 ; sc:name "Sequence signature data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3895, edam:topic_3912 ; sc: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." ; sc:featureList edam:operation_2403, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SINGLe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rocioespci/single" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation ; sc:description "Robust Moiety Model Selection Using Mass Spectrometry Measured Isotopologues." ; sc:featureList edam:operation_3629, edam:operation_3660, edam:operation_3803 ; sc:name "SIRM" ; sc:url "https://pypi.org/project/moiety-modeling/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830, edam:topic_3305, edam:topic_3500, edam:topic_3673 ; sc:citation , "pmcid:PMC7028957", "pubmed:31862714" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SISTR" ; sc:softwareVersion "1.1.2" ; sc:url "https://github.com/phac-nml/sistr_cmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3518 ; sc:citation , "pmcid:PMC6581437", "pubmed:30388204" ; sc:description "Scalable software tool for gene network reverse engineering from big data." ; sc:featureList edam:operation_2495, edam:operation_2497, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SJARACNe" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/jyyulab/SJARACNe" ; biotools:primaryContact "Yu Lab in the Department of Computational Biology at St. Jude Children's Research Hospital" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_2830, edam:topic_3170, edam:topic_3676 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0252, edam:operation_3503, edam:operation_3659 ; sc:name "SKCMhrp" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/skcmhrp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0634, edam:topic_3070, edam:topic_3384 ; sc:citation , "pmcid:PMC4121546", "pubmed:25097821" ; sc: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)""" ; sc:featureList edam:operation_0306, edam:operation_1812, edam:operation_2421 ; sc:license "GPL-3.0" ; sc:name "SKIMMR" ; sc:url "https://github.com/vitnov/SKIMMR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC6528199", "pubmed:31109287" ; sc:description "Fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis." ; sc:featureList edam:operation_0484, edam:operation_2495, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SLAM-DUNK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://t-neumann.github.io/slamdunk" ; biotools:primaryContact , "Philipp Rescheneder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation ; sc:description "Simple Local Alignment Search Tool." ; sc:featureList edam:operation_0491, edam:operation_0495, edam:operation_2421 ; sc:name "SLAST" ; sc:url "https://www.dnaservic.es/dnaresult?ob=2&min=0.5&id=5191&qid=BdZIQbHRnfIsdH0O&tkt=&code=" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0634, edam:topic_3360, edam:topic_3518 ; sc:citation , "pubmed:31598632" ; sc:description "Single-sample landscape entropy reveals the imminent phase transition during disease progression." ; sc:featureList edam:operation_3435, edam:operation_3439, edam:operation_3454 ; sc:name "SLE" ; sc:url "https://github.com/rabbitpei/SLE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3512 ; sc:citation , "pmcid:PMC6330001", "pubmed:29955804" ; sc:description "Systems-Level Interactive Data Exploration (SLIDE) - web-based tool for interactive visualization of large-scale – omics data." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "SLIDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/soumitag/SLIDE" ; biotools:primaryContact "Hyungwon Choi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC6381720", "pubmed:30782112" ; sc:description "Web application for the reproducible processing of environmental DNA metabarcoding data." ; sc:featureList edam:operation_0450, edam:operation_3185, edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SLIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://trtcrd.github.io/SLIM/" ; biotools:primaryContact "Yoann Dufresne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168 ; sc:citation ; sc: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:" ; sc:featureList edam:operation_0524, edam:operation_3216, edam:operation_3798 ; sc:name "SLR-superscaffolder" ; sc:url "https://github.com/BGI-Qingdao/SLR-superscaffolder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2840, edam:topic_3343 ; sc:citation , "pmcid:PMC6509116", "pubmed:31073139" ; sc:description "Database of Chemical Constitutents of Smokeless Tobacco Products." ; sc:featureList edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SLTChemDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bic.icmr.org.in/sltchem" ; biotools:primaryContact "Harpreet Singh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0610, edam:topic_3299 ; sc:citation , , , , "pmcid:PMC10793872", "pmcid:PMC6389312", "pmcid:PMC6393187", "pmcid:PMC6501880", "pubmed:30517680", "pubmed:30565882", "pubmed:30590560", "pubmed:37130229" ; sc: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." ; sc:featureList edam:operation_0230, edam:operation_0550, edam:operation_3946 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SLiM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "4.3" ; sc:url "https://messerlab.org/slim/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "Using Python® language for the validation of the CCI soil moisture products via SM2RAIN." ; sc:featureList edam:operation_2428 ; sc:name "SM2RAIN" ; sc:url "http://hydrology.irpi.cnr.it/research/sm2rain/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6354025", "pubmed:30698691" ; sc:description "SMAGEXP (Statistical Meta-Analysis for Gene EXPression) - galaxy tool suite for transcriptomics data meta-analysis." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SMAGEXP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sblanck/smagexp" ; biotools:primaryContact "Samuel Blanck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_2640, edam:topic_3295 ; sc:citation , "pmcid:PMC6894252", "pubmed:31805986" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3204 ; sc:name "SMART App" ; sc:url "http://www.bioinfo-zs.com/smartapp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "Ultra-fast de novo assembler using long noisy reads" ; sc:featureList edam:operation_0524 ; sc:name "SMARTdenovo" ; sc:url "https://github.com/ruanjue/smartdenovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3399, edam:topic_3421 ; sc:citation , "pmcid:PMC7054179", "pubmed:31531896" ; sc: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)" ; sc:featureList edam:operation_3557 ; sc:name "SMARTp" ; sc:url "https://github.com/bandyopd/SMARTp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3292, edam:topic_3336 ; sc:citation , , "pmcid:PMC7328435", "pubmed:31603667" ; sc:description "Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative." ; sc:featureList edam:operation_2476, edam:operation_3893 ; sc:name "SMIRNOFF99Frosst" ; sc:url "https://github.com/openforcefield/smirnoff99Frosst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070 ; sc:citation , "pubmed:31483262" ; sc: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" ; sc:name "SMOG" ; sc:url "https://github.com/Onto-Med/SMOG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3520 ; sc:citation , "pmcid:PMC6885704", "pubmed:31591261" ; sc: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)""" ; sc:featureList edam:operation_3359, edam:operation_3643, edam:operation_3644, edam:operation_3646 ; sc:license "Apache-2.0" ; sc:name "SMSNet" ; sc:softwareHelp , ; sc:url "https://figshare.com/articles/SMSNet_s_trained_models/8259122" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3304, edam:topic_3334 ; sc:citation ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SMT-Genetic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dewancse/SMT-Genetic" ; biotools:primaryContact "Dewan Sarwar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC6853702", "pubmed:31099385" ; sc:description "Multi-SNP mediation intersection-union test." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SMUT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=SMUT" ; biotools:primaryContact "Wujuan Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC6334411", "pubmed:30646838" ; sc:description "R package for visualization and analysis of single-molecule localization microscopy data." ; sc:featureList edam:operation_3457, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "SMoLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/maartenpaul/SMoLR" ; biotools:primaryContact "Maarten Paul" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3293, edam:topic_3305 ; sc:citation ; sc: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" ; sc:featureList edam:operation_1812, edam:operation_3192, edam:operation_3196 ; sc:license "MIT" ; sc:name "SNAPPy" ; sc:softwareHelp ; sc:url "https://github.com/PMMAraujo/snappy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3325, edam:topic_3337 ; sc:citation "pubmed:17911793" ; sc:description "Web-based browser with comprehensive, scientifically validated clinical healthcare terminology. Enables consistent representation of clinical content in electronic health records." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SNOMED CT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.snomed.org/snomed-ct/five-step-briefing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC6943033", "pubmed:31511885" ; sc: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" ; sc:featureList edam:operation_0428, edam:operation_3196 ; sc:name "SNP2APA" ; sc:url "http://gong_lab.hzau.edu.cn/SNP2APA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2275 ; sc:citation , "pmcid:PMC6448223", "pubmed:30943891" ; sc:description "Modular workflow for standardizing molecular simulation and functional analysis of protein variants." ; sc:featureList edam:operation_0478, edam:operation_2476, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "SNP2SIM" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/mccoymd/SNP2SIM" ; biotools:primaryContact "Matthew McCoy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0208, edam:topic_0625, edam:topic_2885, edam:topic_3303 ; sc:citation ; sc:description "SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence." ; sc:featureList edam:operation_0331, edam:operation_0484, edam:operation_3661 ; sc:name "SNPector" ; sc:url "https://github.com/peterhabib/SNPector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3173, edam:topic_3517, edam:topic_3673 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3778 ; sc:name "SNPnotes" ; sc:url "https://github.com/shraddhapai/SNPNotes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc: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.)" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:name "SNPs" ; sc:url "http://snp-seek.irri.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0194, edam:topic_0610, edam:topic_2885 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3219 ; sc:name "SNiPlay" ; sc:url "http://sniplay.southgreen.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3068, edam:topic_3168, edam:topic_3895 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:name "SOLQC" ; sc:url "https://app.gitbook.com/@yoav-orlev/s/solqc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_3474 ; sc:citation , "pubmed:31603466" ; sc: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." ; sc:featureList edam:operation_0409, edam:operation_3436 ; sc:name "SOLart" ; sc:url "http://babylone.ulb.ac.be/SOLART/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation , "pubmed:25543048" ; sc:description "Python library implementing the full self-organizing map (SOM) analysis workflow." ; sc:featureList edam:operation_2476, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/bougui505/SOM" ; biotools:primaryContact "Guillaume Bouvier", "Michael Nilges" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3306 ; sc:citation ; sc:description "Scalable Open Network Architecture TemplAte (SONATA) Data Format for Efficient Description of Large-Scale Network Models." ; sc:featureList edam:operation_3435, edam:operation_3450, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SONATA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AllenInstitute/sonata" ; biotools:primaryContact "Anton Arkhipov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3316, edam:topic_3673 ; sc:citation , "pmcid:PMC6805285", "pubmed:31639049" ; sc: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""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "SORA" ; sc:softwareHelp ; sc:url "https://github.com/BioHPC/SORA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3673 ; sc:citation ; sc:description "SPAG is a tool for predicting the spatial distribution of adaptive genetic variants under future climatic conditions." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3891 ; sc:name "SPAG" ; sc:url "https://github.com/estellerochat/SPAG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC6488671", "pubmed:31036850" ; sc:description "Efficient algorithm on Apache Spark for aligning multiple similar DNA/RNA sequences with supervised learning." ; sc:featureList edam:operation_0323, edam:operation_0491, edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SPARK-MSNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sourceforge.net/projects/spark-msna/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0621 ; sc:citation ; sc:description "A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3432 ; sc:name "SPARQL" ; sc:url "https://sparql.orthodb.org/sparql" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31598633" ; sc:description "SPARSim is a count data simulator for scRNA-seq data." ; sc:featureList edam:operation_2426, edam:operation_2429, edam:operation_3799 ; sc:name "SPARSim" ; sc:url "https://sysbiobig.dei.unipd.it/software/sparsim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525 ; sc:name "SPAligner" ; sc:url "http://cab.spbu.ru/software/spaligner/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2851 ; sc:encodingFormat edam:format_3814 ; sc:name "Drug structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1696 ; sc:name "Drug report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3314 ; sc:citation , , "pubmed:27419846", "pubmed:27480236" ; sc:description "Structural and physico-chemical interpretation of QSAR models" ; sc:featureList edam:operation_2426, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "SPCI" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://qsar4u.com/pages/sirms_qsar.php" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_3120, edam:topic_3168 ; sc:citation , "pmcid:PMC7523648", "pubmed:31738401" ; sc:description "Data Model for Variants and Applications at NCBI." ; sc:featureList edam:operation_0525, edam:operation_3197, edam:operation_3436 ; sc:name "SPDI" ; sc:url "https://api.ncbi.nlm.nih.gov/variation/v0/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3070, edam:topic_3373 ; sc:citation , "pubmed:31377536" ; sc: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" ; sc:featureList edam:operation_0482 ; sc:license "MIT" ; sc:name "SPDRank" ; sc:url "https://github.com/akiyamalab/SPDRank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC6677810", "pubmed:31375721" ; sc: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" ; sc:featureList edam:operation_3644, edam:operation_3645, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "SPECTRUM" ; sc:url "https://github.com/BIRL/SPECTRUM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3384 ; sc:citation , "pmcid:PMC6498854", "pubmed:31057203" ; sc:description "Tool that computes point-based models using a parametric boundary description for the computing of Shape analysis." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SPHARM-PDM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.nitrc.org/projects/spharm-pdm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "Disentangling microbial associations from hidden environmental and technical factors via latent graphical models." ; sc:featureList edam:operation_2495, edam:operation_3625, edam:operation_3891 ; sc:name "SPIEC-EASI" ; sc:url "https://github.com/zdk123/SpiecEasi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_0736, edam:topic_0798, edam:topic_3168 ; sc:citation , "pmcid:PMC6954442", "pubmed:31745561" ; sc:description """Targeted insertional mutagenesis libraries for deep domain insertion profiling. SPINE: Saturated Programmable INsertion Engineering. Protein domain insertion via programmed oligo libraries""" ; sc:featureList edam:operation_0284, edam:operation_0303, edam:operation_0308 ; sc:license "MIT" ; sc:name "SPINE" ; sc:url "https://github.com/schmidt-lab/SPINE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3056 ; sc:citation , "pmcid:PMC6821363", "pubmed:31077292" ; sc:description "Simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SPLATCHE3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.splatche.com/splatche3" ; biotools:primaryContact "Mathias Currat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444 ; sc:citation "pubmed:266227768" ; sc:description "Statistical Parametric Mapping (SPM) software for the analysis of brain imaging data sequences." ; sc:featureList edam:operation_3435, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SPM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.fil.ion.ucl.ac.uk/spm/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:name "RNA secondary structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , "pmcid:PMC6881452", "pubmed:31776342" ; sc:description "RNA secondary structure predictor" ; sc:featureList edam:operation_0278 ; sc:isAccessibleForFree true ; sc:name "SPOT-RNA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sparks-lab.org/jaswinder/server/SPOT-RNA/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0123, edam:topic_0130, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31800243" ; sc: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.""" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0474, edam:operation_2492, edam:operation_2575 ; sc:license "MIT" ; sc:name "SPROF" ; sc:url "https://github.com/biomed-AI/SPROF" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2209 ; sc:name "Mutation ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1476 ; sc:name "PDB ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0224 ; sc:name "SPROUTS" ; sc:softwareVersion "1.0" ; sc:url "http://sprouts.rpbs.univ-paris-diderot.fr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579, edam:format_3591, edam:format_3592, edam:format_3603 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3682 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3682 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC6298046", "pubmed:30010780" ; sc:description "R package for filtering of spatially related peaks in mass spectrometry imaging data." ; sc:featureList edam:operation_3215, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SPUTNIK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/paoloinglese/SPUTNIK" ; biotools:primaryContact "Paolo Inglese" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3068, edam:topic_3169 ; sc:citation , "pubmed:31116370" ; sc: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." ; sc:featureList edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SPar-K" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/romaingroux/SPar-K" ; biotools:primaryContact "Philipp Bucher", "Romain Groux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC8386606", "pubmed:31752589" ; sc:description "Streamlined particle quantification (SParQ) plug-in is an automated fluorescent vesicle quantification plug-in for particle quantification in Fiji/ImageJ." ; sc:featureList edam:operation_3454, edam:operation_3458, edam:operation_3799 ; sc:name "SParQ" ; sc:url "https://github.com/sparq-plugin/sparq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3520, edam:topic_3697 ; sc:citation , "pmcid:PMC6739102", "pubmed:31506264" ; sc: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 [-d ] [-c ] [-l ] [-m ] [ -o \\] [-p ] [-n ] [-q ] [-v] [-e] | Command driven processing (Windows and Linux supported, MacOS unknown) | This program cannot be run on a Linux subsystem in Windows" ; sc:featureList edam:operation_3627, edam:operation_3637, edam:operation_3860 ; sc:license "MIT" ; sc:name "SPeDE" ; sc:url "https://github.com/LM-UGent/SPeDE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:name "SProCoP" ; sc:url "https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=SProCoP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293 ; sc:citation , "pmcid:PMC6893154", "pubmed:31536115" ; sc: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" ; sc:featureList edam:operation_0325, edam:operation_0551, edam:operation_3478 ; sc:name "SRH" ; sc:url "https://github.com/roblanf/SRHtests" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC7523684", "pubmed:31504202" ; sc: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" ; sc:name "SSASU" ; sc:url "https://github.com/brossetti/ssasu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2828, edam:topic_3306 ; sc:citation , "pmcid:PMC6903780", "pubmed:31570166" ; sc: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.""" ; sc:featureList edam:operation_0302, edam:operation_0320, edam:operation_0479 ; sc:name "SSEThread" ; sc:url "https://github.com/salilab/SSEThread" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0154, edam:topic_0199, edam:topic_3318 ; sc:citation , "pmcid:PMC7178439", "pubmed:31830252" ; sc: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""" ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_2495 ; sc:license "MIT" ; sc:name "SSIPe" ; sc:url "https://zhanglab.ccmb.med.umich.edu/SSIPe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0821, edam:topic_3293 ; sc:citation , "pmcid:PMC6827312", "pubmed:31501245" ; sc: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)" ; sc:license "GPL-3.0" ; sc:name "SSNpipe" ; sc:url "https://github.com/ahvdk/SSNpipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3318, edam:topic_3382 ; sc:citation , "pubmed:31634148" ; sc:description "Scaled Simplex Representation for Subspace Clustering." ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3659 ; sc:name "SSRSC" ; sc:url "https://github.com/csjunxu/SSRSC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3336, edam:topic_3474, edam:topic_3542 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2423 ; sc:name "SSnet" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/ekraka/SSnet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3361, edam:topic_3489 ; sc:citation , "pubmed:31880560" ; sc: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.""" ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:name "ST-SIM" ; sc:url "https://www.raniahassen.com/Research/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3444 ; sc:description "2D and 3D constrained Total Variation using the Split Bregman formulation" ; sc:featureList edam:operation_3359 ; sc:isAccessibleForFree true ; sc:name "HGGM-LIM Split-Bregman-ST-Total-Variation-MRI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/55211-hggm-lim-split-bregman-st-total-variation-mri" ; biotools:primaryContact "Juan Felipe Pérez Juste Abascal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3398 ; sc:citation , "pubmed:31789313" ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:name "STAFF" ; sc:softwareHelp ; sc:url "https://github.com/icbm-iupui/STAFF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0605, edam:topic_0654, edam:topic_3173, edam:topic_3518 ; sc:citation ; sc: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:""" ; sc:featureList edam:operation_3192 ; sc:license "BSD-3-Clause" ; sc:name "START-R" ; sc:url "https://github.com/thomasdenecker/START-R" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3324, edam:topic_3395 ; sc:citation , "pmcid:PMC6708268", "pubmed:31433284" ; sc: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" ; sc:featureList edam:operation_2426 ; sc:name "STEM" ; sc:url "http://www.eclipse.org/stem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885 ; sc:citation , "pubmed:30132900" ; sc:description "Probabilistic genotyping software that combines biological modelling and mathematical processes to interpret a wide range of complex DNA profiles." ; sc:featureList edam:operation_2428, edam:operation_3196, edam:operation_3629 ; sc:isAccessibleForFree false ; sc:license "Other" ; sc:name "STRmix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.strmix.com/" ; biotools:primaryContact "Vic Meles" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC6851049", "pubmed:31781551" ; sc: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""" ; sc:featureList edam:operation_2871, edam:operation_2929, edam:operation_3454 ; sc:name "STS-NLSP" ; sc:url "https://github.com/dqwei-lab/STS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3382, edam:topic_3518 ; sc:citation , "pubmed:30875427" ; sc:description "Tool for analysis and visualization of spatial transcriptomics datasets." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ST viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/SpatialTranscriptomicsResearch/st_viewer" ; biotools:primaryContact "Jose Fernandez Navarro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3305, edam:topic_3489 ; sc:citation ; sc: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/""" ; sc:featureList edam:operation_3211, edam:operation_3227, edam:operation_3472, edam:operation_3482, edam:operation_3840 ; sc:name "STing" ; sc:url "https://github.com/jordanlab/STing" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3603 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140 ; sc:citation , "pmcid:PMC6243280", "pubmed:30373828" ; sc:description "Visualize the human surface proteome (surfaceome) and load your own expression data to inspect and uncover cellular phenotypes and new surfaceome markers." ; sc:featureList edam:operation_2489, edam:operation_2942 ; sc:name "SURFY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://wlab.ethz.ch/surfaceome/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3302, edam:topic_3305, edam:topic_3500 ; sc:citation , "pubmed:31765613" ; sc: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.""" ; sc:name "SURVTOOLS" ; sc:url "https://survtools.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_3474 ; sc:citation , "pmcid:PMC6541270", "pubmed:31141524" ; sc:description "StrUctural Susceptibility PrEdiCTion on BDQ." ; sc:featureList edam:operation_0331, edam:operation_0478, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SUSPECT-BDQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biosig.unimelb.edu.au/suspect_bdq/" ; biotools:primaryContact "David B. Ascher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_2640, edam:topic_3300, edam:topic_3382 ; sc:citation , "pmcid:PMC6899515", "pubmed:31577949" ; sc: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""" ; sc:featureList edam:operation_0313, edam:operation_2436, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "SVCA" ; sc:url "https://github.com/damienArnol/svca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0625, edam:topic_3168, edam:topic_3175 ; sc:citation ; sc: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)""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3198, edam:operation_3227 ; sc:license "AGPL-3.0" ; sc:name "SVJedi" ; sc:url "https://github.com/llecompte/SVJedi.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3175, edam:topic_3512 ; sc:citation , "pmcid:PMC5408916", "pubmed:28031184" ; sc:description "Impact prediction tool for structural variation." ; sc:featureList edam:operation_0484, edam:operation_3436, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SVScore" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/lganel/SVScore" ; biotools:primaryContact "Ira M. Hall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0798, edam:topic_3175, edam:topic_3500 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0525, edam:operation_3198, edam:operation_3228 ; sc:license "GPL-3.0" ; sc:name "SVants" ; sc:url "https://github.com/EpiBlake/SVants" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0196, edam:topic_3170, edam:topic_3303 ; sc:citation , "pmcid:PMC6868818", "pubmed:31747936" ; sc: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." ; sc:featureList edam:operation_0524, edam:operation_2429, edam:operation_3192, edam:operation_3216, edam:operation_3227 ; sc:license "MIT" ; sc:name "SVs" ; sc:url "https://github.com/grocsvs/grocsvs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "Tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight." ; sc:featureList edam:operation_3431, edam:operation_3646 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SW-Tandem" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/Logic09/SW-Tandem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3316 ; sc:citation , "pubmed:31734873" ; sc:description """Counting Kmers for Biological Sequences at Large Scale. This is a distributed kmer counting tools for TB-PB sequencing dataset""" ; sc:featureList edam:operation_0524, edam:operation_3472, edam:operation_3695 ; sc:name "SWAPCounter" ; sc:url "https://github.com/mengjintao/SWAPCounter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3520, edam:topic_3673 ; sc:citation , "pmcid:PMC6743289", "pubmed:31523183" ; sc: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" ; sc:featureList edam:operation_3202, edam:operation_3644, edam:operation_3646 ; sc:name "SWPepNovo" ; sc:url "https://github.com/ChuangLi99/SWPepNovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0593, edam:topic_3047 ; sc:citation , "pmcid:PMC6895709", "pubmed:31711608" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3457, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "SWiFi" ; sc:url "https://github.com/barakgilboa/SWiFi-software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3500 ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SZN Zoological Collection Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://szn.i.hosei.ac.jp/HTML/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:37819886" ; sc: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." ; sc:featureList edam:operation_2428, edam:operation_3631, edam:operation_3633 ; sc:license "MIT" ; sc:name "Sage" ; sc:softwareHelp ; sc:url "https://github.com/lazear/sage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749 ; sc:citation , "pmcid:PMC6720087", "pubmed:31477007" ; sc: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" ; sc:featureList edam:operation_0441, edam:operation_0445, edam:operation_3439 ; sc:name "SalMotifDB" ; sc:url "https://salmobase.org/apps/SalMotifDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3407 ; sc:citation , "pmcid:PMC6727554", "pubmed:31488049" ; sc: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" ; sc:featureList edam:operation_0495, edam:operation_1812, edam:operation_2422 ; sc:name "SamPler" ; sc:url "https://gitlab.bio.di.uminho.pt/merlin-sysbio/merlin-sampler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC6499250", "pubmed:30252043" ; sc:description "Modular and versatile package for the quantitative analysis of high-throughput proteomics experiments." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SanXoT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cnic.es/wiki/proteomica/index.php/SanXoT_software_package" ; biotools:primaryContact "E. Bonzon-Kulichenko", "Jesús María Vázquez Cobos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_3676 ; sc:citation ; sc:description "Genome-wide copy number variants (CNV) calling from off-target reads." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SavvyCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rdemolgen/SavvySuite" ; biotools:primaryContact "Matthew N. Wakeling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3489 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3680 ; sc:name "ScType" ; sc:url "http://session.asuscomm.com:8080/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "Accurate reference-based transcript assembler." ; sc:featureList edam:operation_0264, edam:operation_3258, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Scallop-LR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Kingsford-Group/scallop" ; biotools:primaryContact "Carl Kingsford" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0204, edam:topic_0602, edam:topic_3308 ; sc:description "Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data" ; sc:featureList edam:operation_2437, edam:operation_3792 ; sc:license "AGPL-3.0" ; sc:name "Scan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/zhangjunpeng411/Scan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0160, edam:topic_0166, edam:topic_0622 ; sc:citation , "pmcid:PMC7205576", "pubmed:31711930" ; sc: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)""" ; sc:featureList edam:operation_0238, edam:operation_0502, edam:operation_2441 ; sc:name "ScanFold" ; sc:url "https://mosslabtools.bb.iastate.edu/scanfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "ScanITD: detecting internal tandem duplication with robust variant allele frequency estimation" ; sc:featureList edam:operation_3963 ; sc:name "ScanITD" ; sc:url "https://github.com/ylab-hi/ScanITD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3170 ; sc:citation ; sc: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 -i/--input -at/--aligner_tool " ; sc:featureList edam:operation_3198, edam:operation_3227, edam:operation_3798 ; sc:license "MIT" ; sc:name "Scavenger" ; sc:url "https://github.com/VCCRI/Scavenger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3489 ; sc:citation , "pmcid:PMC5832410", "pubmed:29424689" ; sc: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""" ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_3431 ; sc:name "Sci-Hub" ; sc:url "https://github.com/greenelab/scihub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3305, edam:topic_3810 ; sc:citation , "pmcid:PMC6529016", "pubmed:31071088" ; sc:description "Modeling framework for studying population-scale family trees that combines techniques from the animal and plant breeding literature and from human genetics literature." ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Sci-LMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TalShor/SciLMM" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2422, edam:operation_3208, edam:operation_3454 ; sc:name "SciApps" ; sc:url "https://sciapps.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3293, edam:topic_3297 ; sc:citation , "pmcid:PMC6702558", "pubmed:31528018" ; sc: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" ; sc:featureList edam:operation_0308, edam:operation_3200, edam:operation_3891 ; sc:name "Scientific Educational" ; sc:url "http://www.scied.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_2229 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0547, edam:operation_3196, edam:operation_3557 ; sc:name "ScisTree" ; sc:url "https://github.com/yufengwudcs/ScisTree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation , "pubmed:31116381" ; sc:description "SEquential REmasteriNg to DerIve Profiles for fast and accurate predictions of PPI interface positions." ; sc:featureList edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SeRenDIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.ibi.vu.nl/programs/serendipwww/" ; biotools:primaryContact "K. Anton Feenstra", "Paul de Geest", "Q. Hou" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1475 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1756 ; sc:encodingFormat edam:format_2077 ; sc:name "Protein residue" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_1317 ; sc:description "Annotation of secondary structure elements in proteins." ; sc:featureList edam:operation_0226 ; sc:name "SecStrAnnotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webchem.ncbr.muni.cz/API/SecStr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3794 ; sc:citation , "pubmed:27634948" ; sc:description "Accurate tool for somatic structural variation and virus integration detection." ; sc:featureList edam:operation_0452, edam:operation_3227, edam:operation_3228 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Seeksv" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/qiukunlong/seeksv" ; biotools:primaryContact "Bo Liao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3071, edam:topic_3474 ; sc:citation , "pmcid:PMC7148117", "pubmed:30923381" ; sc:description "PyTorch-based deep learning library for sequence data." ; sc:featureList edam:operation_3278, edam:operation_3279 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Selene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "0.3.1" ; sc:url "https://selene.flatironinstitute.org/" ; biotools:primaryContact "Troyanskaya Laborator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3321, edam:topic_3474 ; sc:citation , "pmcid:PMC6949135", "pubmed:30480667" ; sc:description "Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks (command line version of FORECasT)." ; sc:featureList edam:operation_2238, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SelfTarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/felicityallen/SelfTarget" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3295 ; sc:citation , "pmcid:PMC6612869", "pubmed:31510653" ; sc: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" ; sc:featureList edam:operation_0272, edam:operation_3192, edam:operation_3501 ; sc:name "Selfish" ; sc:url "https://github.com/ucrbioinfo/Selfish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3300, edam:topic_3360 ; sc:citation , "pubmed:31675495" ; sc:description "SeneQuest contains information on gene-to-senescence associations is crucial for increasing our understanding of the molecular mechanisms driving senescence." ; sc:name "SeneQuest" ; sc:url "http://Senequest.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3810 ; sc:citation , "pmcid:PMC6710408", "pubmed:31481971" ; sc: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" ; sc:featureList edam:operation_3227 ; sc:name "Sentieon DNASeq" ; sc:url "https://github.com/ncsa/Sentieon_DNASeq_Benchmarking" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3050, edam:topic_3837 ; sc:citation , "pmcid:PMC6802221", "pubmed:31628336" ; sc:description "Radar vision in the mapping of forest biodiversity from space." ; sc:featureList edam:operation_2429, edam:operation_2940, edam:operation_3435 ; sc:name "Sentinel-1" ; sc:url "https://github.com/So-YeonBae/Sentinel1-Biodiversity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3810 ; sc:citation ; sc:description "A Generic Practice for Generating Dual-pol Covariance Matrix Elements in SNAP S-1 Toolbox." ; sc:license "GPL-3.0" ; sc:name "Sentinel-1 SLC" ; sc:url "https://github.com/mrslab-iitb/sentinel-1-SLC-preprocessing-polarimetry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0199 ; sc:citation , "pubmed:31135038" ; sc: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." ; sc:featureList edam:operation_0250, edam:operation_0267, edam:operation_0455 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Seq2Feature" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.iitm.ac.in/bioinfo/SBFE/index.html" ; biotools:primaryContact "Prof. Michael Gromiha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc: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).." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3891 ; sc:name "SeqBreed" ; sc:url "https://github.com/miguelperezenciso/SeqBreed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0160, edam:topic_0623, edam:topic_3168 ; sc:citation , "pmcid:PMC7022958", "pubmed:31878100" ; sc:description "Graph Theory-Based Sequence Descriptors as Remote Homology Predictors." ; sc:featureList edam:operation_0524, edam:operation_3092, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "SeqDivA" ; sc:url "https://github.com/eancedeg/SeqDivA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC6856333", "pubmed:31540993" ; sc: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)" ; sc:featureList edam:operation_3182, edam:operation_3211, edam:operation_3482 ; sc:license "GPL-2.0" ; sc:name "SeqSero2" ; sc:url "http://denglab.info/SeqSero2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3673 ; sc:citation , "pmcid:PMC6602489", "pubmed:31045209" ; sc:description "Web server for the extraction of DNA or protein sequences from next-generation sequencing data." ; sc:featureList edam:operation_0433, edam:operation_3216, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SeqTailor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://shiva.rockefeller.edu/SeqTailor/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0218, edam:topic_0623, edam:topic_3474 ; sc:citation , "pmcid:PMC6918593", "pubmed:31847804" ; sc: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""" ; sc:featureList edam:operation_0267, edam:operation_0337, edam:operation_0477, edam:operation_2489, edam:operation_3904 ; sc:license "MIT" ; sc:name "SeqVec" ; sc:url "https://github.com/Rostlab/SeqVec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3382 ; sc:citation , "pmcid:PMC6954646", "pubmed:31368484" ; sc: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" ; sc:license "MIT" ; sc:name "Sequence tube maps" ; sc:url "https://vgteam.github.io/sequenceTubeMap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3168 ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Sequencing Initiative Suomi (SISu)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.sisuproject.fi/" ; biotools:primaryContact "Risto Kajanne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3305, edam:topic_3418 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3798, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "SeroCall" ; sc:url "https://github.com/knightjimr/serocall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc: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" ; sc:license "GPL-3.0" ; sc:name "Serosolver" ; sc:url "https://github.com/seroanalytics/serosolver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Evaluation of Cell Type Deconvolution R Packages on Single Cell RNA-seq Data." ; sc:featureList edam:operation_3435, edam:operation_3629, edam:operation_3659 ; sc:name "Seurat SingleR" ; sc:url "https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315 ; sc:citation ; sc:description "Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci | [posMatrix,retVals]=ShNeigh(heatmapMatrix,method_type)" ; sc:name "ShNeigh" ; sc:url "https://github.com/fangzhen-li/ShNeigh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_3474 ; sc:citation , "pmcid:PMC6612843", "pubmed:31510707" ; sc:description "RNA SHAPE prediction using graph kernel | SHApe simulation with graph KERnels | import shaker.rna_tools.rna_io as rio" ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_2441 ; sc:name "ShaKer" ; sc:url "https://github.com/BackofenLab/ShaKer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6366102", "pubmed:30727942" ; sc:description "Platform-agnostic data harmonizer for gene expression data." ; sc:featureList edam:operation_0313, edam:operation_0533, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Shambhala" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/oncobox-admin/harmony" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , ; sc:description "Fast tool for mapping-free gene separation of reads, using Bloom filter." ; sc:featureList edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Shark" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.2.0" ; sc:url "https://github.com/AlgoLab/shark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0632 ; sc:citation , "pmcid:PMC6933856", "pubmed:31730280" ; sc:description "Shift-T is a server for an automated Variable-Temperature NMR Data Analysis." ; sc:featureList edam:operation_0461, edam:operation_2476, edam:operation_3215 ; sc:license "MIT" ; sc:name "Shift-T" ; sc:url "http://meieringlab.uwaterloo.ca/shiftt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3297 ; sc:description "App developed in Shiny and usable in R environment that allows to visualize, explore, filter and extract data from FoodMicrobionet." ; sc:name "ShinyFMBN" ; sc:softwareVersion "1.1" ; sc:url "https://data.mendeley.com/datasets/8fwwjpm79y/1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC7178415", "pubmed:31882993" ; sc:description "ShinyGO is a graphical enrichment tool for animals and plants." ; sc:featureList edam:operation_2422, edam:operation_2436, edam:operation_3083 ; sc:name "ShinyGO" ; sc:url "http://bioinformatics.sdstate.edu/go/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3581 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3391, edam:topic_3473 ; sc:citation ; sc:description "A software framework for performing benchmarks of machine-learning classification algorithms" ; sc:featureList edam:operation_2990 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ShinyLearner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/srp33/ShinyLearner" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:name "Experimental measurement" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229, edam:topic_3934 ; sc:citation , "pmcid:PMC7214046", "pubmed:32049322" ; sc:description "Precise, high-performance FlowSOM-style cytometry data analysis in a browser, in an R Shiny app." ; sc:featureList edam:operation_0313, edam:operation_0571 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ShinySOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.com/exaexa/ShinySOM" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3382 ; sc:citation , "pmcid:PMC6834530", "pubmed:31736735" ; sc: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." ; sc:featureList edam:operation_1812, edam:operation_3450, edam:operation_3799 ; sc:name "ShuTu" ; sc:url "http://personal.psu.edu/dzj2/ShuTu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0625 ; sc:citation , "pmcid:PMC6836738", "pubmed:31628257" ; sc: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""" ; sc:featureList edam:operation_2238, edam:operation_3196, edam:operation_3432 ; sc:name "SiCloneFit" ; sc:url "https://bitbucket.org/hamimzafar/siclonefit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3474 ; sc:citation , "pubmed:31789550" ; sc: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""" ; sc:name "SiRJ" ; sc:url "https://grandjam.shinyapps.io/sirj" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3222, edam:operation_3891 ; sc:name "Sierra" ; sc:url "https://github.com/VCCRI/Sierra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2830, edam:topic_3379 ; sc:citation ; sc:description "Web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials." ; sc:featureList edam:operation_0560 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SieveSifter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sieve.fredhutch.org/viz" ; biotools:primaryContact "Andrew Fiore-Gartland" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0749, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC7703776", "pubmed:31697324" ; sc:description "scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies." ; sc:featureList edam:operation_0277, edam:operation_2428, edam:operation_3439 ; sc:name "SigHotSpotter" ; sc:url "https://SigHotSpotter.lcsb.uni.lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3068, edam:topic_3676 ; sc:citation ; sc:description "Tool for visualizing and exploring patterns of small mutational events." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "SigProfilerMatrixGenerator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AlexandrovLab/SigProfilerMatrixGenerator" ; biotools:primaryContact "Erik Bergstrom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0621, edam:topic_3474, edam:topic_3510 ; sc:citation , "pmcid:PMC6923836", "pubmed:31861981" ; sc: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""" ; sc:featureList edam:operation_0277, edam:operation_0418, edam:operation_3439 ; sc:name "SigUNet" ; sc:url "https://github.com/mbilab/SigUNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3169, edam:topic_3277, edam:topic_3308 ; sc:citation , "pmcid:PMC6823428", "pubmed:31672983" ; sc: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)""" ; sc:featureList edam:operation_0306, edam:operation_0440, edam:operation_0533, edam:operation_3359, edam:operation_3439 ; sc:name "Signaling Pathways Project" ; sc:softwareHelp ; sc:url "https://www.signalingpathways.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC6720940", "pubmed:31477009" ; sc: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" ; sc:featureList edam:operation_0337, edam:operation_3202, edam:operation_3435 ; sc:name "SigsPack" ; sc:url "https://github.com/bihealth/SigsPack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3382 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3501 ; sc:name "SikuliX" ; sc:url "http://sikulix.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3343 ; sc:citation , "pubmed:31066547" ; sc:description "SiliS-PTOXRA (DRY-in Silico Screening & Prediction of Toxic Hazard and Risk Assessment) for the prediction of toxicological endpoints." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SiliS-PTOXRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tomocomd.com/apps/ptoxra" ; biotools:primaryContact "César R. García-Jacas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3855 ; sc:citation ; sc: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:" ; sc:featureList edam:operation_0337, edam:operation_3891 ; sc:name "SimBSI" ; sc:softwareHelp ; sc:url "https://bitbucket.org/neatlabs/simbsi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3173, edam:topic_3308, edam:topic_3315 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2426, edam:operation_2495, edam:operation_3659 ; sc:license "MIT" ; sc:name "SimGEXPwMotifs" ; sc:url "https://github.com/Sim19/SimGEXPwMotifs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6061695", "pubmed:29596608" ; sc:description "Software tool enabling confident phosphosite assignment." ; sc:featureList edam:operation_3501, edam:operation_3627, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SimPhospho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/simphospho/" ; biotools:primaryContact "Garry L Corthals", "Veronika Suni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3168 ; sc:citation , "pmcid:PMC7141864", "pubmed:31764964" ; sc: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) """ ; sc:featureList edam:operation_3196, edam:operation_3562 ; sc:license "GPL-2.0" ; sc:name "SimRVSequences" ; sc:url "https://cran.r-project.org/web/packages/SimRVSequences/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0623, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6916212", "pubmed:31842741" ; sc: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""" ; sc:featureList edam:operation_0232, edam:operation_0491, edam:operation_2499 ; sc:name "SimSpliceEvol" ; sc:url "https://github.com/UdeS-CoBIUS/SimSpliceEvol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC7250144", "pubmed:31446517" ; sc: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" ; sc:name "SimVascular" ; sc:url "http://simvascular.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3512 ; sc:citation , "pubmed:31504187" ; sc: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" ; sc:featureList edam:operation_0476, edam:operation_3472, edam:operation_3644 ; sc:license "AGPL-3.0" ; sc:name "SimkaMin" ; sc:url "https://github.com/GATB/simka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC6917719", "pubmed:31848434" ; sc:description "An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces." ; sc:featureList edam:operation_3562 ; sc:name "SimpactCyan" ; sc:url "https://simpactcyan.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130 ; sc:citation , "pmcid:PMC6933846", "pubmed:31394001" ; sc: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" ; sc:name "SimpleDSFviewer" ; sc:url "https://github.com/hscsun/SimpleDSFviewer-5.0.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634 ; sc:citation , "pmcid:PMC6602488", "pubmed:31114901" ; sc:description "Interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database." ; sc:featureList edam:operation_3197, edam:operation_3436, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Simple ClinVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://simple-clinvar.broadinstitute.org/" ; biotools:primaryContact "Dennis Lal", "Eduardo Pérez-Palma", "Marie Gramm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pmcid:PMC6715530", "pubmed:31377170" ; sc: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" ; sc:featureList edam:operation_3800 ; sc:name "SingleCellNet" ; sc:url "https://github.com/pcahan1/singleCellNet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Inference of intercellular networks from single-cell transcriptomics." ; sc:featureList edam:operation_3083, edam:operation_3659 ; sc:name "SingleCellSignalR" ; sc:url "https://github.com/SCA-IRCM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3474 ; sc:citation , "pmcid:PMC6677298", "pubmed:31374080" ; sc: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" ; sc:featureList edam:operation_2422, edam:operation_3559, edam:operation_3760 ; sc:name "SinoPedia" ; sc:url "http://sinopedia.library.sh.cn/sparql" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3303, edam:topic_3360, edam:topic_3518 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0269, edam:operation_2495, edam:operation_3454 ; sc:name "SkinPhaser" ; sc:url "https://github.com/gangwug/SkinPhaser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6504038", "pubmed:31063501" ; sc:description "Automated sleep stage scoring with sequence to sequence deep learning approach." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SleepEEGNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SajadMo/SleepEEGNet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3512, edam:topic_3534 ; sc:citation , "pubmed:31494246" ; sc: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" ; sc:featureList edam:operation_3096, edam:operation_3901, edam:operation_3902 ; sc:name "SliceIt" ; sc:url "http://sliceit.soic.iupui.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6836736", "pubmed:31519740" ; sc: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" ; sc:featureList edam:operation_0308, edam:operation_2495, edam:operation_3233 ; sc:name "Smart-3SEQ" ; sc:url "https://github.com/jwfoley/Smart-3SEQ_paper_scripts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3360, edam:topic_3421, edam:topic_3512, edam:topic_3577 ; sc:citation , "pmcid:PMC6854692", "pubmed:31754347" ; sc:description "Two predictive precision medicine tools for hepatocellular carcinoma." ; sc:featureList edam:operation_0531, edam:operation_3503, edam:operation_3659 ; sc:name "Smart Cancer Predictive System" ; sc:url "https://zhangzhiqiao2.shinyapps.io/Smart_cancer_predictive_system_HCC_2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3298, edam:topic_3337 ; sc:citation , "pmcid:PMC7115897", "pubmed:31591642" ; sc: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) )""" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3659 ; sc:license "LGPL-2.0" ; sc:name "SmoothWin" ; sc:url "http://CRAN.R-project.org/package=SmoothWin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3315 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3472 ; sc:license "Apache-2.0" ; sc:name "Smudgeplots" ; sc:url "https://github.com/KamilSJaron/smudgeplot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC6879379", "pubmed:31777414" ; sc: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!""" ; sc:name "Snorkel DryBell" ; sc:url "http://snorkel.stanford.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3068, edam:topic_3168 ; sc:citation ; sc:description "Web-server framework to explore and visualize large genomic variation data in lab and its applications to wheat and its progenitors." ; sc:featureList edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SnpHub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://guoweilong.github.io/SnpHub/" ; biotools:primaryContact "Weilong Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3855 ; sc:citation , "pmcid:PMC6411228", "pubmed:30811390" ; sc:description "Script of Scripts (SoS) is a computational environment for the development and execution of scripts in multiple languages for daily computational research." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SoS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://vatlab.github.io/sos-docs/" ; biotools:primaryContact "B. Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3050, edam:topic_3810 ; sc:citation , "pmcid:PMC6530169", "pubmed:31117932" ; sc:description "Identification and resolution of plant taxonomic names." ; sc:featureList edam:operation_0495, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Solr-Plant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bcbi.brown.edu/solrplant" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0091, edam:topic_0797 ; sc:author ; sc:citation , "pmcid:PMC6298048", "pubmed:30032301" ; sc:description "SonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species." ; sc:featureList edam:operation_0292, edam:operation_0324, edam:operation_2423, edam:operation_3209 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SonicParanoid" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.9" ; sc:url "http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6834292", "pubmed:31652275" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3562 ; sc:name "SourceSet" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/SourceSet/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:citation ; sc: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.""" ; sc:name "SouthGreen platform" ; sc:softwareHelp , , ; sc:url "https://southgreen.fr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_1929 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0797, edam:topic_3308, edam:topic_3810 ; sc:citation , , "pmcid:PMC3662865", "pmcid:PMC4383925", "pubmed:23707967", "pubmed:25392413" ; sc: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, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers)." ; sc:featureList edam:operation_0338, edam:operation_2403, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "South Green Genome Hubs" ; sc:softwareHelp ; sc:url "https://www.southgreen.fr/genomehubs" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6747016", "pubmed:31549018" ; sc: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" ; sc:featureList edam:operation_3439, edam:operation_3463, edam:operation_3766 ; sc:name "SoyCSN" ; sc:url "http://soykb.org/SoyCSN" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "A Soybean mine instance with genomic data from the Legume Information Systems (LIS) multi-species chado database and genetic data pulled from Soybase" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "SoyMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/soymine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation , "pubmed:31550555" ; sc: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" ; sc:name "SpCLUST" ; sc:url "https://github.com/johnymatar/SpCLUST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3308, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_3799 ; sc:license "MIT" ; sc:name "SpaCell" ; sc:url "https://github.com/BiomedicalMachineLearning/SpaCell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0310, edam:operation_3432, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SpaRC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/berkeleylab/jgi-sparc/" ; biotools:primaryContact "Zhong Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6598954", "pubmed:31093725" ; sc:description "Encouraging durable memory using spaced testing in pediatric radiology." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Spaced Radiology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.spacedradiology.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Spaniel Spatial Transcriptomics Analysis." ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Spaniel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/RachelQueen1/Spaniel" ; biotools:primaryContact "Rachel Queen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2830, edam:topic_3315, edam:topic_3379, edam:topic_3474 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0252, edam:operation_2495, edam:operation_3659 ; sc:name "Spark" ; sc:url "http://spark.apache.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3168, edam:topic_3316 ; sc:citation , "pmcid:PMC6894754", "pubmed:31805063" ; sc: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)""" ; sc:featureList edam:operation_0487, edam:operation_2409, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "SparkGA2" ; sc:url "https://github.com/HamidMushtaq/SparkGA2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7145543", "pubmed:31713629" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3501 ; sc:name "SpatialDB" ; sc:url "https://www.spatialomics.org/SpatialDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0491, edam:operation_3198, edam:operation_3695 ; sc:name "Spectral Jaccard Similarity" ; sc:url "https://github.com/TavorB/spectral_jaccard_similarity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3802 ; sc:name "SpikeInterface" ; sc:url "http://github.com/SpikeInterface" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382, edam:topic_3406 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3450, edam:operation_3799 ; sc:name "SpineJ" ; sc:url "https://github.com/flevet/SpineJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3320, edam:topic_3474 ; sc:citation , "pmcid:PMC6933889", "pubmed:31881982" ; sc:description """ab initio prediction of splice sites using convolutional neural network. This is the source code for SpliceFinder""" ; sc:featureList edam:operation_0232, edam:operation_0433, edam:operation_3439 ; sc:name "SpliceFinder" ; sc:url "https://gitlab.deepomics.org/wangruohan/SpliceFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3577 ; sc:citation , "pubmed:31617569" ; sc: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""" ; sc:featureList edam:operation_2499, edam:operation_3225, edam:operation_3800 ; sc:license "MIT" ; sc:name "SpliceLauncher" ; sc:url "https://github.com/raphaelleman/SpliceLauncher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6507234", "pubmed:31068132" ; sc:description "Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SpliceV" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/flemingtonlab/SpliceV" ; biotools:primaryContact "Erik Flemington" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3474 ; sc:citation , "pubmed:29580738" ; sc:description "SpliceVec: Distributed feature representations for splice junction prediction" ; sc:featureList edam:operation_0337, edam:operation_2990 ; sc:name "SpliceVec-g" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/aaiitggrp/SpliceVec-g" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_3474 ; sc:citation , "pubmed:31783254" ; sc: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""" ; sc:featureList edam:operation_2990, edam:operation_3083 ; sc:name "SpliceVisuL" ; sc:url "https://github.com/aaiitggrp/SpliceVisuL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:30993321" ; sc:description "Integrative, scalable tool for the discovery of splice-altering variants." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Spliceogen" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/VCCRI/Spliceogen" ; biotools:primaryContact "Steve Monger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3174 ; sc:citation , "pmcid:PMC6765119", "pubmed:31361894" ; sc: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" ; sc:featureList edam:operation_0484, edam:operation_3227, edam:operation_3461 ; sc:name "SpydrPick" ; sc:url "https://anaconda.org/bioconda/spydrpick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3293, edam:topic_3382 ; sc:citation , "pubmed:30247632" ; sc:description "Software tool that automatically generates interactive web-based two-dimensional graphical representations of raw DNA sequences." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Squiggle" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Lab41/squiggle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6700779", "pubmed:31426747" ; sc: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" ; sc:featureList edam:operation_0417, edam:operation_0430, edam:operation_3186 ; sc:name "SssI" ; sc:url "http://bioserv.mps.ohio-state.edu/SssICalc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC6736036", "pubmed:30649230" ; sc:description "R Package for Stacking with Applications to Scenarios Involving Sequential Addition of Samples and Features." ; sc:featureList edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Sstack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://cran.r-project.org/web/packages/Sstack/index.html" ; biotools:primaryContact "Kevin Matlock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_3474 ; sc:citation , "pubmed:31683069" ; sc:description "A stacking based prediction of protein-carbohydrate binding sites from sequence." ; sc:featureList edam:operation_2575 ; sc:name "StackCBPred" ; sc:url "https://bmll.cs.uno.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3304 ; sc:citation , "pmcid:PMC6643891", "pubmed:31040111" ; sc:description "Interscholastic Network To Generate LexA Enhancer Trap Lines in Drosophila." ; sc:featureList edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "StanEx1" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://stanex.stanford.edu/about/" ; biotools:primaryContact "Lutfi Huq", "Seung K. Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3277, edam:topic_3489 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3211, edam:operation_3431, edam:operation_3482, edam:operation_3840 ; sc:license "MIT" ; sc:name "Staphopia" ; sc:url "http://staphopia.emory.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3293 ; sc:citation , , "pmcid:PMC4137710", "pubmed:24899668", "pubmed:30298398" ; sc: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." ; sc:featureList edam:operation_0323, edam:operation_0503 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "StatAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://statalign.github.io/" ; biotools:primaryContact "Adam Novak", "Joe Herman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation ; sc:description "Stereological and Automated Analysis Platform for Assessing Histological Labelling in Cleared Tissue Specimens." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "StereoMate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://imagej.net/StereoMate" ; biotools:primaryContact "David L. Bennett", "Steven J. West" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0166, edam:topic_3169, edam:topic_3179, edam:topic_3794 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_2575, edam:operation_3215, edam:operation_3222, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "StoatyDive" ; sc:url "https://anaconda.org/bioconda/stoatydive" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC8215912", "pubmed:31418766" ; sc: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" ; sc:featureList edam:operation_0545, edam:operation_0555, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "StrainHub" ; sc:url "http://strainhub.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3308, edam:topic_3360, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6923958", "pubmed:31856731" ; sc: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""" ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3196, edam:operation_3565 ; sc:name "StressGenePred" ; sc:url "https://github.com/bhi-kimlab/StressGenePred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_3300, edam:topic_3304, edam:topic_3334 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "String-pulling" ; sc:url "https://github.com/samsoon-inayat/string_pulling_mouse_matlab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885 ; sc:citation , "pmcid:PMC6694510", "pubmed:31412777" ; sc: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" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "Stripes" ; sc:url "https://github.com/CarlborgGenomics/Stripes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154 ; sc:citation , "pubmed:26615437" ; sc:description "Program for alignment of structures of DNA-protein complexes." ; sc:featureList edam:operation_0295, edam:operation_0303, edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "StructAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mouse.genebee.msu.ru/tools/StructAlign.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_0196 ; sc:citation , "pubmed:30124779" ; sc:description "Tool for 3D protein structure profiling." ; sc:featureList edam:operation_0249, edam:operation_0321, edam:operation_0482 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "StructureProfiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.zbh.uni-hamburg.de/forschung/amd/software/structureprofiler.html" ; biotools:primaryContact "Matthias Rarey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3460 ; sc:name "Struo" ; sc:url "https://github.com/leylabmpi/Struo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3379 ; sc:citation , "pmcid:PMC6904404", "pubmed:31823031" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "StudyPortal" ; sc:url "https://studyportal.uni-muenster.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3314, edam:topic_3448 ; sc:citation , "pubmed:31508962" ; sc:description "A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces | SuAVE: Surface Assessment Via grid Evaluation" ; sc:featureList edam:operation_0387, edam:operation_1816 ; sc:name "SuAVE" ; sc:url "http://www.biomatsite.net/suave-software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3336 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_0482, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SuCOS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/susanhleung/SuCOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0621, edam:topic_0634, edam:topic_2229, edam:topic_3407 ; sc:citation , "pubmed:31603468" ; sc: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""" ; sc:featureList edam:operation_0253, edam:operation_2489, edam:operation_3092 ; sc:name "SubMito-XGBoost" ; sc:url "https://github.com/QUST-AIBBDRC/SubMito-XGBoost/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation , "pmcid:PMC6518800", "pubmed:31088372" ; sc:description "Random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Subdyquency" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/weiba/Subdyquency" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_3314 ; sc:citation , "pmcid:PMC6320881", "pubmed:30563078" ; sc: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." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SugarSketcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://glycoproteome.expasy.org/sugarsketcher/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0621, edam:topic_0622, edam:topic_3810 ; sc:author ; sc:citation , "pmcid:PMC6035169", "pubmed:29980662" ; sc:description "The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources." ; sc:featureList edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Sugarcane Genome Hub" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sugarcane-genome.cirad.fr/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_3068, edam:topic_3174, edam:topic_3293 ; sc:citation , "pmcid:PMC9825549", "pubmed:36318251" ; sc: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" ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "SulfAtlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sulfatlas.sb-roscoff.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC6485398", "pubmed:30510236" ; sc:description "Software for estimating confounding bias, SNP heritability, enrichments of heritability and genetic correlations using summary statistics from genome-wide association studies." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SumHer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dougspeed.com/sumher/" ; biotools:primaryContact "Doug Speed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2640 ; sc:citation , "pmcid:PMC6692773", "pubmed:31142576" ; sc:description "An R package for summarizing multiple enrichment analysis results." ; sc:featureList edam:operation_2497, edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Sumer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bzhanglab/sumer" ; biotools:primaryContact "Zhiao Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC6931355", "pubmed:30911754" ; sc:description "Tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SummaryAUC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lsncibb/SummaryAUC" ; biotools:primaryContact "Jianxin Shi", "Lei Song" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3474, edam:topic_3794 ; sc:citation , "pubmed:31545722" ; sc: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:" ; sc:featureList edam:operation_3629 ; sc:name "Super-Resolution" ; sc:url "https://github.com/aamir-mustafa/super-resolution-adversarial-defense" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6798642", "pubmed:31681583" ; sc: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""" ; sc:name "SuperCRF" ; sc:url "https://github.com/Henrik86/SuperCRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6770523", "pubmed:31480377" ; sc: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" ; sc:featureList edam:operation_3432, edam:operation_3458 ; sc:name "SuperCryoEMPicker" ; sc:url "https://github.com/jianlin-cheng/SuperCryoEMPicker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:31116387" ; sc:description "Random Forest and Gaussian Mixture predictor of high confidence genotypes in single cell data." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SureTypeSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/puko818/SureTypeSC" ; biotools:primaryContact "Ivan Vogel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC6509810", "pubmed:31072374" ; sc:description "Pipeline for high-throughput extraction of cell contours from 3D image stacks." ; sc:featureList edam:operation_3446, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CECILL-C" ; sc:name "SurfCut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/sverger/SurfCut" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3399, edam:topic_3421 ; sc:citation "pmcid:PMC6143968" ; sc: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 }}" ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:name "SweGen" ; sc:url "https://swegen-exac.nbis.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0621, edam:topic_0622, edam:topic_3293 ; sc:citation , "pmcid:PMC6812468", "pubmed:31648300" ; sc: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""" ; sc:featureList edam:operation_0327, edam:operation_0544, edam:operation_2421, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "SwiftOrtho" ; sc:url "https://github.com/Rinoahu/SwiftOrtho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6765120", "pubmed:31372651" ; sc:description "> LOW CONFIDENCE! | Nonparametric expression analysis using inferential replicate counts | R scripts used in the Swish paper" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3800 ; sc:name "Swish" ; sc:url "https://github.com/azhu513/swishPaper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3676 ; sc:citation , "pubmed:30565316" ; sc:description "System for Quality-Assured Data Analysis (SyQADA) - workflow management system that seeks to improve reproducibility in as simple a framework as feasible." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SyQADA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://scheetlabsoftware.org/syqada/" ; biotools:primaryContact "Paul Scheet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2885, edam:topic_3168, edam:topic_3175 ; sc:citation , "pmcid:PMC6913012", "pubmed:31842948" ; sc: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.""" ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_3196, edam:operation_3198, edam:operation_3227 ; sc:name "SyRI" ; sc:url "https://schneebergerlab.github.io/syri/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3569 ; sc:citation , ; sc: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.""" ; sc:name "SymPy" ; sc:url "https://www.sympy.org/en/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3398, edam:topic_3895 ; sc:citation , "pmcid:PMC6690502", "pubmed:31423466" ; sc: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" ; sc:featureList edam:operation_2422, edam:operation_3431 ; sc:name "SynBioHub" ; sc:url "https://synbiohub.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8215930", "pubmed:31596456" ; sc: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])""" ; sc:featureList edam:operation_3435, edam:operation_3450, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "SynQuant" ; sc:url "https://github.com/yu-lab-vt/SynQuant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Specific tools for pre-processing datas in order to use them in SynTView." ; sc:name "SynTViewTools" ; sc:url "https://bioweb.pasteur.fr/packages/pack@SynTViewTools@0.0.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC7145678", "pubmed:31728519" ; sc: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""" ; sc:featureList edam:operation_2422 ; sc:name "SyntDB" ; sc:url "http://syntdb.amu.edu.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0102, edam:topic_0749, edam:topic_0797 ; sc:citation , "pmcid:PMC6892358", "pubmed:31776723" ; sc: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""" ; sc:featureList edam:operation_3194, edam:operation_3208, edam:operation_3209 ; sc:license "CC-BY-4.0" ; sc:name "Synteny Browser" ; sc:url "http://syntenybrowser.jax.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0749, edam:topic_3295, edam:topic_3512 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0445, edam:operation_2575, edam:operation_3463 ; sc:name "T-Gene" ; sc:url "http://meme-suite.org/tools/tgene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3379, edam:topic_3473 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0306 ; sc:name "T-Library" ; sc:url "http://www.picoron.com/tlibrary/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6613037", "pubmed:31510645" ; sc: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" ; sc:featureList edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "T-MTSCCA" ; sc:url "https://github.com/dulei323/TMTSCCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC7703783", "pubmed:31580402" ; sc: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.""" ; sc:featureList edam:operation_3196, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "T-lex3" ; sc:url "https://github.com/GonzalezLab/T-lex3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3047, edam:topic_3170, edam:topic_3489 ; sc:citation , "pmcid:PMC7145666", "pubmed:31624839" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0464, edam:operation_2421, edam:operation_2422 ; sc:name "T-psi-C" ; sc:url "http://tpsic.igcz.poznan.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3390, edam:topic_3418 ; sc:citation , "pmcid:PMC6701161", "pubmed:31389338" ; sc: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" ; sc:name "T1D" ; sc:url "http://T1DToolkit.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8594479", "pubmed:34531327" ; sc:description "T1TAdb is a database of Type I Toxin-Antitoxin systems." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0346, edam:operation_2488 ; sc:name "T1TAdb" ; sc:url "https://d-lab.arna.cnrs.fr/t1tadb" ; biotools:primaryContact "Fabien Darfeuille", "Nicolas J. Tourasse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6873396", "pubmed:31757212" ; sc: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." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3435 ; sc:name "TACITuS" ; sc:url "https://tacitus.app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295, edam:topic_3512, edam:topic_3673 ; sc:citation , "pmcid:PMC6933632", "pubmed:31881832" ; sc: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)""" ; sc:featureList edam:operation_0303, edam:operation_0438, edam:operation_2404 ; sc:name "TAD-Lactuca" ; sc:url "https://github.com/LoopGan/TAD-Lactuca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3293, edam:topic_3697 ; sc:citation , "pmcid:PMC6612822", "pubmed:31510701" ; sc: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" ; sc:name "TADA" ; sc:url "https://github.com/tada-alg/TADA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3512, edam:topic_3517 ; sc:citation , "pmcid:PMC6698643", "pubmed:31045203" ; sc:description "Genome-wide supervised learning of non-coding loci associated to complex phenotypes." ; sc:featureList edam:operation_0488, edam:operation_3232, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TAGOOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/aitgon/tagoos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3557, edam:topic_3697 ; sc:citation , "pmcid:PMC6292648", "pubmed:30507938" ; sc:description "Tool for analysis of the morphology of microbial colonies." ; sc:featureList edam:operation_0417, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TAMMiCol" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/HaydenTronnolone/TAMMiCol" ; biotools:primaryContact "H. Tronnolone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3512, edam:topic_3534 ; sc:citation , "pmcid:PMC6454472", "pubmed:30052912" ; sc:description "Tool for alternative polyadenylation site analysis." ; sc:featureList edam:operation_2575, edam:operation_3798, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TAPAS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/arefeen/TAPAS" ; biotools:primaryContact "Tao Jiang", "Xinshu Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6549370", "pubmed:31164077" ; sc:description "Pipeline for TARgeted VIRal strain reconstruction from metagenomic data." ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TAR-VIR" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/chjiao/TAR-VIR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc: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." ; sc:featureList edam:operation_0346 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TARA BLAST Service" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.szn.it/tara-oceans-data-blast-service/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3895 ; sc:citation , "pubmed:31053031" ; sc:description "Package for Calibrated Flow Cytometry Analysis." ; sc:featureList edam:operation_3501, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TASBE Flow Analytics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tasbe.github.io/" ; biotools:primaryContact "Jacob Beal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_0821, edam:topic_3297, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0474, edam:operation_1777, edam:operation_3092 ; sc:license "MIT" ; sc:name "TAXyl" ; sc:url "https://github.com/mehdiforoozandeh/TAXyl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3063, edam:topic_3324, edam:topic_3384 ; sc:citation , , "pubmed:31838261" ; sc: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.""" ; sc:name "TB Portals" ; sc:url "https://tbportals.niaid.nih.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC6752186", "pubmed:31576231" ; sc:description "Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma." ; sc:featureList edam:operation_0531, edam:operation_3503, edam:operation_3659 ; sc:name "TCGA-LGG" ; sc:url "https://portal.gdc.cancer.gov/projects/TCGA-LGG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3293 ; sc:citation , "pmcid:PMC6756559", "pubmed:31509525" ; sc: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:" ; sc:featureList edam:operation_0552, edam:operation_0555, edam:operation_3478 ; sc:name "TCGenerators" ; sc:url "https://github.com/bielcardona/TCGenerators" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0202, edam:topic_0749, edam:topic_3068, edam:topic_3407 ; sc:citation , "pmcid:PMC6874874", "pubmed:31781261" ; sc:description "A Network Pharmacology Approach for Uncovering the Osteogenic Mechanisms of Psoralea corylifolia Linn." ; sc:featureList edam:operation_2436, edam:operation_2489 ; sc:name "TCMSP" ; sc:url "https://old.tcmsp-e.com/tcmsp.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_0749 ; sc:citation ; sc:description "T Cell Relation Extraction (TCRE) - Extracting T Cell Function and Differentiation Characteristics from the Biomedical Literature." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TCRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hammerlab/t-cell-relation-extraction" ; biotools:primaryContact "Eric Czech" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0252, edam:operation_2403, edam:operation_2995, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "TCRex" ; sc:softwareHelp ; sc:softwareVersion "v0.2.1" ; sc:url "https://tcrex.biodatamining.be/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0154, edam:topic_0804, edam:topic_2275 ; sc:citation , "pmcid:PMC6787230", "pubmed:31601838" ; sc: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""" ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3899 ; sc:name "TCRpMHCmodels" ; sc:url "http://www.cbs.dtu.dk/services/TCRpMHCmodels/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC6612886", "pubmed:31510643" ; sc: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)" ; sc:featureList edam:operation_0239, edam:operation_3557 ; sc:license "MIT" ; sc:name "TCSM" ; sc:url "https://github.com/lrgr/tcsm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6889579", "pubmed:31795943" ; sc:description "A novel target convergence set based random walk with restart for prediction of potential LncRNA-disease associations." ; sc:name "TCSRWRLD" ; sc:url "http://www.cuilab.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0224, edam:operation_0436, edam:operation_3644 ; sc:license "GPL-3.0" ; sc:name "TCW" ; sc:url "https://github.com/csoderlund/TCW" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:10964570" ; sc:description "Multiple sequence alignment program. The main characteristic is that it will allow you to combine results obtained with several alignment methods." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "T-Coffee API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/msa/tcoffee_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Cedric Notredame" ; sc:citation , , , "pmcid:PMC11223882", "pmcid:PMC9252731", "pubmed:10964570", "pubmed:35412617", "pubmed:38597606" ; sc:description "Multiple sequence alignment that combines several alignment methods." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "T-Coffee (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CRG", "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/msa/tcoffee/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0622 ; sc:citation , "pmcid:PMC3125728", "pubmed:21558174" ; sc: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." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "T-Coffee (SIB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tcoffee.vital-it.ch/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6663192", "pubmed:31410373" ; sc: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" ; sc:featureList edam:operation_3216, edam:operation_3562 ; sc:name "TDA" ; sc:url "http://www.stat.wisc.edu/~mchung/TDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3168, edam:topic_3519 ; sc:citation , "pmcid:PMC6690219", "pubmed:31428129" ; sc: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" ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3196 ; sc:name "TDNAscan" ; sc:url "https://github.com/noble-research-institute/TDNAscan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3752 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3170, edam:topic_3173, edam:topic_3474 ; sc:citation ; sc: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." ; sc:featureList edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "TDimpute" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "https://github.com/sysu-yanglab/TDimpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3673 ; sc:description "TE-Tracker is a program for detecting germline transposition events through whole-genome resequencing." ; sc:name "TE-Tracker" ; sc:url "http://www.genoscope.cns.fr/externe/tetracker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3305 ; sc:citation , "pmcid:PMC6860463", "pubmed:31705406" ; sc: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""" ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3435 ; sc:name "TECH-VER" ; sc:url "https://www.imta.nl/techver" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:encodingFormat edam:format_1957 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0736 ; sc:citation , "pubmed:30585105" ; sc:description "Graph-based computational method for decomposing protein structures into closed loops." ; sc:featureList edam:operation_0246 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "TEF" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::TEF" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203 ; sc:citation , "pubmed:31095490" ; sc:description "Prediction of essential proteins by integrating network topology, subcellular localization information, gene expression profile and GO annotation data." ; sc:featureList edam:operation_2489, edam:operation_2492, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TEGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wzhangwhu/TEGS" ; biotools:primaryContact "Wei Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3399 ; sc:citation ; sc:description "TEMPO (TEmporal Modeling of Pathway Outliers) - method for modeling and detecting gene sets with disruption of some temporal pattern of expression." ; sc:featureList edam:operation_2436, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TEMPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bcb.cs.tufts.edu/tempo/" ; biotools:primaryContact "Christopher Pietras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3295 ; sc:citation , "pmcid:PMC6899341", "pubmed:31824778" ; sc:description "TEffectR is an R package for studying the potential effects of transposable elements on gene expression with linear regression model." ; sc:featureList edam:operation_2495, edam:operation_3659, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "TEffectR" ; sc:url "https://github.com/karakulahg/TEffectR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199 ; sc:citation , "pubmed:31381222" ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3216 ; sc:name "TEs" ; sc:url "https://mcstitzer.github.io/maize_TEs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0736, edam:topic_0749, edam:topic_0780, edam:topic_3293 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3478 ; sc:name "TEsorter" ; sc:url "https://github.com/zhangrengang/TEsorter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_3169, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC7145579", "pubmed:31665425" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0445, edam:operation_3092, edam:operation_3891, edam:operation_3894 ; sc:name "TFBSshape" ; sc:url "https://tfbsshape.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation , "pubmed:31746988" ; sc: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""" ; sc:featureList edam:operation_0463, edam:operation_3083, edam:operation_3792 ; sc:name "TFmiR2" ; sc:url "http://service.bioinformatik.uni-saarland.de/tfmir2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3173, edam:topic_3512, edam:topic_3674 ; sc:citation , "pmcid:PMC6954419", "pubmed:31754708" ; sc: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." ; sc:featureList edam:operation_0268, edam:operation_0445, edam:operation_3222, edam:operation_3900, edam:operation_3903 ; sc:name "TFregulomeR" ; sc:url "https://github.com/benoukraflab/TFregulomeR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0196, edam:topic_0749, edam:topic_3168 ; sc:citation ; sc:description "TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads." ; sc:featureList edam:operation_0525, edam:operation_3183, edam:operation_3198, edam:operation_3216 ; sc:name "TGS-GapCloser" ; sc:url "https://github.com/BGI-Qingdao/TGS-GapCloser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc: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’" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "TGS-Lite" ; sc:url "https://github.com/sap01/TGS-Lite-supplem/blob/master/README.md" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3067 ; sc:citation , "pmcid:PMC6697955", "pubmed:31419946" ; sc: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" ; sc:featureList edam:operation_2429, edam:operation_3280, edam:operation_3432 ; sc:name "THBP" ; sc:url "https://github.com/xuyanbuaa/THBP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3055 ; sc:citation , , , "pubmed:12165563", "pubmed:15241485", "pubmed:17308338" ; sc:description "Testing Haplotype Effects In Association Studies" ; sc:license "GPL-3.0" ; sc:name "THESIAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.1" ; sc:url "https://github.com/daissi/thesias" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0605, edam:topic_0625, edam:topic_3676 ; sc:citation , "pmcid:PMC6795695", "pubmed:31649706" ; sc: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.""" ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3227, edam:operation_3229, edam:operation_3431 ; sc:name "TILLinG" ; sc:url "http://wheat-tilling.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0821, edam:topic_3314 ; sc:citation , "pubmed:31568581" ; sc: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:""" ; sc:featureList edam:operation_0386, edam:operation_2476 ; sc:name "TITAN" ; sc:url "https://titan-code.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0593, edam:topic_0634 ; sc:citation , "pmcid:PMC5860166", "pubmed:29077808" ; sc:description "Computational tool to assess titin’s role as a disease gene." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TITINdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://fraternalilab.kcl.ac.uk/TITINdb/" ; biotools:primaryContact "Franca Fraternali" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3379, edam:topic_3421 ; sc:citation , "pmcid:PMC6676499", "pubmed:31404154" ; sc: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" ; sc:featureList edam:operation_3557, edam:operation_3659 ; sc:name "TKR" ; sc:url "http://medicalequipoise.com/tkrclinician" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3300 ; sc:citation , "pmcid:PMC6649004", "pubmed:31459527" ; sc: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" ; sc:featureList edam:operation_0267, edam:operation_0306, edam:operation_0480 ; sc:name "TM-IMC" ; sc:url "https://zhanglab.ccmb.med.umich.edu/TM-IMC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6945013", "pubmed:31676507" ; sc:description "A Tagmentation-Mediated 3' Sequencing Approach for Improving Scalability of RNAseq Experiments." ; sc:featureList edam:operation_3196, edam:operation_3200, edam:operation_3435, edam:operation_3800 ; sc:name "TM3 seq" ; sc:url "https://lufpa.github.io/TM3Seq-Pipeline/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation , "pubmed:31504188" ; sc: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" ; sc:featureList edam:operation_0325, edam:operation_0499, edam:operation_3478 ; sc:name "TMAT" ; sc:url "http://healthstat.snu.ac.kr/software/tmat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3176, edam:topic_3368 ; sc:citation , "pubmed:31490686" ; sc: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" ; sc:featureList edam:operation_0244, edam:operation_0478, edam:operation_2476 ; sc:name "TMB" ; sc:url "http://dna.engr.latech.edu/~tmbshare/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0602, edam:topic_0736, edam:topic_0820 ; sc:citation , "pubmed:31682836" ; sc:description "A Web Tool for Predicting Stability of Transmembrane α-Helix Association." ; sc:featureList edam:operation_0279, edam:operation_2415, edam:operation_3767 ; sc:name "TMPfold" ; sc:url "https://opm.phar.umich.edu/tmpfold_server" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6727351", "pubmed:31484546" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3629 ; sc:license "GPL-2.0" ; sc:name "TOAST" ; sc:url "https://bioconductor.org/packages/TOAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation." ; sc:featureList edam:operation_0337, edam:operation_0445, edam:operation_3222 ; sc:license "MIT" ; sc:name "TOBIAS" ; sc:softwareHelp ; sc:url "https://github.com/loosolab/TOBIAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_0749, edam:topic_3300, edam:topic_3489 ; sc:citation , "pmcid:PMC6890663", "pubmed:31796752" ; sc: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""" ; sc:featureList edam:operation_3435, edam:operation_3907 ; sc:name "TOFF" ; sc:url "http://toff-project.univ-lorraine.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3384, edam:topic_3452 ; sc:citation , "pmcid:PMC3493036", "pubmed:23127075" ; sc:description "Proton Monte Carlo platform for research and clinical applications." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "TOPAS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.topasmc.org/home" ; biotools:primaryContact "Joseph Perl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3314, edam:topic_3318 ; sc:citation , "pmcid:PMC6377808", "pubmed:30609382" ; sc:description "Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology." ; sc:isAccessibleForFree true ; sc:name "TOPAS-nBio" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://gray.mgh.harvard.edu/software/258-topas-nbio" ; biotools:primaryContact "Joost Verburg", "Thomas Bortfeld" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC7354698", "pubmed:31804057" ; sc:description """Dose-Response Metabolomics to Understand Biochemical Mechanisms and Off-Target Drug Effects with the TOXcms Software. Job opportunities are available""" ; sc:featureList edam:operation_0490, edam:operation_3435, edam:operation_3891 ; sc:name "TOXcms" ; sc:url "http://pattilab.wustl.edu/software/toxcms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830 ; sc:citation ; sc:description "Therapeutic Peptide Design DataBase." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TP-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dyn.life.nthu.edu.tw/design" ; biotools:primaryContact "Chung-Yu Lan", "Hua-Wen Fu", "Lee-Wei Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3050 ; sc:citation , "pubmed:31471976" ; sc: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) for further information" ; sc:license "GPL-3.0" ; sc:name "TPD" ; sc:url "https://CRAN.R-project.org/package=TPD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC6821153", "pubmed:31099386" ; sc:description "Tumor Purity Estimation from SNVs." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TPES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/l0ka/tpes.git" ; biotools:primaryContact "Alessio Locallo", "Francesca Demichelis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Software to quantify mRNA abundance of genomic features." ; sc:featureList edam:operation_1812, edam:operation_2495, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TPMCalculator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ncbi/TPMCalculator" ; biotools:primaryContact "David Landsman", "Leonardo Mariño-Ramírez", "Lorinc Pongor", "Roberto Vera Alvarez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_0820, edam:topic_3172, edam:topic_3474 ; sc:citation , , , "pmcid:PMC6956793", "pmcid:PMC7703753", "pubmed:31165141", "pubmed:31702773", "pubmed:34477909" ; sc: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." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "TPOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/EpistasisLab/tpot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , , , , "pmcid:PMC3017125", "pmcid:PMC4506239", "pubmed:20013374", "pubmed:20101611", "pubmed:21082435", "pubmed:25631240" ; sc:description "Institute for Systems Biology \"Trans-Proteomic Pipeline\"" ; sc:name "Trans-Proteomic Pipeline (TPP)" ; sc:url "http://tools.proteomecenter.org/software.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3800 ; sc:license "MIT" ; sc:name "TRANSCUP" ; sc:url "https://github.com/plsysu/TRANSCUP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6908688", "pubmed:31831861" ; sc:description "TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3672 ; sc:name "TRANSNAP" ; sc:url "http://plantomics.mind.meiji.ac.jp/nashi/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830 ; sc:citation ; sc:description "Software for reconstruction of T cell receptors (TCR) using short, paired-end single-cell RNA-sequencing." ; sc:featureList edam:operation_0230 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TRAPeS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/YosefLab/TRAPeS" ; biotools:primaryContact "Shaked Afik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3393, edam:topic_3855 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_2428, edam:operation_3799 ; sc:name "TRAX" ; sc:url "http://utahaq.chpc.utah.edu/aq/cgi-bin/mobile_data.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31145698" ; sc:description "Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data." ; sc:featureList edam:operation_3215, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TRC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/dhyeonyu/software" ; biotools:primaryContact "Donghyeon Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2830 ; sc:citation , "pmcid:PMC7525938", "pubmed:32993478" ; sc:description "T-cell Receptor/Immunoglobulin Profiler (TRIP)" ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "tripr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/TRIP" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_3673 ; sc:citation ; sc:description "Chromosome-scale sequence assembly of Triticeae genomes with open-source tools." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TRITEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tritexassembly.bitbucket.io" ; biotools:primaryContact "Martin Mascher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3557 ; sc:citation ; sc:description "Web-tool for prediction of protein–protein Interactions in human Transcriptional Regulation." ; sc:featureList edam:operation_2492, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TRI_tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.vin.bg.ac.rs/180/tools/tfpred.php" ; biotools:primaryContact "Nevena Veljkovic", "Vladimir Perovic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640 ; sc:citation , "pubmed:29028982" ; sc:description "Tool for visualizing and analyzing cancer hallmarks in signaling networks." ; sc:featureList edam:operation_2497, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:license "EPL-1.0" ; sc:name "TROVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://github.com/trove2017/Trove" ; biotools:primaryContact "Huey Eng Chua", "Sourav S. Bhowmick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2229, edam:topic_3047 ; sc:citation , "pubmed:31765328" ; sc: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""" ; sc:featureList edam:operation_2429, edam:operation_3436 ; sc:name "TRamWAy" ; sc:url "http://github.com/DecBayComp/TRamWAy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0736, edam:topic_3512 ; sc:citation ; sc:description "Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "TSDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html" ; biotools:primaryContact "Kenneth Watanabe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_3337, edam:topic_3517 ; sc:citation , "pubmed:31680168" ; sc: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""" ; sc:featureList edam:operation_2428, edam:operation_2436, edam:operation_3196, edam:operation_3232, edam:operation_3431 ; sc:name "TSEA-DB" ; sc:url "https://bioinfo.uth.edu/TSEADB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc: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/""" ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3557, edam:operation_3766 ; sc:name "TSUNAMI" ; sc:url "https://github.com/huangzhii/TSUNAMI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0804, edam:topic_2640 ; sc:citation , "pubmed:31437642" ; sc: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" ; sc:featureList edam:operation_0252, edam:operation_3631 ; sc:name "TTAgP" ; sc:url "https://github.com/reumandc/tsvr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3068 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3799 ; sc:name "TWOMBLI" ; sc:url "https://github.com/wershofe/TWOMBLI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc: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)" ; sc:featureList edam:operation_2945 ; sc:name "TXG-MAPr" ; sc:url "https://txg-mapr.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2275, edam:topic_3385, edam:topic_3452 ; sc:citation , "pmcid:PMC7004880", "pubmed:31768058" ; sc: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""" ; sc:featureList edam:operation_0478, edam:operation_3458 ; sc:name "TYGRESS" ; sc:url "https://www.utsouthwestern.edu/labs/nicastro/tygress/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637, edam:topic_3301 ; sc:citation , "pmcid:PMC6522516", "pubmed:31097708" ; sc:description "Automated high-throughput platform for state-of-the-art genome-based taxonomy." ; sc:featureList edam:operation_0544, edam:operation_3431, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TYGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tygs.dsmz.de" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0637, edam:topic_2885, edam:topic_3174 ; sc:citation , "pmcid:PMC6805505", "pubmed:31638897" ; sc: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""" ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3435 ; sc:name "TZMD" ; sc:url "https://github.com/Yizhuangzhou/TZMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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.""" ; sc:featureList edam:operation_3186, edam:operation_3204 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TaBSAP" ; sc:softwareVersion "1.0.0", "1.0.1", "1.0.2" ; sc:url "https://github.com/pradyumnasagar/TaBSAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_3512 ; sc:citation , "pubmed:30456524" ; sc:description "Web platform for taxonomic profile-based fungal gene prediction." ; sc:featureList edam:operation_0476, edam:operation_3460, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TaF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://taf.genome-report.com/" ; biotools:primaryContact "Theragen Etex Bio Institute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3489 ; sc:citation , "pubmed:31846397" ; sc: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""" ; sc:name "TabSINT" ; sc:url "http://tabsint.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:31410856" ; sc: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" ; sc:featureList edam:operation_0482, edam:operation_2950 ; sc:name "Taba" ; sc:url "https://github.com/azevedolab/taba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC6447449", "pubmed:30936560" ; sc:description "Computational tool that reveals vast protein modification landscapes from large tandem mass spectrometry datasets." ; sc:featureList edam:operation_0417, edam:operation_3645, edam:operation_3649 ; sc:name "TagGraph" ; sc:url "http://kronos.stanford.edu/TAG_GRAPH/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_0780 ; sc:citation , "pmcid:PMC6248703", "pubmed:29236948" ; sc:description "Tool for predicting conserved microRNA targets and target mimics in plants." ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TarHunter" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://tarhunter.genetics.ac.cn/" ; biotools:primaryContact "Xuan Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3518, edam:topic_3519 ; sc:citation , "pmcid:PMC6991699", "pubmed:31851778" ; sc: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.""" ; sc:featureList edam:operation_0463, edam:operation_2495, edam:operation_3223 ; sc:name "TargetScanHuman" ; sc:url "http://www.targetscan.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_3336 ; sc:citation ; sc:description "Connecting genetics and drug discovery | This is the Target Gene Notebook source-code repository | to build TGN backend against git repository:" ; sc:featureList edam:operation_3196 ; sc:license "MIT" ; sc:name "Target Gene Notebook" ; sc:url "http://tgn.broadinstitute.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6905110", "pubmed:31857821" ; sc:description """in-field counting of wheat spikes with context-augmented local regression networks. This is the repository for TasselNetv2, presented in:""" ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3799 ; sc:name "TasselNetv2" ; sc:url "https://tinyurl.com/TasselNetv2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0781, edam:topic_3520 ; sc:citation ; sc:description "An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples." ; sc:featureList edam:operation_3460, edam:operation_3649, edam:operation_3767 ; sc:name "TaxIt" ; sc:url "https://gitlab.com/rki_bioinformatics/TaxIt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0140, edam:topic_2229, edam:topic_3520 ; sc:citation , "pmcid:PMC6902019", "pubmed:31849937" ; sc: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.""" ; sc:featureList edam:operation_2428, edam:operation_2489, edam:operation_3630 ; sc:name "TcellSubC" ; sc:url "https://tcellatlas.kaust.edu.sa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3519 ; sc:citation , "pmcid:PMC6715295", "pubmed:31425522" ; sc: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" ; sc:featureList edam:operation_0372, edam:operation_3233, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "TeXP" ; sc:url "https://github.com/gersteinlab/texp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0769, edam:topic_2258, edam:topic_2840, edam:topic_3474 ; sc:citation , "pubmed:31612715" ; sc:description "A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows." ; sc:featureList edam:operation_0337, edam:operation_3695 ; sc:license "CC-BY-4.0" ; sc:name "TeachOpenCADD-KNIME" ; sc:url "https://hub.knime.com/volkamerlab/space/TeachOpenCADD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC3436826", "pubmed:22962446" ; sc: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." ; sc:featureList edam:operation_0310 ; sc:name "Telescope" ; sc:url "https://github.com/Mangul-Lab-USC/telescope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6786656", "pubmed:31568525" ; sc: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.""" ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3198, edam:operation_3800, edam:operation_3891 ; sc:license "MIT" ; sc:name "Telescope" ; sc:softwareHelp ; sc:url "https://github.com/mlbendall/telescope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6540518", "pubmed:31138115" ; sc:description "In silico estimation of telomere content and composition from cancer genomes." ; sc:featureList edam:operation_3435, edam:operation_3798, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TelomereHunter" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html" ; biotools:primaryContact "Lina Sieverling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3315 ; sc:citation , "pubmed:30957838" ; sc:description "Package to study genetic variation in tera-scale genotypes as it performs PCA of large-scale datasets." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TeraPCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/aritra90/TeraPCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3512, edam:topic_3542 ; sc:citation , "pmcid:PMC7145512", "pubmed:31732725" ; sc: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""" ; sc:featureList edam:operation_2441, edam:operation_2488, edam:operation_3902 ; sc:name "Terminome-seq" ; sc:url "https://github.com/BenoitCastandet/Terminome_Seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3316, edam:topic_3810 ; sc:citation , "pmcid:PMC6764783", "pubmed:31565027" ; sc:description "Terra Populus' Architecture for Integrated Big Geospatial Services | Boundaries are missing for the selected sample geography. Please select a different sample geography" ; sc:name "Terra" ; sc:url "https://data.terrapop.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168 ; sc:citation , "pubmed:31392327" ; sc: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" ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3798 ; sc:license "MIT" ; sc:name "Tersect" ; sc:url "https://github.com/tomkurowski/tersect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2269 ; sc:citation , "pmcid:PMC6663104", "pubmed:31360055" ; sc: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)" ; sc:name "Tetrad" ; sc:url "https://github.com/sbauldry/tetrad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC6836478", "pubmed:31699079" ; sc: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""" ; sc:name "ThalPred" ; sc:url "http://codes.bio/thalpred/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "ThaleMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "4.3.1-20210109" ; sc:url "https://bar.utoronto.ca/thalemine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc: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." ; sc:name "The Great Genotyper" ; sc:url "https://github.com/dib-lab/TheGreatGenotyper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3063, edam:topic_3071 ; sc:citation , "pubmed:28003258" ; sc:description "Web-based data management tool for health and medical research." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "The Ark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sphinx.org.au/the-ark/" ; biotools:primaryContact "Adrian Bickerstaffe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3307, edam:topic_3318 ; sc:citation , "pubmed:31117786" ; sc:description "Theoretical Reims-Tomsk Spectral data." ; sc:featureList edam:operation_0386, edam:operation_0476, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TheoReTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://theorets.univ-reims.fr" ; biotools:primaryContact "Andrei Nikitin", "Michael Rey", "Vladimir G. Tyuterev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154 ; sc:citation , "pmcid:PMC6943036", "pubmed:31555805" ; sc: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]" ; sc:featureList edam:operation_0279, edam:operation_2518, edam:operation_3095 ; sc:name "Thera-SAbDab" ; sc:url "http://opig.stats.ox.ac.uk/webapps/therasabdab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:31078672" ; sc:description "High-throughput analysis software for non-invasive thermal assessment of laboratory mic." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ThermoLabAnimal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ThermoLabAnimal/ThermoLabAnimal_FreeVersion" ; biotools:primaryContact "Paulo Aguiar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3474, edam:topic_3794 ; sc:citation , "pmcid:PMC6752863", "pubmed:31483777" ; sc: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" ; sc:featureList edam:operation_0278, edam:operation_3901, edam:operation_3902 ; sc:name "ThermoNet" ; sc:url "https://github.com/suyufeng/ThermoNet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc: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" ; sc:featureList edam:operation_3215, edam:operation_3434, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ThermoRawFileParser" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/compomics/ThermoRawFileParser" ; biotools:primaryContact "Computational Omics and Systems Biology Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3520 ; sc:citation , "pmcid:PMC7012383", "pubmed:31363206" ; sc: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)!" ; sc:featureList edam:operation_0417, edam:operation_3216, edam:operation_3629 ; sc:name "Thesaurus" ; sc:url "http://bitbucket.org/searleb/thesaurus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170 ; sc:citation , "pmcid:PMC5870860", "pubmed:28203700" ; sc:description "Tool for determining the threshold in short RNA-seq datasets." ; sc:featureList edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Threshold-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cm.jefferson.edu/threshold-seq/" ; biotools:primaryContact "Isidore Rigoutsos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation , "pmcid:PMC6931271", "pubmed:31077294" ; sc:description "Software for scalable execution of portable pipelines on the cloud." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Tibanna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/4dn-dcic/tibanna" ; biotools:primaryContact "Burak H. Alver", "Peter J. Park" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC6612900", "pubmed:31510677" ; sc: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)" ; sc:featureList edam:operation_3192, edam:operation_3195, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "TideHunter" ; sc:url "https://github.com/yangao07/TideHunter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3277, edam:topic_3678 ; sc:citation , "pmcid:PMC6833352", "pubmed:31709289" ; sc:description "Time-energy measured data on modern multicore systems running shared-memory applications." ; sc:name "Time-energy" ; sc:url "https://github.com/dloghin/multicores-time-energy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3168, edam:topic_3386 ; sc:citation , "pubmed:31523773" ; sc: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" ; sc:featureList edam:operation_1812, edam:operation_3192, edam:operation_3461 ; sc:name "Tn-seq" ; sc:url "https://github.com/WhiteleyLab/Tn-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0637 ; sc:citation , "pmcid:PMC6323299", "pubmed:30624651" ; sc:description "Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TogoGenome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://togogenome.org/" ; biotools:primaryContact "Keita Urashima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0637, edam:topic_3489 ; sc:citation , "pmcid:PMC6323299", "pubmed:30624651" ; sc:description "Generic Web framework for rendering an information block." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TogoStanza" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://togostanza.org/" ; biotools:primaryContact "Keita Urashima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , "pmcid:PMC2323670", "pubmed:18387209" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Tomato Genome Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://cab.unina.it/cgi-bin/gb2/gbrowse/SL250/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:30715205" ; sc:description "Tool for selecting high-quality top-down proteomics mass spectra." ; sc:featureList edam:operation_3627, edam:operation_3637, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Top-Down Garbage Collector" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://patternlabforproteomics.org/tdgc/" ; biotools:primaryContact "Diogo B. Lima", "Julia Chamot-Rooke", "Paulo C. Carvalho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6858545", "pubmed:31591578" ; sc: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." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3458 ; sc:license "GPL-3.0" ; sc:name "Topaz" ; sc:url "http://topaz.csail.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. 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Topological-tumour-graphs""" ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3659 ; sc:name "Topological Tumor Graphs" ; sc:url "https://github.com/Henrik86/Topological-tumour-graphs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A post sequencing QC tool for Oxford Nanopore sequencers." ; sc:featureList edam:operation_3218 ; sc:name "ToulligQC" ; sc:url "https://github.com/GenomicParisCentre/toulligQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3343 ; sc:citation , "pmcid:PMC6792352", "pubmed:31566444" ; sc: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" ; sc:featureList edam:operation_3642 ; sc:name "Tox21" ; sc:url "https://tripod.nih.gov/tox21/samples" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC6950642", "pubmed:31874186" ; sc:description "A method for merging multiple independent neuronal traces." ; sc:featureList edam:operation_3552 ; sc:name "TraceMontage" ; sc:url "https://www.cai-lab.org/tracemontage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382, edam:topic_3421 ; sc:citation ; sc:description "Track-Control is an automatic video-based real-time closed-loop behavioral control toolbox." ; sc:name "Track-Control" ; sc:url "https://github.com/GuangWei-Zhang/TraCon-Toolbox/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_3071 ; sc:citation ; sc: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." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TrackFind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://trackfind.elixir.no/" ; biotools:primaryContact "Dmytro Titov", "Eivind Hovig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3377 ; sc:citation , "pubmed:31070721" ; sc:description "Genome-wide tool for preliminary assessment of therapeutic target druggability." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TractaViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/NeilPearson-Lilly/TractaViewer" ; biotools:primaryContact "Neil Pearson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation , , "pubmed:32447016" ; sc: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" ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TractoFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/scilus/tractoflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:28369169" ; sc:description "Machine learning tool for microscopy pixel classification." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Trainable Weka Segmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.2.33" ; sc:url "https://imagej.net/Trainable_Weka_Segmentation" ; biotools:primaryContact "Ignacio Arganda-Carreras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0335, edam:operation_3185, edam:operation_3198, edam:operation_3258 ; sc:name "Trans-NanoSim" ; sc:url "https://github.com/bcgsc/NanoSim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0622, edam:topic_3170, edam:topic_3512, edam:topic_3673 ; sc: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." ; sc:featureList edam:operation_0436, edam:operation_0524, edam:operation_3644 ; sc:name "TransDecoder" ; sc:url "https://github.com/TransDecoder/TransDecoder/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6480747", "pubmed:31014374" ; sc:description "De novo transcriptome assembler that uses line graph iteration." ; sc:featureList edam:operation_0524, edam:operation_3258, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TransLiG" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://sourceforge.net/projects/transcriptomeassembly/files/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_0780, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6827441", "pubmed:31695967" ; sc: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""" ; sc:featureList edam:operation_0440, edam:operation_3196, edam:operation_3659, edam:operation_3663 ; sc:license "GPL-2.0" ; sc:name "TransPrise" ; sc:url "https://github.com/StepanAbstro/TransPrise" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084 ; sc:citation , "pmcid:PMC5348085", "pubmed:28469416" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Transcriptologs" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/LucaAmbrosino/Transcriptologs.git" ; biotools:primaryContact "Luca Ambrosino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3659 ; sc:name "Transformer-CNN" ; sc:url "https://github.com/bigchem/transformer-cnn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pubmed:31835003" ; sc:description "A Computational Theory for the Discretized Entorhinal Cortex." ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "Transition Scale-Spaces" ; sc:url "https://github.com/rochus/transitionscalespace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3314, edam:topic_3512 ; sc:citation , "pmcid:PMC6803931", "pubmed:31557893" ; sc: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" ; sc:featureList edam:operation_0334, edam:operation_0337, edam:operation_3891 ; sc:name "Transitivity" ; sc:url "http://www.vhcsgroup.com/transitivity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0798, edam:topic_3512 ; sc:citation , "pmcid:PMC6510757", "pubmed:31076573" ; sc: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." ; sc:featureList edam:operation_0427 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Transposons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AlexShein/transposons/" ; biotools:primaryContact "Maria Poptsova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation "pmcid:PMC6980320", "pubmed:31797618" ; sc:description "Tree-Weighting for Multi-Study Ensemble Learners." ; sc:name "Tree-Weighting" ; sc:url "https://github.com/m-ramchandran/tree-weighting" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3293, edam:topic_3305 ; sc:citation , "pmcid:PMC6705769", "pubmed:31437182" ; sc: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)" ; sc:featureList edam:operation_0546, edam:operation_0557, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "TreeCluster" ; sc:url "https://github.com/niemasd/TreeCluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3293 ; sc:citation , "pubmed:31114853" ; sc: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." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TreeExp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/hr1912/TreeExp" ; biotools:primaryContact "Hang Ruan", "Xun Gu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3168, edam:topic_3301, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0540, edam:operation_0547, edam:operation_3478 ; sc:name "TreeFix-TP" ; sc:url "https://compbio.engr.uconn.edu/software/treefix-tp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3512 ; sc:citation , "pmcid:PMC6612878", "pubmed:31510668" ; sc: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)" ; sc:featureList edam:operation_0544, edam:operation_0547, edam:operation_0555 ; sc:name "TreeMerge" ; sc:url "http://github.com/ekmolloy/treemerge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0623, edam:topic_3293 ; sc:citation ; sc:description "Treerecs is an open-source (species- and gene-) tree reconciliation software distributed under the GNU AGPL licence." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0492 ; sc:license "AGPL-3.0" ; sc:name "Treerecs" ; sc:url "https://project.inria.fr/treerecs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3500 ; sc:citation , "pubmed:31418539" ; sc: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 |  Fan 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" ; sc:featureList edam:operation_0484, edam:operation_0525, edam:operation_3216 ; sc:name "TreeshrewDB" ; sc:url "http://www.treeshrewdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6662310", "pubmed:30566622" ; sc:description "Software tool to prioritize important genes in pathways and their non-coding regulators." ; sc:featureList edam:operation_0533, edam:operation_3223, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TriPOINT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.uconn.edu/ajt06004/TriPOINT" ; biotools:primaryContact "Asa Thibodeau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31070854" ; sc:description "Efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species." ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Trimitomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bplese/Trimitomics" ; biotools:primaryContact "Ana Riesgo", "Bruna Plese" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3489 ; sc:citation , "pmcid:PMC6829499", "pubmed:31688940" ; sc: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""" ; sc:featureList edam:operation_0282, edam:operation_0490, edam:operation_2421 ; sc:name "Tripal MapViewer" ; sc:url "https://gitlab.com/mainlabwsu/tripal_map" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3810 ; sc:description "TropGeneDB is a database that manages genomic, genetic and phenotypic information about tropical crops. It is organised on a crop basis." ; sc:name "TropGeneDB" ; sc:url "http://tropgenedb.cirad.fr/tropgene/JSP/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3173, edam:topic_3512 ; sc:citation ; sc:description "Toolkit for rapidly simulating ChIP-seq data using statistical models of the experimental steps." ; sc:featureList edam:operation_3222, edam:operation_3798, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Tulip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gymreklab/Tulip" ; biotools:primaryContact "An Zheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0625, edam:topic_3673 ; sc:citation , "pubmed:31125057" ; sc:description "Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs." ; sc:featureList edam:operation_3196, edam:operation_3233 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TumorCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yongzhuang/TumorCNV" ; biotools:primaryContact "Yongzhuang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6710255", "pubmed:31451757" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3216, edam:operation_3501 ; sc:name "TupaiaBase" ; sc:url "http://tupaiabase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Protein MD Setup tutorial using BioExcel Building Blocks - a Jupyter Notebook tutorial." ; sc:name "Tutorial: MD Setup" ; sc:url "https://github.com/bioexcel/biobb_wf_md_setup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3399, edam:topic_3697 ; sc:citation , "pubmed:31526404" ; sc: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" ; sc:name "TwinsUK" ; sc:url "http://twinsuk.ac.uk/resources-for-researchers/access-our-data/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3170, edam:topic_3295, edam:topic_3673 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3183, edam:operation_3196, edam:operation_3227 ; sc:name "TypeTE" ; sc:url "https://github.com/clemgoub/TypeTE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3517 ; sc:citation , "pubmed:31400194" ; sc: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" ; sc:featureList edam:operation_3659 ; sc:license "MIT" ; sc:name "U-PASS" ; sc:url "https://github.com/Pill-GZ/U-PASS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC5516091", "pubmed:28732212" ; sc:description "Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data." ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "UALCAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://ualcan.path.uab.edu/analysis.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Suite" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071 ; sc: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.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "UniBioDicts" ; sc:url "https://github.com/UniBioDicts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Utilities for handling sequences and assemblies from the UCSC Genome Browser project." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "UCSC Genome Browser Utilities" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hgdownload.cse.ucsc.edu/downloads.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3305, edam:topic_3412, edam:topic_3421 ; sc:citation , "pmcid:PMC6773358", "pubmed:31575580" ; sc: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." ; sc:featureList edam:operation_3454 ; sc:name "UGICR" ; sc:url "https://ugicr.org.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC6508075", "pubmed:31080962" ; sc: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" ; sc:featureList edam:operation_0368, edam:operation_0452 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ULTRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TravisWheelerLab/ULTRA" ; biotools:primaryContact "Daniel Olson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3120, edam:topic_3168 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0232, edam:operation_3225, edam:operation_3227 ; sc:license "MIT" ; sc:name "UMI-VarCal" ; sc:url "https://gitlab.com/vincent-sater/umi-varcal-master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3336 ; sc:citation , "pmcid:PMC6550413", "pubmed:31120875" ; sc:description "Efficient algorithms to discover alterations with complementary functional association in cancer." ; sc:featureList edam:operation_3219, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "UNCOVER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/VandinLab/UNCOVER" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC4117748", "pubmed:24970867" ; sc:description "Method and associated software for discovering somatic mutations using the integration of DNA and RNA sequencing." ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UNCeqR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://lbc.unc.edu/~mwilkers/unceqr_dist/" ; biotools:primaryContact "Matt Wilkerson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6923391", "pubmed:31857624" ; sc: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""" ; sc:license "GPL-3.0" ; sc:name "UNI-EM" ; sc:url "https://github.com/urakubo/UNI-EM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1775, edam:topic_3518 ; sc:citation , "pmcid:PMC6694573", "pubmed:31412768" ; sc: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 }}" ; sc:featureList edam:operation_1777, edam:operation_3083, edam:operation_3439 ; sc:name "UNIPred-Web" ; sc:url "http://unipred.di.unimi.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3337, edam:topic_3384 ; sc:citation , "pmcid:PMC6712144", "pubmed:31134468" ; sc:description "Big data analytics research data platform to improve care of patients with cardiomyopathies using routine electronic health records and standardized biobanking." ; sc:featureList edam:operation_0306, edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "UNRAVEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.unravelrdp.nl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC7357299", "pubmed:31841402" ; sc: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""" ; sc:featureList edam:operation_0479, edam:operation_3436 ; sc:license "MIT" ; sc:name "UNet++" ; sc:url "https://github.com/MrGiovanni/UNetPlusPlus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31369377" ; sc: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)" ; sc:featureList edam:operation_2939, edam:operation_3891 ; sc:name "UOVOS" ; sc:url "https://www.github.com/visiontao/uovos" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:description "A Convolution Neural Network (CNN) model to classify publications with accession annotations according to UniProtKB categories" ; sc:featureList edam:operation_3927 ; sc:name "UPCLASS" ; sc:url "http://goldorak.hesge.ch/bioexpclass/upclass/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_0637, edam:topic_0821, edam:topic_3293 ; sc:citation , "pmcid:PMC6902001", "pubmed:31820805" ; sc: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""" ; sc:featureList edam:operation_0239, edam:operation_2421, edam:operation_2995, edam:operation_3092, edam:operation_3431 ; sc:name "UPObase" ; sc:url "http://upobase.bioinformaticsreview.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC6829132", "pubmed:31690598" ; sc:description "Expression-Based Cell Lineage Analysis in Drosophila Through a Course-Based Research Experience for Early Undergraduates." ; sc:featureList edam:operation_2421, edam:operation_3463 ; sc:name "URCFG" ; sc:url "http://www.urcfg.ucla.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6980905", "pubmed:31689538" ; sc:description """Sample sizes and population differences in brain template construction. Caucasian and Chinese Brain templates [US200 CN200]""" ; sc:featureList edam:operation_3435 ; sc:name "US200 CN200" ; sc:url "https://www.nitrc.org/projects/us200_cn200/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3335, edam:topic_3379 ; sc:citation , "pmcid:PMC6717797", "pubmed:31496866" ; sc: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:" ; sc:featureList edam:operation_2426 ; sc:name "UT-Heart" ; sc:url "http://ut-heart.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6434621", "pubmed:30909881" ; sc: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." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "UTAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://utap.readthedocs.io/en/latest/index.html" ; biotools:primaryContact "Refael Kohen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6886508", "pubmed:31744903" ; sc: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 .""" ; sc:featureList edam:operation_0428, edam:operation_0463, edam:operation_3792 ; sc:name "UTRome" ; sc:url "http://www.UTRome.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3301 ; sc:author ; sc:citation , "pmcid:PMC6194142", "pubmed:30337678" ; sc:description "The Unified Variant Pipeline (UVP) is used to identify variants and assign lineage from Mycobacterium tuberculosis sequence data." ; sc:featureList edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UVP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "2.6.0", "2.7.0" ; sc:url "https://github.com/CPTR-ReSeqTB/UVP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6846653", "pubmed:31435647" ; sc: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:" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "Ularcirc" ; sc:url "https://github.com/VCCRI/Ularcirc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3891 ; sc:name "Umbria" ; sc:url "http://dati.umbria.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0605, edam:topic_3306, edam:topic_3474, edam:topic_3895 ; sc:citation , "pmcid:PMC7067682", "pubmed:31636460" ; sc: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""" ; sc:featureList edam:operation_0476, edam:operation_1777, edam:operation_3630 ; sc:name "UniRep" ; sc:url "https://github.com/churchlab/UniRep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3068, edam:topic_3316, edam:topic_3473 ; sc: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)\"""" ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-2.5" ; sc:name "Unicorn Papers" ; sc:softwareHelp ; sc:url "http://unicornpapers.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_0637, edam:topic_3071 ; sc:citation , "pubmed:31843688" ; sc:description """Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase). Retrieving Information of Proteins from Uniprot. Connect to Uniprot 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""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "UniprotR" ; sc:url "https://cran.r-project.org/web/packages/UniprotR/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3810 ; sc:citation , "pubmed:31436473" ; sc: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" ; sc:featureList edam:operation_0308 ; sc:name "Uniqprimer" ; sc:url "https://github.com/SouthGreenPlatform/Uniqprimer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0176, edam:topic_0602, edam:topic_0821 ; sc:citation , "pmcid:PMC6933841", "pubmed:31710727" ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_0409, edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "UnityMol-APBS" ; sc:url "https://sourceforge.net/projects/unitymol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0622, edam:topic_0623, edam:topic_0781 ; sc:citation ; sc:description "Classification and annotation of viral sequences based on RefSeq annotation." ; sc:featureList edam:operation_0361, edam:operation_0363, edam:operation_0447, edam:operation_3431 ; sc:name "VADR" ; sc:url "https://github.com/nawrockie/vadr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC6735694", "pubmed:31494667" ; sc: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:" ; sc:featureList edam:operation_2939, edam:operation_3227, edam:operation_3891 ; sc:name "VAPPER" ; sc:url "https://github.com/PGB-LIV/VAPPER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3375, edam:topic_3577 ; sc:citation , "pmcid:PMC6943059", "pubmed:31495872" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3202 ; sc:name "VARIDT" ; sc:url "http://varidt.idrblab.net/ttd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6842140", "pubmed:31703556" ; sc: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""" ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3258, edam:operation_3431 ; sc:name "VARUS" ; sc:url "https://github.com/Gaius-Augustus/VARUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_2814, edam:topic_2828 ; sc:citation , "pmcid:PMC6933850", "pubmed:31724231" ; sc: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." ; sc:featureList edam:operation_0292, edam:operation_0295, edam:operation_0319, edam:operation_0570, edam:operation_2488 ; sc:name "VASE" ; sc:url "https://github.com/cmbi/vase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:31425086" ; sc: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:" ; sc:featureList edam:operation_3891 ; sc:name "VASSL" ; sc:url "https://vassl.new-dimension.co" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3676 ; sc:citation , "pubmed:31442673" ; sc: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" ; sc:featureList edam:operation_3225, edam:operation_3227 ; sc:name "VCF-DART" ; sc:url "https://github.com/sirselim/diagnostics_exome_reporting" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3168, edam:topic_3473 ; sc:citation , "pmcid:PMC6625089", "pubmed:31127704" ; sc:description "A web-based visualization tool for high-throughput variant data mining and management." ; sc:featureList edam:operation_1812, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VCF-Server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://diseasegps.sjtu.edu.cn/VCF-Server?lan=eng" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0625, edam:topic_2885 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3196 ; sc:license "MIT" ; sc:name "VCF2PopTree" ; sc:url "https://github.com/sansubs/vcf2pop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6513159", "pubmed:30351394" ; sc: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." ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VCPA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.niagads.org/resources/tools-and-software/vcpa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3452 ; sc:citation , "pmcid:PMC6890217", "pubmed:31794595" ; sc:description "Use of three points to determine the accuracy of guided implantation." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "VDING" ; sc:url "https://github.com/coolleafly/VDING" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_0804 ; sc:citation , "pmcid:PMC6943044", "pubmed:31602484" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_0487, edam:operation_2421, edam:operation_3196 ; sc:name "VDJbase" ; sc:url "https://www.vdjbase.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0160, edam:topic_0219, edam:topic_2830 ; sc:citation , "pubmed:31588507" ; sc:description "VDJdb is a database extension, new analysis infrastructure and a T-cell receptor motif compendium." ; sc:featureList edam:operation_0224, edam:operation_0238, edam:operation_0416 ; sc:name "VDJdb" ; sc:url "https://vdjdb.cdr3.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3474, edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:31873730" ; sc: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""" ; sc:featureList edam:operation_3227, edam:operation_3359, edam:operation_3675, edam:operation_3695 ; sc:license "MIT" ; sc:name "VEF" ; sc:url "http://github.com/ChuanyiZ/vef" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3304, edam:topic_3500 ; sc:citation , "pmcid:PMC6753167", "pubmed:31572120" ; sc: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""" ; sc:featureList edam:operation_0337 ; sc:name "VETA" ; sc:url "https://github.com/greenhouselab/Veta/tree/master/data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203 ; sc:author ; sc: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""" ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "VEnCode" ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/AndreMacedo88/VEnCode" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3372 ; sc:citation , "pmcid:PMC6886159", "pubmed:31787090" ; sc: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." ; sc:featureList edam:operation_3359 ; sc:name "VGE" ; sc:url "https://github.com/SatoshiITO/VGE" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3620 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3489 ; sc:author , "Bryan Brancotte" ; sc:citation , "pmcid:PMC8428608", "pubmed:33594411" ; sc:contributor ; sc: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.""" ; sc:featureList edam:operation_3436 ; sc:license "MIT" ; sc:name "Viral Host Range database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://viralhostrangedb.pasteur.cloud/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3174, edam:topic_3407, edam:topic_3697 ; sc:citation , ; sc: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""" ; sc:featureList edam:operation_0362, edam:operation_3192, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "VIBRANT" ; sc:url "https://wiki.cyverse.org/wiki/display/DEapps/VIBRANT-1.0.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3400 ; sc:citation , "pmcid:PMC6708137", "pubmed:31443733" ; sc: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 ]" ; sc:featureList edam:operation_1812, edam:operation_3225, edam:operation_3227 ; sc:name "VIC" ; sc:url "https://github.com/HGLab/VIC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_3421 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0416, edam:operation_3196, edam:operation_3891 ; sc:name "VICTOR" ; sc:url "http://www.transplanttoolbox.org/victor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_3308, edam:topic_3379, edam:topic_3400 ; sc:citation , "pmcid:PMC6927110", "pubmed:31865910" ; sc: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""" ; sc:featureList edam:operation_0560, edam:operation_3431, edam:operation_3435, edam:operation_3501 ; sc:name "VIO" ; sc:url "http://www.ontobee.org/ontology/VIO" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3752 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654, edam:format_3834 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3382, edam:topic_3520 ; sc:citation "pubmed:17545182" ; sc: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." ; sc:featureList edam:operation_3203, edam:operation_3432, edam:operation_3627, edam:operation_3628, edam:operation_3694, edam:operation_3695 ; sc:license "Apache-2.0" ; sc:name "VIPER LC-MS" ; sc:url "https://omics.pnl.gov/software/viper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC6943068", "pubmed:31598702" ; sc: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""" ; sc:featureList edam:operation_0238, edam:operation_0440, edam:operation_0463 ; sc:name "VISDB" ; sc:url "https://bioinfo.uth.edu/VISDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation ; sc: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" ; sc:featureList edam:operation_0441, edam:operation_3557 ; sc:name "VISION" ; sc:url "http://usevision.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2914 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence features metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3175, edam:topic_3511 ; sc:author ; sc:citation , "pubmed:31589307" ; sc:description "Haplotype-aware structural variants simulator for short, long and linked reads" ; sc:featureList edam:operation_2426, edam:operation_2928, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "VISOR" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/davidebolo1993/VISOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3379, edam:topic_3577 ; sc:citation , "pmcid:PMC6697931", "pubmed:31419935" ; sc:description "a Variant-Information Search Tool for precision oncology | The Variant Information Search Tool developed @ WBI" ; sc:featureList edam:operation_2421, edam:operation_3280 ; sc:name "VIST" ; sc:url "https://vist.informatik.hu-berlin.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3489, edam:topic_3892 ; sc:citation , "pubmed:31682440" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3436 ; sc:name "VMD Store" ; sc:url "https://biosim.pt/how-to-install-vmd-store/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407, edam:topic_3697 ; sc:citation , "pmcid:PMC6323901", "pubmed:30371894" ; sc: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." ; sc:featureList edam:operation_3501, edam:operation_3660, edam:operation_3715 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VMH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://vmh.life" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3416, edam:topic_3452 ; sc:citation , "pmcid:PMC7790441", "pubmed:31840849" ; sc: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." ; sc:featureList edam:operation_2428, edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "VNA" ; sc:url "http://github.com/McBrideGagyiLab/VNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pubmed:31791122" ; sc: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.""" ; sc:featureList edam:operation_3432, edam:operation_3801, edam:operation_3803 ; sc:name "VOCCluster" ; sc:url "https://github.com/Yaser218/Untargeted-Metabolomics-Clustering/tree/master/VOCCluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3400, edam:topic_3697 ; sc:citation , "pmcid:PMC6701114", "pubmed:31429723" ; sc: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" ; sc:featureList edam:operation_1812, edam:operation_3501, edam:operation_3659 ; sc:name "VOLARE" ; sc:url "http://aasix.cytoanalytics.com/volare/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154 ; sc:citation , "pmcid:PMC6602475", "pubmed:31114895" ; sc:description "VOLPES (Visualization Of PhysicochEmical Sequence properties) - interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences." ; sc:featureList edam:operation_0279, edam:operation_2518, edam:operation_3095 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VOLPES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://volpes.univie.ac.at" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6509870", "pubmed:31074382" ; sc:description "Variational projection for accurate clustering of single-cell transcriptomic data." ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VPAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ShengquanChen/VPAC" ; biotools:primaryContact "Rui Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC7056850", "pubmed:31765830" ; sc: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""" ; sc:featureList edam:operation_3226, edam:operation_3461, edam:operation_3675 ; sc:license "GPL-3.0" ; sc:name "VPOT" ; sc:url "https://github.com/VCCRI/VPOT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3292, edam:topic_3315, edam:topic_3332 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:name "VRTK" ; sc:url "http://www.vrtk.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0611, edam:topic_3170 ; sc:citation , "pmcid:PMC6972656", "pubmed:31374129" ; sc: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" ; sc:featureList edam:operation_3192, edam:operation_3501 ; sc:name "VTA" ; sc:url "https://gitlab.com/mlinitaur/vta-expression-data-extractor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3334, edam:topic_3384, edam:topic_3399, edam:topic_3577 ; sc:citation , "pmcid:PMC6857688", "pubmed:31730697" ; sc: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\"""" ; sc:featureList edam:operation_1812, edam:operation_3432, edam:operation_3557 ; sc:license "LGPL-2.1" ; sc:name "VaDER" ; sc:url "https://github.com/johanndejong/VaDER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3277 ; sc:citation , "pubmed:31751680" ; sc: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.""" ; sc:name "VarCover" ; sc:url "https://github.com/erscott/varcover" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3325 ; sc: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." ; sc:license "MIT" ; sc:name "VarFish" ; sc:url "https://github.com/bihealth/varfish-server" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31834354" ; sc: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." ; sc:featureList edam:operation_0484, edam:operation_2422, edam:operation_3675 ; sc:license "MIT" ; sc:name "VarGen" ; sc:url "https://github.com/MCorentin/VarGen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2533 ; sc:citation , "pmcid:PMC6291943", "pubmed:30541431" ; sc: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." ; sc:isAccessibleForFree true ; sc:name "VarGenius" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/frankMusacchia/VarGenius" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0166, edam:topic_0654 ; sc:citation , "pmcid:PMC6853667", "pubmed:31192369" ; sc:description "Tool for mapping a list of chromosome coordinates, and their variants, to the corresponding protein residues in the canonical UniProt protein sequence." ; sc:featureList edam:operation_0321, edam:operation_2422, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VarMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/DisaStr/GetPage.pl?varmap=TRUE" ; biotools:primaryContact "James Stephenson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation , "pubmed:30192923" ; sc:description "Package for variable selection in model-based clustering of mixed-data with missing values." ; sc:featureList edam:operation_3432, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VarSelLCM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "2.1.3" ; sc:url "https://CRAN.R-project.org/package=VarSelLCM/" ; biotools:primaryContact "Mohammed Sedki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3325, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC6792253", "pubmed:31615419" ; sc: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\"""" ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227, edam:operation_3675 ; sc:name "VarSight" ; sc:url "https://github.com/HudsonAlpha/VarSight" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0634, edam:topic_2814, edam:topic_3120 ; sc:citation , "pmcid:PMC6933866", "pubmed:31606900" ; sc:description """Disease variants and protein structure. Disease Variants and Structure""" ; sc:featureList edam:operation_0477, edam:operation_0570, edam:operation_2488, edam:operation_3227 ; sc:name "VarSite" ; sc:url "https://www.ebi.ac.uk/thornton-srv/databases/VarSite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0495, edam:operation_2422, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:license "MIT" ; sc:name "Vargas" ; sc:url "https://github.com/langmead-lab/vargas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2885, edam:topic_3320 ; sc:citation ; sc:description "Benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction." ; sc:featureList edam:operation_0331, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VariBench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://structure.bmc.lu.se/VariBench/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0219, edam:topic_3068, edam:topic_3168, edam:topic_3298 ; sc:citation , "pubmed:31705629" ; sc: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.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3436 ; sc:name "VariCarta" ; sc:url "http://varicarta.msl.ubc.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3174 ; sc:citation , "pmcid:PMC6612864", "pubmed:31510647" ; sc: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" ; sc:featureList edam:operation_0524, edam:operation_3211, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "VariMerge" ; sc:url "https://github.com/cosmo-team/cosmo/tree/VARI-merge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3577 ; sc:citation ; sc:description "A Large-Scale Genomic Variant Search Index." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3211, edam:operation_3226, edam:operation_3227 ; sc:name "VariantStore" ; sc:url "https://github.com/Kingsford-Group/variantstore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203 ; sc:citation , "pmcid:PMC5765404", "pubmed:28967166" ; sc: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/""" ; sc:featureList edam:operation_1812, edam:operation_3227 ; sc:license "AGPL-3.0" ; sc:name "VariantValidator" ; sc:url "http://variantvalidator.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3325 ; sc:author "Sofia Papadomitriou" ; sc:citation , , "pmcid:PMC10152795", "pmcid:PMC6575632", "pubmed:31127050", "pubmed:37127601" ; sc: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.""" ; sc:featureList edam:operation_2423, edam:operation_3197, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Variant Combination Pathogenicity Predictor (VarCoPP) 2.0" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Interuniversity Institute of Bioinformatics in Brussels" ; sc:softwareVersion "1.0", "2.0" ; sc:url "http://varcopp.ibsquare.be" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3676 ; sc:citation , "pubmed:31086968" ; sc:description "Variant Score Ranker (VSR) - web application for intuitive missense variant prioritization." ; sc:featureList edam:operation_0331, edam:operation_3225, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Variant Score Ranker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://vsranker.broadinstitute.org" ; biotools:primaryContact "Dennis Lal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053 ; sc:citation , "pmcid:PMC6624979", "pubmed:31300006" ; sc:description "Variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens." ; sc:featureList edam:operation_0487 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Variational Bayes approach (GEMINI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/sellerslab/gemini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3168, edam:topic_3303 ; sc:citation ; sc:description """a complete and efficient tool to support NGS data analysis. High precision on genetic analysis""" ; sc:featureList edam:operation_2428, edam:operation_3197 ; sc:name "Varstation" ; sc:url "http://varstation.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3489 ; sc:citation , "pmcid:PMC6776151", "pubmed:31598083" ; sc: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""" ; sc:featureList edam:operation_0415, edam:operation_3196, edam:operation_3432 ; sc:name "VegMarks" ; sc:url "https://vegmarks.nivot.affrc.go.jp/resource/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6941187", "pubmed:31881980" ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_2497, edam:operation_3501 ; sc:name "Venn-diaNet" ; sc:url "http://biohealth.snu.ac.kr/software/venndianet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pubmed:31286135" ; sc:description "R package for the analysis of nucleic acids structural data, with an emphasis in complex RNA structures." ; sc:featureList edam:operation_0279, edam:operation_2518, edam:operation_3095 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VeriNA3d" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d" ; biotools:primaryContact "Modesto Orozco", "Pablo D. Dans" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6685253", "pubmed:31406507" ; sc: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" ; sc:featureList edam:operation_2942, edam:operation_3436, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "ViSEAGO" ; sc:url "https://bioconductor.org/packages/ViSEAGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3436 ; sc:name "ViSiElse" ; sc:url "https://cran.csiro.au/web/packages/ViSiElse/ViSiElse.pdf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC6658840", "pubmed:31372596" ; sc: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.." ; sc:featureList edam:operation_3196 ; sc:name "ViVa" ; sc:url "http://plantsynbiolab.bse.vt.edu/ViVa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "VICTOR is an interactive and dependency-free visual analytics web application which allows the comparison and visualization of various clustering outputs." ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:name "VICTOR" ; sc:url "http://bib.fleming.gr:3838/VICTOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_3474 ; sc:citation , "pubmed:31583641" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:name "VieClus" ; sc:softwareHelp ; sc:url "http://vieclus.taa.univie.ac.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC7703770", "pubmed:31580400" ; sc: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""" ; sc:featureList edam:operation_3196, edam:operation_3436, edam:operation_3791 ; sc:name "VikNGS" ; sc:url "https://vikngsdocs.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0625, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC6829986", "pubmed:31684876" ; sc:description "The method is essentially an EM algorithm." ; sc:featureList edam:operation_0487, edam:operation_3216, edam:operation_3432, edam:operation_3798 ; sc:name "VirBin" ; sc:url "https://github.com/chjiao/VirBin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6764358", "pubmed:31579606" ; sc: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""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "ViralPlaque" ; sc:url "https://sourceforge.net/projects/viralplaque/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6909514", "pubmed:31836005" ; sc:description "Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference." ; sc:featureList edam:operation_3196, edam:operation_3200, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Vireo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/single-cell-genetics/vireo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2229 ; sc:citation , "pmcid:PMC9883706", "pubmed:31373613" ; sc: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" ; sc:featureList edam:operation_2495 ; sc:name "VirtualCytometry" ; sc:url "https://www.grnpedia.org/cytometry/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:31504195" ; sc: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" ; sc:featureList edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "VisFeature" ; sc:url "https://github.com/wangjun1996/VisFeature" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2333, edam:format_3751 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation , "pmcid:PMC4559603", "pubmed:26328469" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "VisR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.4" ; sc:url "https://visrsoftware.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2830, edam:topic_3520 ; sc:citation , "pmcid:PMC6698994", "pubmed:31452600" ; sc: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" ; sc:featureList edam:operation_3629, edam:operation_3633 ; sc:name "VisioProt-MS" ; sc:url "https://masstools.ipbs.fr/mstools/visioprot-ms/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:29091996" ; sc:description "Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains." ; sc:featureList edam:operation_3202, edam:operation_3798 ; sc:name "VizGVar" ; sc:softwareHelp ; sc:softwareVersion "1.5" ; sc:url "http://vizport.io/vizgvar/" ; biotools:primaryContact "Allan Orozco-Solano", "Antonio Solano-Román" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0102, edam:topic_0798 ; sc:citation , "pmcid:PMC7703779", "pubmed:31589313" ; sc:description "Web-Assisted Symbolic Plasmid Synteny Server." ; sc:featureList edam:operation_0578, edam:operation_2421 ; sc:name "WASPS" ; sc:url "https://archaea.i2bc.paris-saclay.fr/wasps/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_2275 ; sc:citation , "pubmed:26198103" ; sc:description "Tool for improving the design of drugs based on protein-water interactions." ; sc:featureList edam:operation_0482, edam:operation_2415, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "WATCLUST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://watclust.wordpress.com/" ; biotools:primaryContact "Adrian G. Turjanski", "Marcelo A. Marti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3372 ; sc:author "Marc Chakiachvili" ; sc:citation , "pubmed:30052762" ; sc: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." ; sc:featureList edam:operation_3763 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "WAVES" ; sc:operatingSystem "Linux" ; sc:provider "LIRMM" ; sc:softwareHelp , ; sc:softwareVersion "1.6" ; sc:url "http://www.atgc-montpellier.fr/waves/" ; biotools:primaryContact "Vincent Lefort" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3344, edam:topic_3382 ; sc:description "This code is implementation of an algorithm to segment the nucleus of white blood cells (WBCs)" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "An Efficient Technique for White Blood Cells Nuclei Automatic Segmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/36634-an-efficient-technique-for-white-blood-cells-nuclei-automatic-segmentation" ; biotools:primaryContact "Mostafa M. A. Mohamed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6757419", "pubmed:31547811" ; sc: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" ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:name "WBNPMD" ; sc:url "https://github.com/Dicrop/WBNPMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2815, edam:topic_3673 ; sc:citation ; sc:description "Wengan is a new genome assembler that unlike most of the current long-reads assemblers avoids entirely the all-vs-all read comparison." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3644 ; sc:license "AGPL-3.0" ; sc:name "WENGAN" ; sc:url "https://github.com/adigenova/wengan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6375192", "pubmed:30760221" ; sc:description "Pipeline for detecting whole genome duplication events using the genome or transcriptome annotations." ; sc:featureList edam:operation_3258 ; sc:isAccessibleForFree true ; sc:name "WGDdetector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yongzhiyang2012/WGDdetector" ; biotools:primaryContact "Yongzhi Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3534 ; sc:author ; sc:citation , "pubmed:16450362" ; sc: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." ; sc:name "WHISCY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://bianca.science.uu.nl/whiscy/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3168 ; sc:citation , "pmcid:PMC7759745", "pubmed:31860070" ; sc: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.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3454, edam:operation_3644 ; sc:license "MIT" ; sc:name "WHdenovo" ; sc:url "https://github.com/shilpagarg/WHdenovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3810 ; sc:citation , "pubmed:31057068" ; sc:description "Fast and Memory Efficient Approach for Mapping NGS Reads to a Reference Genome." ; sc:featureList edam:operation_3198, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "WIT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.algorithm-skg.com/wit/home.html" ; biotools:primaryContact "Sanjeev Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0637, edam:topic_0659, edam:topic_3050, edam:topic_3697 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "WITOD" ; sc:url "https://github.com/johncava/WITOD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3399 ; sc:citation , "pmcid:PMC6707408", "pubmed:31463184" ; sc: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" ; sc:name "WPD" ; sc:url "http://www.wpdk.ivi.int/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0659, edam:topic_0749, edam:topic_0780, edam:topic_3512 ; sc:citation , "pubmed:31693067" ; sc: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""" ; sc:featureList edam:operation_0463, edam:operation_3454, edam:operation_3792 ; sc:name "WPMIAS" ; sc:url "https://cbi.njau.edu.cn/WPMIAS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3314, edam:topic_3315 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "WPTherml" ; sc:url "https://github.com/FoleyLab/wptherml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736 ; sc:citation , "pmcid:PMC6929547", "pubmed:31874617" ; sc: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""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0474 ; sc:name "Wang-xiaoheng" ; sc:url "https://github.com/Xiaoheng-Wang12/Wang-xiaoheng/tree/master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3314, edam:topic_3372 ; sc:citation , "pubmed:31658458" ; sc:description "Wannier90 is a tool for obtaining maximally localized wannier functions from DFT calculations." ; sc:featureList edam:operation_0337 ; sc:name "Wannier90" ; sc:url "http://aiida-wannier90.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3306, edam:topic_3316, edam:topic_3382 ; sc:citation , "pmcid:PMC6858868", "pubmed:31591575" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3458 ; sc:license "GPL-3.0" ; sc:name "Warp" ; sc:url "http://github.com/cramerlab/warp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC7820865", "pubmed:31838514" ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3778 ; sc:name "WebAnno" ; sc:url "http://webanno.github.io/webanno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3375, edam:topic_3534 ; sc:citation , "pubmed:30052776" ; sc:description "Cleavage sites analysis tool for natural and unnatural substrates from diverse data source." ; sc:featureList edam:operation_3216, edam:operation_3501, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "WebMetabase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webmetabase.com:8182/WebMetabaseBioinformatics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_3172, edam:topic_3473, edam:topic_3474, edam:topic_3489 ; sc:author "Miguel Rocha", "Sara Cardoso", "Telma Afonso" ; sc:citation , "pmcid:PMC6835413", "pubmed:31635085" ; sc:contributor "Marcelo Maraschin" ; sc: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." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "WebSpecmine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webspecmine.bio.di.uminho.pt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0478, edam:operation_3454 ; sc:name "Webina" ; sc:url "http://durrantlab.com/webina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC6558888", "pubmed:31185910" ; sc:description "Web application for the analysis of fluorescent reporter gene data." ; sc:featureList edam:operation_1812, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "WellInverter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://team.inria.fr/ibis/wellinverter/" ; biotools:primaryContact "Hidde de Jong", "Johannes Geiselmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3512, edam:topic_3810, edam:topic_3912 ; sc:citation , "pmcid:PMC6836449", "pubmed:31694550" ; sc: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""" ; sc:featureList edam:operation_0440, edam:operation_3096 ; sc:name "WheatCRISPR" ; sc:url "https://crispr.bioinfo.nrc.ca/WheatCrispr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0610, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0227, edam:operation_2421, edam:operation_3625, edam:operation_3908 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "WheatIS" ; sc:softwareHelp , , , ; sc:url "https://urgi.versailles.inrae.fr/wheatis/" ; biotools:primaryContact "Support service" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Wheat IWGSC RefSeq v1.0" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "WheatMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://urgi.versailles.inra.fr/WheatMine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318 ; sc:citation , "pmcid:PMC6773861", "pubmed:31575870" ; sc: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.""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3659 ; sc:license "MIT" ; sc:name "When2Heat" ; sc:url "https://github.com/oruhnau/when2heat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "Whisper 2" ; sc:url "https://github.com/refresh-bio/whisper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:description "Automatic white blood cells detector using differential evolution (DE)" ; sc:featureList edam:operation_2429, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "White blood cells detection using differential evolution (DE)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.6.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47111-white-blood-cells-detection-using-differential-evolution-de" ; biotools:primaryContact "Erik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3172, edam:topic_3474 ; sc:citation , "pmcid:PMC6780109", "pubmed:31438611" ; sc: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" ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3629 ; sc:license "MIT" ; sc:name "WiPP" ; sc:url "https://github.com/bihealth/WiPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pmcid:PMC6838453", "pubmed:31720321" ; sc: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""" ; sc:featureList edam:operation_3359 ; sc:name "WiseNET" ; sc:url "https://wisenet.checksem.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_3293, edam:topic_3500 ; sc:citation ; sc:description "Complete genome assembly of the Wolbachia endosymbiont of the horn fly Haematobia irritans irritans." ; sc:featureList edam:operation_0525, edam:operation_3431, edam:operation_3840 ; sc:name "Wolbachia" ; sc:url "https://github.com/gerthmicha/wolbachia-mlst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0602, edam:topic_0654 ; sc:citation , "pmcid:PMC3083346", "pubmed:21473782" ; sc: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." ; sc:featureList edam:operation_2436, edam:operation_2497, edam:operation_3432, edam:operation_3501 ; sc:name "WordCloud Cytoscape Plugin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://baderlab.org/Software/WordCloudPlugin" ; biotools:primaryContact "Layla Oesper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2640, edam:topic_3405 ; sc:citation , "pmcid:PMC6531084", "pubmed:31096452" ; sc:description "Interactive web-based platform presenting global cancer statistics , which can be used for cancer research." ; sc:featureList edam:operation_2429, edam:operation_2942 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "World Cancer Map" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://worldmap.csmu-liawyp.tw" ; biotools:primaryContact "Yung-Po Liaw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2830, edam:topic_3512 ; sc:citation , "pubmed:31552661" ; sc: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" ; sc:name "WormBook" ; sc:url "http://www.wormbook.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0625, edam:topic_0634, edam:topic_3382 ; sc:citation , "pmcid:PMC6925079", "pubmed:31728898" ; sc: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""" ; sc:featureList edam:operation_3503 ; sc:name "WormBot" ; sc:url "http://wormbot.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Intermine data mining platform for C. elegans and related nematodes" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "WormMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "273" ; sc:url "http://intermine.wormbase.org/tools/wormmine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation ; sc:description "an interactive platform for systems genetics in Caenorhabditis elegans | eQTL visualization and investigation | All eQTL patterns for a single trait" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:name "WormQTL2" ; sc:url "http://www.bioinformatics.nl/WormQTL2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3489 ; sc:citation , "pubmed:31094692" ; sc:description "Massive XML-based biological data management platform." ; sc:featureList edam:operation_0224, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "X2H" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lyotvincent/X2H" ; biotools:primaryContact "Jian Liu", "Lei Zhang", "Qiuru Liu", "Shuhui Su", "Yongzhuang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9883676", "pubmed:31400221" ; sc: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:" ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3800 ; sc:name "XAEM" ; sc:url "https://github.com/WenjiangDeng/XAEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0659 ; sc:citation , "pmcid:PMC7772933", "pubmed:31698618" ; sc: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""" ; sc:name "XCI" ; sc:url "http://dna.cs.miami.edu/3D-XCI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation , , "pmcid:PMC7580946", "pubmed:33091000" ; sc:description "An algorithm for extracting ion chromatograms." ; sc:featureList edam:operation_3203, edam:operation_3636 ; sc:name "XFlow" ; sc:url "https://github.com/optimusmoose/jsms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3295 ; sc:citation , "pubmed:31392406" ; sc: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" ; sc:name "XG-PseU" ; sc:url "http://www.bioml.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2828, edam:topic_3448 ; sc:citation , "pmcid:PMC6718201", "pubmed:31475914" ; sc:description "extended gradient descent algorithm for lattice finding | Directory Algorithm documentation | Directory precomputedSamplePoints" ; sc:license "LGPL-3.0" ; sc:name "XGANDALF" ; sc:url "https://stash.desy.de/users/gevorkov/repos/xgandalf/browse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6933652", "pubmed:31881847" ; sc:description "Putative biomarkers for predicting tumor sample purity based on gene expression data." ; sc:featureList edam:operation_2454, edam:operation_3463, edam:operation_3659 ; sc:license "Apache-2.0" ; sc:name "XGBoost" ; sc:url "https://cran.r-project.org/web/packages/xgboost/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:27153693" ; sc:description "XIBD (X chromosome Identity by Descent) performs pairwise identity by descent (IBD) mapping on the autosomes and the X chromosome." ; sc:featureList edam:operation_0484, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "XIBD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.wehi.edu.au/software/XIBD/" ; biotools:primaryContact "Lyndal Henden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0593, edam:topic_3678 ; sc:citation , "pubmed:31748843" ; sc: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""" ; sc:featureList edam:operation_0320, edam:operation_3214, edam:operation_3695 ; sc:name "XIPP" ; sc:url "https://spin.niddk.nih.gov/dgarrett/Xipp/xipp.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3678 ; sc:citation , ; sc:description "XL-mHG is a Semiparametric Test for Enrichment in Ranked Lists." ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "XL-mHG" ; sc:url "https://github.com/flo-compbio/xlmhg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3304, edam:topic_3337, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc: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)""" ; sc:featureList edam:operation_3435 ; sc:name "XTRACT" ; sc:url "http://www.fmrib.ox.ac.uk/fsl/XTRACT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Search and retrieve integrated Xenopus tropicalis and Xenopus laevis data" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "XenMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "b BETA bUpdated on:Sep-02-2015" ; sc:url "http://www.xenmine.org/xenmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2640, edam:topic_3170, edam:topic_3304, edam:topic_3673 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "XenoCP" ; sc:url "https://pecan.stjude.cloud/permalink/xenocp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3360 ; sc:citation , "pubmed:31142512" ; sc:description "Integrative pharmacogenomics analysis of patient-derived xenografts." ; sc:featureList edam:operation_0533, edam:operation_3501, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Xeva" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bhklab/Xeva" ; biotools:primaryContact "Benjamin Haibe-Kains" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2259, edam:topic_3382 ; sc:citation , "pmcid:PMC6842926", "pubmed:31749833" ; sc: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""" ; sc:featureList edam:operation_2426, edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "XitoSBML" ; sc:url "https://github.com/spatialsimulator/XitoSBML/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0780, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material." ; sc:featureList edam:operation_3472, edam:operation_3840 ; sc:name "Xylella" ; sc:url "https://github.com/lfaino/xylella" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC6873394", "pubmed:31757199" ; sc: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""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3211, edam:operation_3472 ; sc:license "MIT" ; sc:name "YALFF" ; sc:url "https://github.com/yhhshb/yalff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6670153", "pubmed:31366376" ; sc: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}}" ; sc:featureList edam:operation_0440, edam:operation_0441, edam:operation_2495 ; sc:name "YAPP" ; sc:url "http://www.bioinformatics.org/yapp/cgi-bin/yapp.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation , "pmcid:PMC6693274", "pubmed:31409274" ; sc: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" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3800 ; sc:name "Yanagi" ; sc:url "https://github.com/HCBravoLab/yanagi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Search and retrieve S. cerevisiae data, populated by SGD and powered by InterMine" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "YeastMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "Data Updated on: Nov-19-2019" ; sc:url "https://yeastmine.yeastgenome.org/yeastmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382 ; sc:citation , "pmcid:PMC6821424", "pubmed:31095270" ; sc:description "Accurate and parameter-free web segmentation for microscopy images of yeast cells." ; sc:featureList edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "YeastSpotter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://yeastspotter.csb.utoronto.ca/" ; biotools:primaryContact "Alan Moses", "Alex Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0632, edam:topic_3168, edam:topic_3293, edam:topic_3305 ; sc:citation , "pmcid:PMC6861861", "pubmed:31580794" ; sc:description "Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization." ; sc:featureList edam:operation_3192, edam:operation_3431, edam:operation_3460, edam:operation_3840 ; sc:name "Yersinia" ; sc:url "https://bigsdb.pasteur.fr/yersinia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0623, edam:topic_0821 ; sc:citation , "pmcid:PMC6602428", "pubmed:31106356" ; sc:description "Yosshi (YOur web-server for S-S bond HarvestIng) - web server for disulfide engineering by bioinformatic analysis of diverse protein families." ; sc:featureList edam:operation_0303, edam:operation_0471, edam:operation_1850 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Yosshi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://biokinet.belozersky.msu.ru/yosshiserver/" ; biotools:primaryContact "Dmitry Suplatov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0154, edam:topic_2830 ; sc:citation , "pmcid:PMC6602444", "pubmed:31106372" ; sc:description "Antibody high-density alignment visualization and analysis platform with an integrated database." ; sc:featureList edam:operation_3431, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Yvis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.icb.ufmg.br/yvis/" ; biotools:primaryContact , "Liza F Felicori" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2840, edam:topic_3304 ; sc:citation , "pubmed:30615594" ; sc:description "Application for quantification of spontaneous tail movement in zebrafish embryos." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ZebraSTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lcc.ens.uabc.mx/~zebrastm/" ; biotools:primaryContact "Ulises Bardullas" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description """ZebrafishMine is powered by the InterMIne data warehouse system, and integrates biological data sets from multiple sources.\r It currently includes updates of data from ZFIN, the zebrafish model organism database. There is also data from the Panther database.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "ZebrafishMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "Last Build: 03.28.2013" ; sc:url "http://zebrafishmine.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621 ; sc:description "Zebrafish is an online database of standardized Zebrafish (a marine vertebrate model) neuroanatomy, accessible via an interactive interface for 3D visualisation." ; sc:featureList edam:operation_0337 ; sc:name "Zebrafish neuroanatomy" ; sc:url "https://zebrafish.tefor.net/#/home?_k=3p8igq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3489, edam:topic_3534 ; sc:citation , "pmcid:PMC6361820", "pubmed:30722040" ; sc:description "Database of zinc binding sites." ; sc:featureList edam:operation_0389, edam:operation_0445, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "ZincBind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://zincbind.bioinf.org.uk/" ; biotools:primaryContact "Sam Ireland" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC6706154", "pubmed:31453251" ; sc: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. 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'aba_enrich' interfaces the ontology enrichment software FUNC to perform the statistical analyses." ; sc:featureList edam:operation_2436 ; sc:license "GPL-2.0" ; sc:name "ABAEnrichment" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ABAEnrichment.html" ; biotools:primaryContact "Steffi Grote" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2830, edam:topic_3474, edam:topic_3930 ; sc:citation , "pmcid:PMC9813736", "pubmed:36618397" ; sc:description "A deep learning method for predicting antibody-antigen interactions based on sequence information." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0478, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AbAgIntPre" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.zzdlab.com/AbAgIntPre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2830, edam:topic_3168, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC10320167", "pubmed:37207341" ; sc:description "A comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires." ; sc:featureList edam:operation_0292, edam:operation_0416, edam:operation_0553 ; sc:isAccessibleForFree true ; sc:name "Abalign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cao.labshare.cn/abalign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3293, edam:topic_3308 ; sc:citation , "pmcid:PMC6778792", "pubmed:31413154" ; sc:description "The Abalomics community portal is a community driven project to increase genetic knowledge of the abalone species." ; sc:featureList edam:operation_3192, edam:operation_3216 ; sc:name "abalonedb" ; sc:url "http://abalonedb.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3751 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_3751 ; sc:name "Resource metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3617 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2032 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2269, edam:topic_3518 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2409, edam:operation_2428, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "ABarray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.42.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ABarray.html" ; biotools:primaryContact "Yongming Andrew Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3895 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0438, edam:operation_1781, edam:operation_2437, edam:operation_3431 ; sc:name "Abasy Atlas" ; sc:url "https://abasy.ccg.unam.mx/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation , "pubmed:26083755" ; sc: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." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "abawaca" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/CK7/abawaca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174 ; sc:citation , "pubmed:18818729" ; sc: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." ; sc:featureList edam:operation_0523, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "ABBA" ; sc:operatingSystem "Linux" ; sc:url "http://www.biofacebook.com/?p=250" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC4668780", "pubmed:25995231" ; sc:description "Computational tool that identifies allele specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs." ; sc:featureList edam:operation_0445 ; sc:name "ABC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/mlupien/ABC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0736, edam:topic_0769, edam:topic_3300 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0303, edam:operation_0337, edam:operation_3767 ; sc:license "GPL-3.0" ; sc:name "ABC-finder" ; sc:url "http://abc-finder.osdd.jnu.ac.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_2885, edam:topic_3173, edam:topic_3517 ; sc:citation , "pmcid:PMC7379852", "pubmed:32765587" ; sc:description "A web application for analysis of breast cancer GWAS variants." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3431, edam:operation_3661 ; sc:name "ABC-GWAS" ; sc:url "http://education.knoweng.org/abc-gwas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3179 ; sc:citation , "pmcid:PMC8896320", "pubmed:35240993" ; sc:description "abc4pwm is a software tool for clustering of pwms, classficiation of pwms to their DNA binding Domain, motif search, and other supportive modules." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_3192, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "abc4pwm" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://omer0191.github.io/abc4pwm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3277, edam:topic_3697 ; sc:citation , "pmcid:PMC10767846", "pubmed:37994699" ; sc:description "The atlas of biosynthetic gene clusters in the human microbiome." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "ABC-HuMi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ccb.uni-saarland.de/abc_humi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3400, edam:topic_3408 ; sc:citation , "pmcid:PMC9825444", "pubmed:35920330" ; sc:description "ABC portal provides web-based interactive analysis modules, especially a comprehensive cell-cell communication analysis and disease-related gene signature analysis." ; sc:license "Not licensed" ; sc:name "ABC portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://abc.sklehabc.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pmcid:PMC3597143", "pubmed:23357921" ; sc:contributor ; sc: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)." ; sc:featureList edam:operation_2422 ; sc:license "Not licensed" ; sc:name "AbCD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://yunliweb.its.unc.edu/AbCD.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3360 ; sc:citation , "pmcid:PMC6722159", "pubmed:31501752" ; sc: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." ; sc:featureList edam:operation_2495, edam:operation_3501 ; sc:name "Alzheimers Disease Biomarker Comprehensive Database (ABCD)" ; sc:url "http://www.bioinfoindia.org/abcd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workbench" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_0780, edam:topic_3390, edam:topic_3810 ; sc:citation ; sc:description "The Aliment to Bodily Condition knowledgebase (ABCkb) is a database connecting plants and human health." ; sc:featureList edam:operation_1812, edam:operation_2421 ; sc:license "GPL-3.0" ; sc:name "Aliment to Bodily Condition knowledgebase (ABCkb)" ; sc:url "https://github.com/atrautm1/ABCkb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3473, edam:topic_3474 ; sc:citation , "pubmed:33057581" ; sc: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.""" ; sc:featureList edam:operation_3436, edam:operation_3936, edam:operation_3937 ; sc:license "GPL-3.0" ; sc:name "ABCModeller" ; sc:url "http://lishuyan.lzu.edu.cn/ABCModeller.rar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3361 ; sc:citation , "pubmed:34460364" ; sc:description "Adaptive Bezier-Curve Network for Real-time End-to-end Text Spotting." ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "ABCNet" ; sc:softwareVersion "V.2" ; sc:url "https://git.io/AdelaiDet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3400, edam:topic_3948, edam:topic_3966 ; sc:citation , "pmcid:PMC9581038", "pubmed:36303781" ; sc: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)." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0480, edam:operation_3891 ; sc:license "Other" ; sc:name "AbCPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.unipune.ac.in/AbCPE/Home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_3400 ; sc:citation , "pubmed:16894596" ; sc: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." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "ABCpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/abcpred/" ; biotools:primaryContact "Gajendra P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3047, edam:topic_3474 ; sc:citation , "pubmed:34609711" ; sc:description "ABCpred is a webserver for the discovery of acetyl- and butyryl-cholinesterase inhibitors." ; sc:isAccessibleForFree true ; sc:name "ABCpred" ; sc:url "http://codes.bio/abcpred/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description "Prediction of antibiotic resistant strains of bacteria from their beta-lactamases protein." ; sc:featureList edam:operation_0321, edam:operation_3482, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "ABCRpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webs.iiitd.edu.in/raghava/abcrpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3315, edam:topic_3407 ; sc:citation , "pubmed:35657711" ; sc:description "ABCstats is an R package for metabolomics data transformation. Adaptive Box-Cox (ABC) transformation improves the data normality for statistical analysis." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ABCstats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HuanLab/ABCstats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0196, edam:topic_0623, edam:topic_0736, edam:topic_0821 ; sc:citation , "pmcid:PMC7737780", "pubmed:33040418" ; sc:description "The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes." ; sc:featureList edam:operation_0249, edam:operation_0310, edam:operation_0479, edam:operation_2488 ; sc:name "AbDesign" ; sc:url "https://github.com/Fleishman-Lab/AbDesign_for_enzymes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_2830, edam:topic_3297 ; sc:citation ; sc:description "Integrated online application for identification of optimal immunizing peptides for antibody production using peptide-based strategy." ; sc:featureList edam:operation_0252 ; sc:name "AbDesigner3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sysbio.chula.ac.th/AbDesigner3D/" ; biotools:primaryContact "Trairak Pisitkun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2830, edam:topic_3168, edam:topic_3374 ; sc:citation ; sc:description "AbDiver is a tool to explore the natural antibody landscape to aid therapeutic design." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "AbDiver" ; sc:softwareHelp ; sc:url "http://research.naturalantibody.com/abdiver" ; biotools:primaryContact "Konrad Krawczyk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3324, edam:topic_3343, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC10954100", "pubmed:38345040" ; sc:description "Prediction of active antimicrobial compounds using supervised machine learning techniques." ; sc:featureList edam:operation_3436, edam:operation_3482, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "ABDpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://clinicalmedicinessd.com.in/abdpred/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1917 ; sc:encodingFormat edam:format_2330 ; sc:name "Atomic property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3332 ; sc:citation , "pubmed:16381078" ; sc:description "Calculates partial atomic charges for small organic molecules, drug-like molecules." ; sc:featureList edam:operation_2480 ; sc:isAccessibleForFree true ; sc:name "ABEEM Solver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-CZ" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "http://ncbr.muni.cz/~svobodova/eem_abeem" ; biotools:primaryContact "Radka Svobodová Vařeková" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0634, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC9563686", "pubmed:36063052" ; sc: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." ; sc:featureList edam:operation_3435, edam:operation_3454, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ABEILLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://jlabory.shinyapps.io/ABEILLE-main/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2830, edam:topic_3382 ; sc:citation , "pmcid:PMC10898366", "pubmed:37188806" ; sc:description "Web server for the prediction of antibody epitopes." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0479, edam:operation_0480, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "AbEMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://abemap.cluspro.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0219 ; sc:citation , "pmcid:PMC4384359", "pubmed:25627673" ; sc:description "Framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies." ; sc:featureList edam:operation_3559 ; sc:name "Aber-OWL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://aber-owl.net/#/" ; biotools:primaryContact "Robert Hoehndorf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625 ; sc:description "abi2link is designed to create linkage files out of ABI genotype and phenotype files." ; sc:featureList edam:operation_0335 ; sc:name "abi2link" ; sc:url "http://www.imbs-luebeck.de/imbs/node/40" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "abi2xml is a command line utility to convert an abi trace file to an xml file. 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The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. 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sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ABSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ABSP-methylation-tool/ABSP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2032 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3617 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2032 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Plug-in" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3170 ; sc:citation , "pmcid:PMC4973090", "pubmed:27488180" ; sc:description "An R package which provides RNA-Seq analysis based on modelling absolute expression differences." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2426, edam:operation_2495, edam:operation_3223 ; 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sc:url "https://github.com/YuWang28/acPCoA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3474 ; sc:citation , "pmcid:PMC8146440", "pubmed:33925812" ; sc:description "AC2 is an efficient protein sequence compression tool using artificial neural networks and cache-hash models." ; sc:featureList edam:operation_0267, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "AC2" ; sc:url "https://github.com/cobilab/ac2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3382 ; sc:citation "pmcid:PMC8299461", "pubmed:34308361" ; sc:description "Adaptive Checkpoint Adjoint Method for Gradient Estimation in Neural ODE." ; sc:name "ACA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; 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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." ; sc:featureList edam:operation_3233, edam:operation_3435 ; sc:name "Accucopy" ; sc:url "https://www.yfish.org/display/PUB/Accucopy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2229, edam:topic_3168, edam:topic_3295, edam:topic_3474 ; sc:citation ; sc:description """Accurate enhancer prediction by integration of multiple cell type data with deep learning. 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Moreover, we also tested joint training for multiple cell types to boost the model performance.""" ; sc:featureList edam:operation_0440, edam:operation_2575, edam:operation_3222 ; sc:name "accuEnhancer" ; sc:url "https://github.com/callsobing/accuEnhancer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC9825286", "pubmed:36610711" ; sc: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." ; sc:featureList edam:operation_0292, edam:operation_0525, edam:operation_3196 ; sc:license "Not licensed" ; sc:name "AccuVIR" ; sc:url "https://github.com/rainyrubyzhou/AccuVIR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3370, edam:topic_3524 ; sc:citation , "pubmed:12779216" ; sc: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. 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sc:license "GPL-3.0" ; sc:name "acdpretty" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/acdpretty.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Generate an HTML table of parameters from an application ACD file." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "acdtable" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/acdtable.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "Web-server for the generic analysis of large data sets of counts." ; sc:name "acdtool" ; sc:url "http://www.igs.cnrs-mrs.fr/acdtool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Trace processing of an application ACD file (for testing)." ; sc:featureList edam:operation_0336 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "acdtrace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/acdtrace.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Validate an application ACD file." ; sc:featureList edam:operation_0336 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "acdvalid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/acdvalid.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation , "pubmed:26026137" ; sc:description "Corrects substitution errors in an Illumina archive using a k-mer trie." ; sc:featureList edam:operation_3195 ; sc:name "ACE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/sheikhizadeh/ACE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3314, edam:topic_3372 ; sc:citation , "pubmed:32241122" ; sc:description "Advanced Computational Engine for Molecule (ACE-Molecule) is a quantum chemistry package based on a real-space numerical grid." ; sc:license "GPL-3.0" ; sc:name "ACE-Molecule" ; sc:softwareHelp ; sc:url "https://gitlab.com/aceteam.kaist/ACE-Molecule" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_0804, edam:topic_2885, edam:topic_3404 ; sc:citation ; sc:description "In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227 ; sc:name "ACE2 Netlas" ; sc:url "https://gpwhiz.github.io/ACE2Netlas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3324, edam:topic_3930 ; sc:citation , "pmcid:PMC10768796", "pubmed:38180831" ; sc: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." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3629, edam:operation_3631, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ACE" ; sc:url "https://github.com/pirl-unc/ace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc: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." ; sc:featureList edam:operation_2423, edam:operation_2454 ; sc:name "AcE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.5" ; sc:url "http://www.bioinformatics.org/project/?group_id=39" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3170, edam:topic_3511 ; sc:citation , "pmcid:PMC5504734", "pubmed:28693417" ; sc:description "Efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data." ; sc:featureList edam:operation_3482 ; sc:name "ACE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.zju.edu.cn/software/ace/" ; biotools:primaryContact "Dianhao Guo", "Jiapeng Luo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3063, edam:topic_3303, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC8279796", "pubmed:33712854" ; sc:description "ACEapi is the API for the the Advanced Cohort Engine for searching longitudinal patient records." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3436 ; sc:license "MIT" ; sc:name "ACEapi" ; sc:url "https://github.com/som-shahlab/ACEapi" ; biotools:primaryContact "Alison Callahan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3315, edam:topic_3374 ; sc:description "PKPD model for ACE inhibition with benazapril or cilazapril; ducational drug dosing app for treatment of high blood pressure" ; sc:isAccessibleForFree true ; sc:name "ACEInhibPKPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/61167-ashleefv-aceinhibpkpd" ; biotools:primaryContact "Ashlee N. Ford Versypt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0602, edam:topic_2815, edam:topic_3474 ; sc:citation , "pmcid:PMC2586757", "pubmed:19025694" ; sc:description "Tool that aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations." ; sc:featureList edam:operation_2409, edam:operation_3280, edam:operation_3778 ; sc:name "ACELA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nactem.ac.uk/acela/" ; biotools:primaryContact "Yoshimasa Tsuruoka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0160, edam:topic_3400, edam:topic_3474 ; sc:citation , "pmcid:PMC7455913", "pubmed:32859150" ; sc: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." ; sc:featureList edam:operation_0239, edam:operation_0267, edam:operation_0303, edam:operation_0337, edam:operation_3482 ; sc:name "ACEP" ; sc:url "https://github.com/Fuhaoyi/ACEP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources." ; sc:featureList edam:operation_0226, edam:operation_0310, edam:operation_0335, edam:operation_2928 ; sc:name "AceParser" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.33" ; sc:url "http://www.personal.psu.edu/jhm10/Vera/SoftwareC.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3168, edam:topic_3293, edam:topic_3512 ; sc:citation ; sc: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.""" ; sc:featureList edam:operation_0224, edam:operation_0323, edam:operation_0492, edam:operation_0552, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ACES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TNTurnerLab/ACES" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2292 ; sc:name "GenBank accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2803 ; sc:name "Clone ID (RefSeq)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2704 ; sc:name "Clone ID (IMAGE)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:name "Gene ID (NCBI)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene transcript report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3512 ; sc:citation , "pmcid:PMC3272079", "pubmed:20064451" ; sc: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)." ; sc:featureList edam:operation_0224 ; sc:name "AceView genes database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "NCBI" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3056 ; sc:citation , "pmcid:PMC3575405", "pubmed:23379678" ; sc: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." ; sc:featureList edam:operation_2478 ; sc:name "ACG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://arup.utah.edu/acg/" ; biotools:primaryContact "Brendan O'Fallon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3175, edam:topic_3518 ; sc:citation , "pubmed:16159913" ; sc: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." ; sc:featureList edam:operation_3443 ; sc:license "GPL-2.0" ; sc:name "aCGH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.52.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/aCGH.html" ; biotools:primaryContact "Peter Dimitrov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0121, edam:topic_0154, edam:topic_0166 ; sc:citation , "pmcid:PMC10320090", "pubmed:37158246" ; sc:description "Application for fast calculation of partial atomic charges of structures from the Alphafold database." ; sc:featureList edam:operation_0474, edam:operation_0478, edam:operation_3431, edam:operation_3893 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "aCharges" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://alphacharges.ncbr.muni.cz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:14962935" ; sc:description "The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. 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sc:softwareHelp ; sc:url "http://design.rxnfinder.org/addictedchem/prediction/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0203, edam:topic_3295, edam:topic_3419 ; sc:citation , "pmcid:PMC8113760", "pubmed:34025933" ; sc:description "AddictGene is an integrated knowledge base for differentially expressed genes associated with psychostimulants," ; sc:featureList edam:operation_2422, edam:operation_3223, edam:operation_3431, edam:operation_3672 ; sc:name "AddictGene" ; sc:softwareHelp ; sc:url "http://159.226.67.237/sun/addictgedb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC8496238", "pubmed:34544122" ; sc: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.""" ; sc:featureList edam:operation_0308, edam:operation_3096, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "AddTag" ; sc:url "https://github.com/tdseher/addtag-project" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8424397", "pubmed:33401309" ; sc:description "ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0463, edam:operation_2441, edam:operation_3223 ; sc:name "ADeditome" ; sc:url "https://ccsm.uth.edu/ADeditome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3295, edam:topic_3948 ; sc:citation , "pmcid:PMC8344678", "pubmed:34254996" ; sc:description "An integrated platform of age-dependent expression and immune profiles across human tissues." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3463, edam:operation_3800 ; sc:name "ADEIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://geneyun.net/ADEIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3473 ; sc:citation , "pubmed:33074804" ; sc: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." ; sc:featureList edam:operation_3359, edam:operation_3436 ; sc:name "AdelaiDet" ; sc:url "http://git.io/AdelaiDet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0654, edam:topic_3303 ; sc:citation , "pmcid:PMC7470936", "pubmed:32692355" ; sc: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." ; sc:featureList edam:operation_0570, edam:operation_2442, edam:operation_3216 ; sc:license "BSD-3-Clause" ; sc:name "Adenita" ; sc:url "https://github.com/edellano/Adenita-SAMSON-Edition-Linux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2258 ; sc:citation , "pubmed:23127988" ; sc: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." ; sc:featureList edam:operation_2406 ; sc:name "Adenosiland" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:url "http://mms.dsfarm.unipd.it/Adenosiland/" ; biotools:primaryContact "Stefano Moro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3379 ; sc:author "Nicole Mentenich" ; sc:citation , "pubmed:32529631" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "Animation of Adverse Event Profiles (AdEPro)" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=adepro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0769, edam:topic_3378, edam:topic_3379 ; sc:citation , "pmcid:PMC7660953", "pubmed:33215076" ; sc: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." ; sc:featureList edam:operation_3778 ; sc:license "Apache-2.0" ; sc:name "Adverse drug event presentation and tracking (ADEPT)" ; sc:url "https://github.com/hms-dbmi/adept" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0154, edam:topic_0166, edam:topic_2275, edam:topic_3382 ; sc:citation , "pmcid:PMC3692060", "pubmed:23609539" ; sc: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." ; sc:featureList edam:operation_0387, edam:operation_0478, edam:operation_2950 ; sc:name "Adepth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biodev.cea.fr/adepth" ; biotools:primaryContact "Adepth coordinator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:21121022" ; sc:description "Software package for peptide identification using two different types of MS/MS spectra." ; sc:featureList edam:operation_3631 ; sc:name "ADEPTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cs.uwaterloo.ca/~l22he/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1147 ; sc:name "GEO accession number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2984 ; sc:name "Pathway or network report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3295, edam:topic_3308 ; sc:citation , "pmcid:PMC8223391", "pubmed:34167460" ; sc: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." ; sc:featureList edam:operation_0313, edam:operation_0571, edam:operation_2495, edam:operation_3431, edam:operation_3436, edam:operation_3501, edam:operation_3927, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "ADEx: Autoimmune Diseases Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://adex.genyo.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3168, edam:topic_3320 ; sc:citation , "pubmed:32246828" ; sc:description "ADFinder is an efficient detector of programmed DNA eliminations using NGS high-throughput sequencing data. 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It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information." ; sc:featureList edam:operation_2436, edam:operation_2495, edam:operation_3223, edam:operation_3762 ; sc:name "ADGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.btool.org/ADGO2" ; biotools:primaryContact "ADGO Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0108, edam:topic_0128, edam:topic_3474, edam:topic_3957 ; sc:citation , "pmcid:PMC9576568", "pubmed:36267921" ; sc:description "An attention-based deep hybrid model for protein-protein interaction prediction." ; sc:featureList edam:operation_0267, edam:operation_2492, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ADH-PPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://opendfki.de/PPI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0637, edam:topic_3303, edam:topic_3375 ; sc:citation , , "pmcid:PMC5405929", "pubmed:28445530", "pubmed:31438176" ; sc:description "Computation of adherence to medications from Electronic Healthcare Data." ; sc:featureList edam:operation_0224, edam:operation_0337 ; sc:name "AdhereR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://cran.r-project.org/web/packages/AdhereR/index.html" ; biotools:primaryContact "Dan Dediu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in", "Script" ; sc:applicationSubCategory edam:topic_0153, edam:topic_2229, edam:topic_3382, edam:topic_3407 ; sc:citation , "pmcid:PMC9635306", "pubmed:35947507" ; sc:description "A simple toolbox of two ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AdipoQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hansenjn/AdipoQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "A scalable tool to visualize the adjacency matrix with values on the edges, direction, and the sum of value as the node size." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Adjacency-Matrix-Visualizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/73772-adjacency-matrix-visualizer" ; biotools:primaryContact "Chaohan Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3418, edam:topic_3474 ; sc:citation , "pmcid:PMC7402217", "pubmed:32185818" ; sc:description "Adjusted-ADJUST is a script for the automatic identification of artifacts in electroencephalograph (EEG) data." ; sc:featureList edam:operation_3432, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "Adjusted-ADJUST" ; sc:url "https://github.com/ChildDevLab/MADE-EEG-preprocessing-pipeline/tree/master/adjusted_adjust_scripts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3444 ; sc:description "ALC is a dynamic fMRI connectivity toolbox for single-subject validation." ; sc:featureList edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Adjusted Local Connectivity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.3" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/61814-adjusted-local-connectivity" ; biotools:primaryContact "Mangor Pedersen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3653 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3653 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3653 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3653 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3520, edam:topic_3572 ; sc: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." ; sc:featureList edam:operation_3203, edam:operation_3628 ; sc:name "adjustPKL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://blog.binfalse.de/software/adjustpkl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089 ; sc: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." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ADL Workbench" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0.6" ; sc:url "https://openehr.github.io/adl-tools/adl_workbench_guide.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373, edam:topic_3375, edam:topic_3379 ; sc:citation , "pubmed:34176369" ; sc:description "Validating ADME QSAR Models Using Marketed Drugs." ; sc:featureList edam:operation_0409, edam:operation_2428, edam:operation_3799 ; sc:name "ADME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://opendata.ncats.nih.gov/adme/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0634, edam:topic_0654, edam:topic_3295 ; sc:citation , "pubmed:35617175" ; sc:description "A manually curated database for the differential methylation in Alzheimer's disease." ; sc:featureList edam:operation_2421 ; sc:license "Not licensed" ; sc:name "ADmeth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.biobdlab.cn/ADmeth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3314 ; sc:citation , "pmcid:PMC6020094", "pubmed:29943074" ; sc: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." ; sc:featureList edam:operation_0322 ; sc:name "ADMETlab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://admet.scbdd.com/" ; biotools:primaryContact "Dong-Sheng Cao" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3303, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC10029263", "pubmed:36941726" ; sc:description "Chemical Rules for Optimization of Chemical Mutagenicity via Matched Molecular Pairs Analysis and Machine Learning Methods." ; sc:featureList edam:operation_2428, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "ADMETopt2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lmmd.ecust.edu.cn/admetsar2/admetopt2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3056 ; sc:citation , "pmcid:PMC10980565", "pubmed:38490256" ; sc:description "An integrated toolkit and pipeline for genetic analyses of admixed populations." ; sc:featureList edam:operation_3196, edam:operation_3891, edam:operation_3920 ; sc:isAccessibleForFree true ; sc:name "admix-kit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KangchengHou/admix-kit" . a sc:SoftwareApplication ; 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This pipeline takes raw reads as an input, compares the composition (Jellyfish hashes) of the two parents and identifies uniquely segregating k-mers. 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biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3314, edam:topic_3318, edam:topic_3344, edam:topic_3382 ; sc:description "Atomic Force Microscopy Image Analysis" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "AFM Image Analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29645-afm-image-analysis" ; biotools:primaryContact "Prashant Patil" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0870 ; sc:name "Sequence distance matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3556 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation , "pmcid:PMC5224691", "pubmed:28105314" ; sc:description "Alignment-free network of 143 Bacteria and Archaea genomes." ; sc:featureList edam:operation_0567 ; sc:isAccessibleForFree true ; sc:name "AFnetwork" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.org.au/tools/AFnetwork/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0623, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7188683", "pubmed:32345989" ; sc:description "Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs." ; sc:featureList edam:operation_0418, edam:operation_3891, edam:operation_3937 ; sc:name "AFP-LSE" ; sc:url "https://github.com/Shujaat123/AFP-LSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "Prediction of antifreeze proteins (AFPs)" ; sc:name "AFProPred" ; sc:url "https://webs.iiitd.edu.in/raghava/afpropred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2229, edam:topic_3334 ; sc:citation , "pmcid:PMC5838108", "pubmed:29507333" ; sc:description "Browser-based visualization tools for AFQ results." ; sc:featureList edam:operation_3744 ; sc:name "AFQ-Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://yeatmanlab.github.io/AFQBrowser-demo/?table[prevSort][count]=2&table[prevSort][order]=ascending&table[prevSort][key]=&table[sort][count]=2&table[sort][order]=ascending&table[sort][key]=" ; biotools:primaryContact "Yeatman Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_0621 ; sc:citation , "pmcid:PMC10656092", "pubmed:37947313" ; sc:description "Database of protein mutations responsible for antifungal resistance." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0337, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "AFRbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://proteininformatics.org/mkumar/afrbase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0820, edam:topic_2275, edam:topic_3047 ; sc:citation , "pubmed:35348582" ; sc:description "An integrated web-based platform for molecular modeling and screening" ; sc:featureList edam:operation_0269, edam:operation_3937, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AFSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://noveldelta.com/AFSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3512 ; sc:citation ; sc:description "AFST(Abnormality Filtering and Sequence Trimming for ESTs)is a software tool using a pattern analysis approach." ; sc:featureList edam:operation_3192, edam:operation_3695 ; sc:name "AFST" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "1.0" ; sc:url "http://code.google.com/p/afst/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation , "pmcid:PMC5374548", "pubmed:28361673" ; sc: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.""" ; sc:featureList edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "afterqc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/OpenGene/AfterQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0736, edam:topic_0820, edam:topic_2815 ; sc:citation , "pmcid:PMC10013729", "pubmed:36917599" ; sc: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." ; sc:featureList edam:operation_0269, edam:operation_0417, edam:operation_0420, edam:operation_0477, edam:operation_2241 ; sc:isAccessibleForFree true ; sc:name "AFTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://conglab.swmed.edu/AFTM" ; biotools:primaryContact "Qian Cong" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1870 ; sc:name "Genus name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2530 ; sc:encodingFormat edam:format_2331 ; sc:name "Organism report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation , "pubmed:21652303" ; sc:description "Fungal structural and biochemical database." ; sc:featureList edam:operation_0224 ; sc:name "Assembling the Fungal Tree of Life (AFTOL)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.aftol.org/index.php" ; biotools:primaryContact "Dr. Joseph Spatafora" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0622, edam:topic_3308 ; sc:citation , "pmcid:PMC3840672", "pubmed:24252138" ; sc:description "Automated tool that constructs matrices for phylogenomic analyses.  It builds alignments of homologous genes and preliminary species trees from genomic and transcriptome data." ; sc:featureList edam:operation_0310, edam:operation_3258 ; sc:name "Agalma" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.6.0" ; sc:url "https://bitbucket.org/caseywdunn/agalma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3170, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC10382368", "pubmed:37460664" ; sc: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)." ; sc:featureList edam:operation_0525, edam:operation_3096, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "AgAnimalGenomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://AgAnimalGenomes.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC3013706", "pubmed:21075795" ; sc: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." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3672 ; sc:name "AgBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.agbase.msstate.edu/" ; biotools:primaryContact "AgBase Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622 ; sc:citation , "pmcid:PMC3137228", "pubmed:21697127" ; sc:description "A tool to evaluate agreement of differential expression for cross-species genomics." ; sc:featureList edam:operation_0315 ; sc:license "GPL-2.0" ; sc:name "AGDEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AGDEX.html" ; biotools:primaryContact "Cuilan lani Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation , "pmcid:PMC3042181", "pubmed:21233167" ; sc:description "Tool that implements an algorithm for optimal alignment of sequences with SVs." ; sc:featureList edam:operation_0292 ; sc:license "CC-BY-NC-4.0" ; sc:name "AGE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sv.gersteinlab.org/age" ; biotools:primaryContact "Abyzov Alexej" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3295, edam:topic_3360 ; sc:citation , "pmcid:PMC9825500", "pubmed:36200838" ; sc: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.""" ; sc:featureList edam:operation_3223, edam:operation_3501, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "AgeAnno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://relab.xidian.edu.cn/AgeAnno/#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3360, edam:topic_3399, edam:topic_3474, edam:topic_3489 ; sc:citation , "pmcid:PMC6823431", "pubmed:31672994" ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "AgeGuess" ; sc:url "http://www.ageguess.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0622, edam:topic_0797, edam:topic_3168 ; sc:citation , "pmcid:PMC441524", "pubmed:15215399" ; sc: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." ; sc:featureList edam:operation_0232, edam:operation_0292, edam:operation_0448, edam:operation_2454 ; sc:name "AGenDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/agenda/" ; biotools:primaryContact "Alexander Sczyrba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_0780, edam:topic_3512, edam:topic_3957 ; sc:citation ; sc:description "AGENT is the the Arabidopsis Gene Regulatory Network Tool for Exploring and Analyzing GRNs." ; sc:featureList edam:operation_0239, edam:operation_2437, edam:operation_3925 ; sc:name "AGENT" ; sc:url "https://bar.utoronto.ca/AGENT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3056, edam:topic_3399 ; sc:citation , "pubmed:20100220" ; sc: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." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AgeStructure" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.zsl.org/science/software/agestructure" ; biotools:primaryContact "Dr Jinliang Wang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1288 ; sc:encodingFormat edam:format_2572 ; sc:name "Genome map" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "Maureen Smith", "Roland Wittler" ; sc:citation , "pmcid:PMC3549816", "pubmed:23369161" ; sc: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." ; sc:featureList edam:operation_0291, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:name "AggloIndel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BiBiServ", "Bielefeld University", "CeBiTec" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bibiserv.cebitec.uni-bielefeld.de/agglodel" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3005 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3572 ; sc:citation , , "pmcid:PMC4987906", "pubmed:27137889" ; sc:description "Such as phastCons, GERP, binCons, and others for a set of genomic intervals." ; sc:featureList edam:operation_2428, edam:operation_3436 ; sc:name "aggregate_scores_in_intervals" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.3" ; sc:url "https://github.com/bxlab/bx-python" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:author , ; sc:citation , "pmcid:PMC8504643", "pubmed:33970215" ; sc:contributor ; sc:description "aggregateBioVar is a R library for differential gene expression analysis for multi-subject single cell RNA sequencing studies." ; sc:featureList edam:operation_0315, edam:operation_3196, edam:operation_3223, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "aggregateBioVar" ; sc:url "https://www.bioconductor.org/packages/release/bioc/html/aggregateBioVar.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3444 ; sc:description "This code solves the aggregation problem using global inputs given N particles in a 2D environment." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "Aggregation of particles in 2D grid using global control" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/60810-aggregation-of-particles-in-2d-grid-using-global-control" ; biotools:primaryContact "Aaron T. Becker's Robot Swarm Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517, edam:topic_3974 ; sc:citation , "pmcid:PMC10371492", "pubmed:37471595" ; sc: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." ; sc:featureList edam:operation_3196, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AGHmatrix" ; sc:url "https://cran.r-project.org/web/packages/AGHmatrix/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation , "pubmed:21088030" ; sc: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." ; sc:featureList edam:operation_0492, edam:operation_0496, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:name "AGILE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.ece.northwestern.edu/%7Esmi539/agile.html" ; biotools:primaryContact "Misra S." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3676 ; sc:citation , "pmcid:PMC4285299", "pubmed:24307375" ; sc: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." ; sc:featureList edam:operation_3197 ; sc:name "AgileExomeFilter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://dna.leeds.ac.uk/agile/AgileExomeFilter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3168 ; sc: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" ; sc:featureList edam:operation_0335 ; sc:name "AgileFileConverter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "20130213" ; sc:url "http://dna.leeds.ac.uk/agile/AgileFileConverter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0654 ; sc: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." ; sc:featureList edam:operation_2421 ; sc:name "AgileGeneFilter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "20120105" ; sc:url "http://dna.leeds.ac.uk/agile/AgileGeneFilter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0654, edam:topic_2885 ; sc: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." ; sc:featureList edam:operation_2429, edam:operation_3196 ; sc:name "AgileGenotyper" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "20130204" ; sc:url "http://dna.leeds.ac.uk/agile/AgileGenotyper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc: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." ; sc:featureList edam:operation_0335 ; sc:name "AgilePairedEndReadsCombiner" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "20140923" ; sc:url "http://dna.leeds.ac.uk/agile/AgilePairedEndReadsCombiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3056, edam:topic_3676 ; sc:citation , "pmcid:PMC4285299", "pubmed:24307375" ; sc: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." ; sc:featureList edam:operation_3197 ; sc:name "AgilePindelFilter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://dna.leeds.ac.uk/agile/AgilePindelFilter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "AgileQualityFilter performs a number of pre-alignment tasks on sequence data from an Illumina GA-II clonal sequencer. 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AH-DB is designed to provide an easy and unified way to prepare apo-holo structure pair data for studies. 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Deep learning model (Temporal conv net, using dilated conv layers) detects post-translational modified peptides based on their ms/ms spectrum." ; sc:featureList edam:operation_3644, edam:operation_3646, edam:operation_3755, edam:operation_3860 ; sc:license "MIT" ; sc:name "AHLF" ; sc:url "http://gitlab.com/dacs-hpi/ahlf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3301, edam:topic_3339, edam:topic_3340 ; sc:citation "pubmed:12824404" ; sc:description "This tool offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_2421, edam:operation_3431 ; sc:name "AHMII" ; sc:url "http://www.wdcm.org/AHMII/ahmii.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "AhNGE is a Database for Arachis hypogaea nodule developmental gene expression." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_2422, edam:operation_3672 ; sc:name "AhNGE" ; sc:url "http://nipgr.ac.in/AhNGE/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2814, edam:topic_3534 ; sc:citation , "pmcid:PMC9750100", "pubmed:36282546" ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "AHoJ: Apo Holo Protein Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.4.7" ; sc:url "http://apoholo.cz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3376 ; sc:citation , "pmcid:PMC4383949", "pubmed:25392419" ; sc: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." ; sc:featureList edam:operation_0226, edam:operation_2409 ; sc:name "AHTPDB" ; sc:softwareHelp , ; sc:url "https://webs.iiitd.edu.in/raghava/ahtpdb/" ; biotools:primaryContact "DR. Gajendra P. S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation , "pmcid:PMC4702812", "pubmed:26538599" ; sc:description "AHTpin is an in silico method developed to predict and design efficient antihypertensive peptides." ; sc:featureList edam:operation_2415 ; sc:name "AHTpin" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/ahtpin/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3335, edam:topic_3474 ; sc:citation , "pubmed:35474167" ; sc:description "Accurate prediction of anti-hypertensive peptides based on convolutional neural network and gated recurrent unit" ; sc:featureList edam:operation_0267, edam:operation_0433, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AHTPs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ahtps.zhanglab.site/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC8360022", "pubmed:33719168" ; sc: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'""" ; sc:featureList edam:operation_3443 ; sc:license "MIT" ; sc:name "AI-biopsy" ; sc:url "https://ai-biopsy.eipm-research.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation ; sc: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." ; sc:name "AI-CT-COVID-19" ; sc:url "http://www.ai-ct-covid.team/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC7671397", "pubmed:33575629" ; sc: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." ; sc:featureList edam:operation_0331, edam:operation_3227 ; sc:name "AI-Driver" ; sc:url "http://aidriver.maolab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3373, edam:topic_3474 ; sc:citation ; sc:description "AI4AMP is a sequence-based antimicrobial peptides (AMP) predictor based on PC6 protein encoding method and deep learning." ; sc:featureList edam:operation_2492, edam:operation_3927 ; sc:name "AI4AMP" ; sc:url "http://symbiosis.iis.sinica.edu.tw/PC_6/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3393, edam:topic_3940 ; sc:citation , "pmcid:PMC9040017", "pubmed:34273560" ; sc:description "A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis." ; sc:featureList edam:operation_0337, edam:operation_3218, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:name "AIAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Zhang-lab/ATAC-seq_QC_analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:20047774" ; sc:description "Lightweight, non-intrusive MVC-based Java application framework that eases the connection, execution and integration of operations with well defined input/output." ; sc:featureList edam:operation_2409 ; sc:name "AIBench" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.aibench.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_0196, edam:topic_0736 ; sc:citation , , "pmcid:PMC4086082", "pmcid:PMC4481839", "pubmed:24831546", "pubmed:25701568" ; sc: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." ; sc:featureList edam:operation_0246, edam:operation_0303, edam:operation_0310, edam:operation_0476, edam:operation_0478 ; sc:name "AIDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ffas.burnham.org/AIDA/" ; biotools:primaryContact "Adam Godzik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3334 ; sc:citation , ; sc: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." ; sc:featureList edam:operation_3096, edam:operation_3680, edam:operation_3891 ; sc:name "AIDD" ; sc:url "https://github.com/RNAdetective/AIDD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC8501087", "pubmed:34625565" ; sc: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." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3553 ; sc:license "LGPL-2.1" ; sc:name "AIDE" ; sc:url "https://github.com/lich0031/AIDE" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3382, edam:topic_3421, edam:topic_3474, edam:topic_3934 ; sc:citation ; sc: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)." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3802 ; sc:license "BSD-3-Clause" ; sc:name "AIDeveloper" ; sc:url "https://github.com/maikherbig/AIDeveloper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3336, edam:topic_3373, edam:topic_3379, edam:topic_3400 ; sc:citation ; sc:description "AIdrug2cov is a network representation learning-based methodology to discover drug mechanism and anti-inflammatory response for patients with COVID-19." ; sc:name "AIdrug2cov" ; sc:url "https://github.com/pengsl-lab/AIdrug2cov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3375, edam:topic_3474 ; sc:citation ; sc:description "Artificial Intelligence-based Web-App for Virtual Screening of Inhibitors against SARS-COV-2." ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:name "AIDrugApp" ; sc:url "https://sars-covid-app.herokuapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3324, edam:topic_3412, edam:topic_3577 ; sc:citation , "pmcid:PMC10229817", "pubmed:37266419" ; sc:description "An easy-to-use AIHF-nomogram to predict advanced liver fibrosis in patients with autoimmune hepatitis." ; sc:featureList edam:operation_2428, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "AIHF-nomogram" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ndth-zzy.shinyapps.io/AIHF-nomogram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3332, edam:topic_3473, edam:topic_3524 ; sc:citation , , "pmcid:PMC5686034", "pmcid:PMC7479590", "pubmed:29138947", "pubmed:32901044" ; sc: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." ; sc:featureList edam:operation_3762 ; sc:license "MIT" ; sc:name "AiiDA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.aiida.net/" ; biotools:primaryContact "Andrius Merkys" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3299, edam:topic_3332, edam:topic_3336, edam:topic_3371 ; sc:citation , "pmcid:PMC7267738", "pubmed:32498019" ; sc: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." ; sc:featureList edam:operation_0531, edam:operation_3216, edam:operation_3938 ; sc:name "AILDE" ; sc:softwareHelp ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/AILDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation , "pubmed:15376910" ; sc: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." ; sc:featureList edam:operation_0571, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AIM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/aim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC8820645", "pubmed:35081109" ; sc:description "Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments." ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "AIME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tianwei-yu/AIME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0749, edam:topic_0821, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC8385923", "pubmed:34368837" ; sc:description "A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe." ; sc:featureList edam:operation_0478, edam:operation_3937, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AIMEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SIAT-code/AIMEE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3315, edam:topic_3512, edam:topic_3519 ; sc:citation ; sc:description "A generic modular response analysis R package and its application to estrogen and retinoic acid receptors crosstalk." ; sc:featureList edam:operation_3799, edam:operation_3927 ; sc:name "aiMeRA" ; sc:softwareHelp ; sc:url "https://github.com/bioinfo-ircm/aiMeRA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3169, edam:topic_3512 ; sc:citation ; sc:description "AIModules enables you to find transcription factor binding sites (TFBSs) and modules on DNA using own matrices or the JASPAR 2022 database." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0337, edam:operation_0445 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "AIModules" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo-wuerz.de/aimodules/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:encodingFormat edam:format_2330 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_2640 ; sc:citation , "pubmed:25479802" ; sc:description "This package contains the necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). 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It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_0496 ; sc:name "Align-m" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.vub.ac.be/software/software.html" ; biotools:primaryContact "Ivo Van Walle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0602 ; sc:citation ; sc:description "Inference of Pathway Decomposition Across Multiple Species Through Gene Clustering." ; sc:featureList edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Align-paths" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/align-paths" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0654, edam:topic_3382 ; sc:citation , "pmcid:PMC6644830", "pubmed:31363407" ; sc: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" ; sc:featureList edam:operation_0487, edam:operation_3660, edam:operation_3745 ; sc:license "GPL-3.0" ; sc:name "align3d" ; sc:url "https://github.com/heltilda/align3d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0654, edam:topic_3473, edam:topic_3511, edam:topic_3512 ; sc:citation , "pubmed:9788350" ; sc: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." ; sc:featureList edam:operation_0239, edam:operation_0415, edam:operation_3196 ; sc:name "AlignACE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://arep.med.harvard.edu/mrnadata/mrnasoft.html" ; biotools:primaryContact "Maryanne Fenerjian (HMS Office of Technology Licensing contact)", "Zhou Zhu (questions or comments)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3510 ; sc:citation , "pubmed:26231432" ; sc: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." ; sc:featureList edam:operation_0292, edam:operation_3359 ; sc:name "AlignBucket" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.biocomp.unibo.it/~giuseppe/partitioning.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Read and write alignments." ; sc:featureList edam:operation_2089 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "aligncopy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/aligncopy.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Read and write pairs from alignments." ; sc:featureList edam:operation_2409 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "aligncopypair" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/aligncopypair.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0121, edam:topic_0128, edam:topic_3957 ; sc:citation , "pmcid:PMC7672851", "pubmed:33203353" ; sc:description "An R-package for alignment of protein-protein interaction networks." ; sc:featureList edam:operation_0491, edam:operation_0496, edam:operation_2492, edam:operation_3094 ; sc:name "AligNet" ; sc:url "https://github.com/biocom-uib/AligNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196 ; sc:citation , "pmcid:PMC4058956", "pubmed:24932000" ; sc:description "Software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism." ; sc:featureList edam:operation_0310, edam:operation_0525, edam:operation_3217 ; sc:name "AlignGraph" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/baoe/AlignGraph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769 ; sc:citation , "pubmed:33621981" ; sc: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." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3198, edam:operation_3216, edam:operation_3798 ; sc:name "AlignGraph2" ; sc:url "https://github.com/huangs001/AlignGraph2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_0820 ; sc:citation , , , "pmcid:PMC3587630", "pmcid:PMC4086118", "pubmed:21073167", "pubmed:23469223", "pubmed:24753425" ; sc: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. 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The annotated and colorized alignment can be downloaded as an interactive HTML file for web browsers." ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_0564 ; sc:name "Alignment-Annotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/strap/aa/" ; biotools:primaryContact "Christoph Gille" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1433, edam:format_1912, edam:format_1929, edam:format_3160 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_3160 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3070, edam:topic_3307 ; sc:author "Ben Stöver" ; sc:contributor "Kai Müller" ; sc:description "An application to efficiently visualize and annotate differences between alternative multiple sequence alignments of the same dataset." ; sc:featureList edam:operation_0292, edam:operation_0564 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AlignmentComparator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioinfweb.info/AlignmentComparator/" ; biotools:primaryContact "Ben Stöver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0160, edam:topic_0623, edam:topic_3168 ; sc:citation , "pmcid:PMC7570326", "pubmed:33123346" ; sc: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." ; sc:featureList edam:operation_0492, edam:operation_0564, edam:operation_2479 ; sc:license "MIT" ; sc:name "AlignmentViewer" ; sc:url "http://alignmentviewer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_3168 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_1812, edam:operation_3198, edam:operation_3695 ; sc:name "alignparse" ; sc:url "https://jbloomlab.github.io/alignparse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0092, edam:topic_2814 ; sc:citation , "pubmed:28961944" ; sc:description "Viewing protein secondary structure predictions within large multiple sequence alignments. The module is part of the ANTHEPROT package." ; sc:featureList edam:operation_0570 ; sc:name "ALIGNSEC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://antheprot-pbil.ibcp.fr/" ; biotools:primaryContact "Gilbert Deleage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269 ; sc:citation , "pmcid:PMC5081975", "pubmed:27784265" ; sc:description "AlignStat is a web-tool and R package for statistical comparison of alternative multiple sequence alignments." ; sc:featureList edam:operation_2451 ; sc:license "Other" ; sc:name "AlignStat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.2" ; sc:url "http://alignstat.science.latrobe.edu.au/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pmcid:PMC9633278", "pubmed:36329619" ; sc:description "LC-MS alignment algorithm based on Wasserstein distance." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Alignstein" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/grzsko/Alignstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc: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." ; sc:featureList edam:operation_0292, edam:operation_0491, edam:operation_0495, edam:operation_0496 ; sc:name "ALION" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "http://motif.stanford.edu/distributions/alion/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3170, edam:topic_3293, edam:topic_3308 ; sc:citation , "pubmed:32180108" ; sc:description """A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. 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Comparative genomic analysis coupled with stress-treated transcriptome profiling uncovers a set of unique saline- and alkaline-responsive genes in alkaligrass""" ; sc:featureList edam:operation_0525, edam:operation_2429, edam:operation_2495 ; sc:name "alkaligrass" ; sc:url "http://xhhuanglab.cn/data/alkaligrass.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1088 ; sc:name "Article ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1086 ; sc:name "Compound identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation , "pmcid:PMC4086102", "pubmed:24838570" ; sc:description "Chemicals prioritization for topics of interest using gene-related PubMed abstracts." ; sc:featureList edam:operation_0305 ; sc:name "Alkemio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbdm.uni-mainz.de/medlineranker" ; biotools:primaryContact "Jean Fred Fontaine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3321 ; sc:citation , "pubmed:22833229" ; sc: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." ; sc:featureList edam:operation_2406, edam:operation_2423, edam:operation_3630 ; sc:name "ALL-P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pappso.inra.fr/bioinfo/all_p/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3676 ; sc:citation ; sc: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." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "All2" ; sc:url "https://github.com/abyzovlab/All2" ; biotools:primaryContact "Alexej Abyzov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_3047, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:37664900" ; sc:description "Curation of ion mobility collision cross-section atlas for small molecules using comprehensive molecular representations." ; sc:featureList edam:operation_2421, edam:operation_3927, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "AllCCS2" ; sc:url "http://allccs.zhulab.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_3316 ; sc:citation , "pmcid:PMC7542712", "pubmed:33028201" ; sc: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." ; sc:featureList edam:operation_3432, edam:operation_3478, edam:operation_3840 ; sc:license "MIT" ; sc:name "AllCoPol" ; sc:url "https://github.com/AGOberprieler/allcopol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_0749 ; sc:citation , "pmcid:PMC2655690", "pubmed:19151090" ; sc: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." ; sc:featureList edam:operation_0238 ; sc:name "Allegro" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://acgt.cs.tau.ac.il/allegro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0208, edam:topic_2830, edam:topic_3056, edam:topic_3305 ; sc:citation , "pmcid:PMC3013710", "pubmed:21062830" ; sc: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." ; sc:featureList edam:operation_0487, edam:operation_0542, edam:operation_3196, edam:operation_3221, edam:operation_3227 ; sc:name "Allele frequency net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.allelefrequencies.net" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3299 ; sc:citation , "pubmed:22925629" ; sc: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." ; sc:featureList edam:operation_2426 ; sc:name "AlleleRetain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/alleleretain/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pmcid:PMC8212829", "pubmed:34178449" ; sc:description "AlleleShift is an R package to predict and visualize population-level changes in allele frequencies in response to climate change." ; sc:featureList edam:operation_0337, edam:operation_0554, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AlleleShift" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RoelandKindt/AlleleShift" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_2830 ; sc:citation , "pubmed:31677971" ; sc:description "A Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire." ; sc:featureList edam:operation_3658 ; sc:name "allelic inclusion" ; sc:url "https://github.com/JasonACarter/Allelic_inclusion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3170 ; sc:citation , "pmcid:PMC4465016", "pubmed:26066318" ; sc:contributor ; sc:description "Provides a framework for allelic specific expression investigation using RNA-seq data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "AllelicImbalance" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AllelicImbalance.html" ; biotools:primaryContact "Jesper R Gadin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3304, edam:topic_3382, edam:topic_3444, edam:topic_3512 ; sc:citation , "pmcid:PMC3531093", "pubmed:23193282" ; sc: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." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_0315, edam:operation_2495, edam:operation_3223 ; sc:name "Allen Brain Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.brain-map.org" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pubmed:17151600" ; sc:description "Integration of gene expression data, connectivity data and neuroanatomical information for the adult and developing brain in mouse, human and non-human primate." ; sc:featureList edam:operation_2495 ; sc:name "Allen Brain Atlas-API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://help.brain-map.org/display/api/RESTful+Model+Access+%28RMA%29" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3173 ; sc:citation , "pmcid:PMC7076970", "pubmed:32183716" ; sc: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. 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Franssen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3336 ; sc:citation , "pmcid:PMC6030990", "pubmed:29757429" ; sc: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. 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sc:license "Not licensed" ; sc:name "AlloMAPS 2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://allomaps.bii.a-star.edu.sg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pmcid:PMC4619270", "pubmed:26493317" ; sc:description "Web server uses normal mode analysis and pocket features to predict allosteric pockets on proteins." ; sc:featureList edam:operation_2575 ; sc:license "MIT" ; sc:name "AlloPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "hotmail.co.uk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.sbg.bio.ic.ac.uk/allopred/home" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; 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Jaffe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3418 ; sc:citation ; sc:description "RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia." ; sc:featureList edam:operation_0314, edam:operation_3225, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ALLSorts" ; sc:softwareHelp ; sc:url "https://github.com/Oshlack/AllSorts/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2275, edam:topic_2814 ; sc:citation , "pubmed:24676684" ; sc:description "This modelling environment provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations." ; sc:featureList edam:operation_0477 ; sc:name "ALMOST" ; sc:operatingSystem "Linux" ; sc:url "http://www-mvsoftware.ch.cam.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3393, edam:topic_3572 ; sc:citation , "pmcid:PMC5167069", "pubmed:27559158" ; sc:description "Simplifying quality control of high-throughput sequencing data." ; sc:featureList edam:operation_3218 ; sc:name "AlmostSignificant" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/bartongroup/AlmostSignificant" ; biotools:primaryContact "Joe Ward" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_3512 ; sc:citation , "pmcid:PMC8386716", "pubmed:34447886" ; sc: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. 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It can simulate sequence and SNP data, pedigrees, QTL effects, and breeding values. Pre-specified pedigrees can also be supplied." ; sc:featureList edam:operation_2476 ; sc:name "AlphaDrop beta" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/hickeyjohn/alphadrop" ; biotools:primaryContact "John Hickey" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation , "pubmed:38718922" ; sc:description "A database for the comparison of structural models predicted by ESMFold and AlphaFold2 for human proteins." ; sc:featureList edam:operation_2483 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "AlphaESM hFolds" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://alpha-esmhfolds.biocomp.unibo.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_3047, edam:topic_3421 ; sc:citation , "pmcid:PMC9911346", "pubmed:36424442" ; sc:description "AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. 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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. 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Partition/Decomposition of Breeding Values by Paths of Information." ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:license "GPL-2.0" ; sc:name "AlphaPart" ; sc:url "http://CRAN.R-project.org/package=AlphaPart" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "Framework for MS-based proteomics." ; sc:featureList edam:operation_3630, edam:operation_3631, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AlphaPept" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MannLabs/alphapept" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC9700817", "pubmed:36433986" ; sc:description "A modular deep learning framework to predict peptide properties for proteomics." ; sc:featureList edam:operation_0417, edam:operation_3629, edam:operation_3631, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AlphaPeptDeep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MannLabs/alphapeptdeep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0121 ; sc:citation , "pubmed:14997542" ; sc: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." ; sc:featureList edam:operation_0267, edam:operation_0492 ; sc:name "AlphaPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/alphapred/" ; biotools:primaryContact "Dr. G.P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3047, edam:topic_3957 ; sc:citation , "pmcid:PMC9805587", "pubmed:36413069" ; sc:description "A Python package for protein-protein interaction screens using AlphaFold-Multimer." ; sc:featureList edam:operation_0474, edam:operation_2464, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AlphaPulldown" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.embl-hamburg.de/AlphaPulldown" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description "AlphaSimR is the successor to the AlphaSim software for breeding program simulation and a package for the R software environment." ; sc:featureList edam:operation_2426, edam:operation_3196 ; sc:license "MIT" ; sc:name "AlphaSimR" ; sc:softwareHelp ; sc:url "https://alphagenes.roslin.ed.ac.uk/wp/software-2/alphasimr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_2275 ; sc:citation , "pmcid:PMC7093224", "pubmed:31995373" ; sc:description "AlphaSpace2 is a surface topographical mapping tool." ; sc:featureList edam:operation_2429, edam:operation_2464, edam:operation_2492 ; sc:name "AlphaSpace2" ; sc:softwareHelp ; sc:url "http://www.nyu.edu/projects/yzhang/AlphaSpace2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC8526765", "pubmed:34543758" ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3436 ; sc:license "Apache-2.0" ; sc:name "AlphaTims" ; sc:url "https://github.com/MannLabs/alphatims" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3500 ; sc:citation ; sc: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." ; sc:featureList edam:operation_2938, edam:operation_3432 ; sc:name "AlphaTracker" ; sc:url "https://github.com/ZexinChen/AlphaTracker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0769, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC10203375", "pubmed:37084271" ; sc:description "Predicting the pathogenicity of missense variants using features derived from AlphaFold2." ; sc:featureList edam:operation_0331, edam:operation_3431, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AlphScore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Ax-Sch/AlphScore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC5143225", "pubmed:27669167" ; sc:description "Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation." ; sc:featureList edam:operation_2426 ; sc:license "GPL-2.0" ; sc:name "alpine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/alpine.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0769, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:31930381" ; sc:description "AlpsNMR is an R package that can load Bruker and JDX samples as well as preprocess them." ; sc:featureList edam:operation_3215, edam:operation_3435, edam:operation_3803 ; sc:license "MIT" ; sc:name "AlpsNMR" ; sc:softwareVersion "3.1.4" ; sc:url "https://sipss.github.io/AlpsNMR/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308 ; sc:citation ; sc:description "A method for imputation of missing values in single cell RNA-sequencing data" ; sc:featureList edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "ALRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KlugerLab/ALRA" ; biotools:primaryContact "Yuval Kluger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2258 ; sc: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." ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "alsace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/alsace.html" ; biotools:primaryContact "Ron Wehrens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC2978646", "pubmed:18604217" ; sc:description "Alta-Cyclic is a Illumina Genome-Analyzer (Solexa) base caller." ; sc:featureList edam:operation_3185 ; sc:name "Alta-Cyclic" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://hannonlab.cshl.edu/Alta-Cyclic/main.html" ; biotools:primaryContact "Yaniv Erlich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3303, edam:topic_3307, edam:topic_3308 ; sc:contributor , ; sc: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.""" ; sc:featureList edam:operation_2403 ; sc:funder ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AltaiR" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0.1" ; sc:url "https://github.com/cobilab/altair" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC2896198", "pubmed:20513647" ; sc: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)." ; sc:featureList edam:operation_0276, edam:operation_0303, edam:operation_2495, edam:operation_2499, edam:operation_3223 ; sc:name "AltAnalyze" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.altanalyze.org" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2060 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203 ; sc:citation , "pmcid:PMC514699", "pubmed:15310390" ; sc:description "Convenience data structures and functions to handle cdfenvs." ; sc:featureList edam:operation_0527 ; sc:license "GPL-2.0" ; sc:name "altcdfenvs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/altcdfenvs.html" ; biotools:primaryContact "Laurent Gautier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0654 ; sc:citation , "pmcid:PMC2896128", "pubmed:20439312" ; sc:description "ALTER is a program-oriented web tool for the conversion between DNA and protein alignments." ; sc:featureList edam:operation_0260, edam:operation_2479 ; sc:name "ALTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sing.ei.uvigo.es/ALTER/" ; biotools:primaryContact "ALTER Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602 ; sc:citation , "pmcid:PMC5233954", "pubmed:28084397" ; sc: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)." ; sc:featureList edam:operation_2497 ; sc:name "Altered Pathway Analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://bioinfo.icgeb.res.in/APA/" ; biotools:primaryContact "Abhinav Kaushik", "Dinesh Gupta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3120, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC506815", "pubmed:15292448" ; sc: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." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0433, edam:operation_0526, edam:operation_2499 ; sc:name "Alternative Splicing Gallery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://statgen.ncsu.edu/asg/" ; biotools:primaryContact "Jeremy Leipzig", "Steffen Heber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC6041798", "pubmed:29514179" ; sc: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." ; sc:featureList edam:operation_0487, edam:operation_3680 ; sc:name "AltHapAlignR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jknightlab/AltHapAlignR" ; biotools:primaryContact "Julian C Knight", "Peter Humburg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2275, edam:topic_2814, edam:topic_2828, edam:topic_3474 ; sc:citation , "pmcid:PMC6938380", "pubmed:31846452" ; sc: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]""" ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3454 ; sc:name "altMOD" ; sc:url "https://github.com/pymodproject/altmod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC4756442", "pubmed:26883204" ; sc:description "Altools is a software package that allows the precise detection of polymorphisms and structural variations." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "Altools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/altools/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3360, edam:topic_3500, edam:topic_3518 ; sc:citation , "pubmed:35303580" ; sc:description "AltWOA is a novel feature selection algorithm where Altruistic property of candidate whales are embedded to the Whale Optimization Algorithm (WOA)." ; sc:featureList edam:operation_0314, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AltWOA" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/Rohit-Kundu/AltWOA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_0769, edam:topic_3047, edam:topic_3474 ; sc:citation , "pmcid:PMC9655980", "pubmed:36361669" ; sc:description "Alvascience: A New Software Suite for the QSAR Workflow Applied to the Blood-Brain Barrier Permeability" ; sc:featureList edam:operation_2428, edam:operation_3799, edam:operation_4009 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Alvascience" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.alvascience.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC9759058", "pubmed:36528564" ; sc:description "A web browser-based tool to analyze lung intravital microscopy." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3937 ; sc:license "Other" ; sc:name "Alveolus Analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/uic-evl/AlveolusAnalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_2640, edam:topic_3307 ; sc:citation , "pmcid:PMC4573065", "pubmed:26417198" ; sc:description "Fast bam file viewer from the National Cancer Informatics Program." ; sc:featureList edam:operation_3208 ; sc:name "Alview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbiit.nci.nih.gov/ncip" ; biotools:primaryContact "Richard P. Finney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3300, edam:topic_3315 ; sc:citation ; sc: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""" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3435 ; sc:name "Alvin" ; sc:url "https://ge.gitlab-pages.informatik.uni-wuerzburg.de/Dev/alveolus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3382 ; sc:citation , "pmcid:PMC7967992", "pubmed:33726674" ; sc: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." ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_0450, edam:operation_1812, edam:operation_3198 ; sc:name "Alvis" ; sc:softwareHelp ; sc:url "https://github.com/SR-Martin/alvis" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3304, edam:topic_3474 ; sc:citation , "pmcid:PMC7580783", "pubmed:32603655" ; sc:description "Selective Neuronal Vulnerability in Alzheimer's Disease." ; sc:featureList edam:operation_2436, edam:operation_3450, edam:operation_3799 ; sc:name "Selective Neuronal Vulnerability Alzheimer Disease" ; sc:url "http://alz.princeton.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:35619290" ; sc:description "A tool to discriminate disease-causing and neutral mutations in Alzheimer's disease." ; sc:featureList edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Alz-disc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://web.iitm.ac.in/bioinfo2/alzdisc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3170 ; sc:citation , "pubmed:35040932" ; sc: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." ; sc:featureList edam:operation_1781, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "AlzCode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.alzcode.xyz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0202, edam:topic_0602, edam:topic_3375, edam:topic_3379 ; sc:citation ; sc: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." ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3925 ; sc:name "AlzGPS" ; sc:url "https://alzgps.lerner.ccf.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "AlzScPred - A Package to Predict Alzheimer's Disease Using Single Cell Data" ; sc:name "AlzScPred" ; sc:url "https://webs.iiitd.edu.in/raghava/alzscpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC8742670", "pubmed:35035265" ; sc:description "AM-UNet: Automated Mini 3D End-to-End U-NetBased Network For Brain Claustrum Segmentation." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AM-UNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AhmedAlbishri/AM-UNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_0634, edam:topic_3407, edam:topic_3941 ; sc:citation , "pmcid:PMC8317061", "pubmed:34335304" ; sc:description "A Comprehensive Database for Association Between Microbiota and Disease." ; sc:featureList edam:operation_2421, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "Amadis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gift2disease.net/GIFTED/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0611, edam:topic_2828, edam:topic_3373, edam:topic_3474 ; sc:citation , "pmcid:PMC10853961", "pubmed:38134445" ; sc:description "A machine learning platform for predicting drug-induced phosphol ipidosis." ; sc:featureList edam:operation_2428, edam:operation_3891, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "AMALPHI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ba.ic.cnr.it/softwareic/amalphiportal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3379 ; sc:citation , "pmcid:PMC8722753", "pubmed:34406360" ; sc:description "An R package for Meta-analysis of metabolomics non-integral data." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Amanida" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mariallr/amanida" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0194, edam:topic_2269, edam:topic_3293 ; sc:citation , "pmcid:PMC4734057", "pubmed:26835189" ; sc: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." ; sc:featureList edam:operation_2478, edam:operation_2479 ; sc:license "GPL-3.0" ; sc:name "AMAS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/marekborowiec/AMAS" ; biotools:primaryContact "Marek L. Borowiec" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3464, edam:format_3579, edam:format_3591, edam:format_3603, edam:format_3752 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3508, edam:format_3752 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3464, edam:format_3579, edam:format_3591, edam:format_3603, edam:format_3752 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC3190602", "pubmed:21800894" ; sc: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. 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Banga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , "pmcid:PMC2639003", "pubmed:19033274" ; sc:description "The GO Consortium GO browser and search engine." ; sc:featureList edam:operation_0224, edam:operation_2451, edam:operation_2495, edam:operation_3559 ; sc:name "AmiGO 2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://amigo.geneontology.org/amigo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0621, edam:topic_0654 ; sc:citation , "pubmed:35385068" ; sc:description "AMIGOS III is a plugin to PyMOL for pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids." ; sc:featureList edam:operation_0249, edam:operation_0570, edam:operation_1812, edam:operation_2518 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "AMIGOS III" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pylelab/AMIGOSIII. a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3070, edam:topic_3344 ; sc:description "Analysis of amino acid conservation using conservation index" ; sc:featureList edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "Amino acid conservation.zip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47155-amino-acid-conservation-zip" ; biotools:primaryContact "Guangdi Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3342, edam:topic_3376, edam:topic_3382, edam:topic_3383, edam:topic_3679 ; sc:citation , "pubmed:38052317" ; sc:description "AMIS (A Mouse Imaging Server) is a still growing webserver providing imaging information about the distribution of certain GPCRs in mice." ; sc:name "AMIS" ; sc:url "https://amis.docking.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3295, edam:topic_3577 ; sc:citation , "pmcid:PMC7176885", "pubmed:32150667" ; sc:description "a web‐based prognostic model to predict the prognosis of Acute myeloid leukaemia patients. Using log-rank test and univariate COX regression analysis as well as LASSO-COX, AML patients were divided into high-risk and low-risk groups based on AML risk score (AMLRS) which was constituted by 10 survival-related genes." ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3659, edam:operation_3891 ; sc:name "AMLRS" ; sc:url "https://tcgi.shinyapps.io/amlrs_nomogram/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168, edam:topic_3577 ; sc:citation , "pmcid:PMC7001226", "pubmed:32019565" ; sc:description "AMLVaran, the AML Variant Analyzer is a web-based software platform for variant analysis on targeted NGS data, addressing the requirements of a clinical setting." ; sc:featureList edam:operation_3225, edam:operation_3227, edam:operation_3675 ; sc:license "GPL-3.0" ; sc:name "AMLVaran" ; sc:url "https://amlvaran.uni-muenster.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:citation , "pubmed:35394910" ; sc:description "Adaptive Multilinear Meshes (AMMs) is a new framework to represent piecewise multilinear volumetric data using mixed-precision adaptive meshes." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "AMM" ; sc:url "https://github.com/llnl/amm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3071 ; sc:citation , "pmcid:PMC5830045", "pubmed:29489825" ; sc:description "Tool which helps enable adaptive management by codifying knowledge in the form of models generated from numerous analyses and data sets. Facilitates this process by storing all models and data sets in a single object that can be updated and saved, thus tracking changes in knowledge through time. A shiny application called AM Model Manager (modelMgr()) enables the use of these functions via a GUI." ; sc:featureList edam:operation_2409 ; sc:name "AMModels" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/AMModels/index.html" ; biotools:primaryContact "Jon Katz" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3816 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3816 ; sc:name "Small molecule structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154 ; sc:citation , , "pmcid:PMC2588602", "pmcid:PMC5570140", "pubmed:18925937", "pubmed:28486703" ; sc:description "Automatic Molecular Mechanics Optimization for in silico Screening 2. Efficient computational refinement of protein–small organic molecule complexes. Employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes." ; sc:featureList edam:operation_0322 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "AMMOS" ; sc:softwareVersion "1.0", "2.0" ; sc:url "http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php" ; biotools:primaryContact "Maria A. Miteva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0219, edam:topic_0780, edam:topic_3303, edam:topic_3375 ; sc:citation , "pmcid:PMC10172712", "pubmed:37120901" ; sc:description "Curated database of Indian anti-tubercular medicinal plants." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "AMMPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ammpdb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3293, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC3013638", "pubmed:20974635" ; sc:description "It is a new functional genomic databases serving the amoebozoa research communities. It contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. Importantly it utilizes the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_2422 ; sc:name "AmoebaDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://AmoebaDB.org" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174 ; sc:citation , "pmcid:PMC4184256", "pubmed:24974201" ; sc:description "Database engine for comparing metagenomic data at massive scale. It first obtains the sequence signature of metagenomes and organizes them as points in high dimensional space." ; sc:featureList edam:operation_0310, edam:operation_2478 ; sc:name "Amordad" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://smithlabresearch.org/software/amordad/" ; biotools:primaryContact "Andrew Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation "pubmed:15383210" ; sc:description "AMOS is a Modular, Open-Source whole genome assembler." ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_3180, edam:operation_3184 ; sc:name "AMOS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://amos.sourceforge.net/" ; biotools:primaryContact "AMOS team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "A pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. This tool aims to search active modules in multi-layer WGCN using a continuous optimization approach." ; sc:featureList edam:operation_2425 ; sc:license "GPL-2.0" ; sc:name "AMOUNTAIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AMOUNTAIN.html" ; biotools:primaryContact "Dong Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_3301, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9793967", "pubmed:36461699" ; sc:description "Prediction of antimicrobial peptide function based on a BERT model." ; sc:featureList edam:operation_2995, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AMP-BERT" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/GIST-CSBL/AMP-BERT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3063, edam:topic_3474 ; sc:citation , "pubmed:32750857" ; sc:description "AMPZero is a predictor designed for predicting the effectiveness of a peptide sequence against various microbial species. The predictor takes the peptide sequence and any N/C-termini modifications together with the genomic sequence of a microbial species to generate targeted predictions." ; sc:featureList edam:operation_3482, edam:operation_3631, edam:operation_3938 ; sc:name "AMP0" ; sc:url "http://ampzero.pythonanywhere.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3301, edam:topic_3474 ; sc:citation , "pmcid:PMC9487607", "pubmed:35988923" ; sc:description "Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data." ; sc:featureList edam:operation_3431, edam:operation_3461, edam:operation_3968 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AMPBenchmark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://BioGenies.info/AMPBenchmark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3168, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9511757", "pubmed:36163001" ; sc:description "A tool for hemolytic activity prediction of antimicrobial peptides using transfer learning." ; sc:featureList edam:operation_2995, edam:operation_3436, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AMPDeep" ; sc:url "https://github.com/milad73s/AMPDeep" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2332 ; sc:name "Experiment report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2332 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Suite", "Web service" ; sc:applicationSubCategory edam:topic_3336 ; sc:citation ; sc:description "Annotated collection of normalized data describing antimicrobial peptides, their sources, their 3D structures, and their target organisms. It enables users to perform quick queries and allows the entire peptide community to contribute to the repository." ; sc:featureList edam:operation_0224, edam:operation_2424, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Antimicrobial Peptide Database (AMPed)" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://amped.uri.edu/" ; biotools:primaryContact "Lenore M Martin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_0780 ; sc:citation , "pubmed:33135060" ; sc:description "AmPEPpy is a Python application that implements a random forest classifier for predicting antimicrobial peptide sequences using the distribution descriptor set from the global protein sequence descriptors. amPEPpy has improved portability, increased accuracy relative to similar methods, and includes utilities for easily training and optimizing random forest classifiers on novel training data." ; sc:featureList edam:operation_3631 ; sc:license "GPL-3.0" ; sc:name "amPEPpy" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/tlawrence3/amPEPpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0621 ; sc:citation , "pubmed:37236434" ; sc:description "A computational model to identify antimicrobial peptides and their functions based on sequence-derived information." ; sc:featureList edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "AMPFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/abcair/AMPFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation , "pmcid:PMC2760878", "pubmed:18851752" ; sc:description "Automated Phylogenomic Inference Pipeline for bacterial sequences. From a given a set of protein sequences, it automatically identifies 31 phylogenetic marker genes. It then generates high-quality multiple sequence alignments for these genes and make tree-based phylotype assignments." ; sc:featureList edam:operation_2478 ; sc:license "CC-BY-4.0" ; sc:name "AMPHORA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "https://phylogenomics.me/software/amphora/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3293 ; sc:citation , "pubmed:24144838" ; sc:description "Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data and genomic data." ; sc:featureList edam:operation_0525, edam:operation_2478 ; sc:name "AmphoraNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pitgroup.org/amphoranet/" ; biotools:primaryContact "PIT Bioinformatics Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0194, edam:topic_3174 ; sc:citation , "pubmed:25296554" ; sc:description "Visualize outputs generated by the metagenomic and genomic analysis tool AMPHORA2 or its webserver implementation AmphoraNet." ; sc:featureList edam:operation_3184, edam:operation_3208 ; sc:name "AmphoraVizu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pitgroup.org/amphoravizu/" ; biotools:primaryContact "PIT Bioinformatics Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "An R package for fast genome-wide prediction of antimicrobial peptides. It is fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs." ; sc:name "ampir" ; sc:url "https://github.com/legana/ampir" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2275, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC7189366", "pubmed:32243153" ; sc:description """AMPL is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery. The ATOM Modeling PipeLine (AMPL) extends the functionality of DeepChem and supports an array of machine learning and molecular featurization tools. AMPL is an end-to-end data-driven modeling pipeline to generate machine learning models that can predict key safety and pharmacokinetic-relevant parameters. AMPL has been benchmarked on a large collection of pharmaceutical datasets covering a wide range of parameters.""" ; sc:featureList edam:operation_3359, edam:operation_3799, edam:operation_3938 ; sc:license "MIT" ; sc:name "AMPL" ; sc:url "https://github.com/ATOMconsortium/AMPL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_2828 ; sc:citation , "pubmed:23151627" ; sc:description "A program for Molecular Replacement with search ensembles generated from uncoventional models." ; sc:featureList edam:operation_3454 ; sc:name "Ample" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ccp4.ac.uk/ample/" ; biotools:primaryContact "D. J. Rigden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3519 ; sc:citation ; sc:description "It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems." ; sc:featureList edam:operation_2928, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "amplican" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/amplican.html" ; biotools:primaryContact "Eivind Valen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation , , "pmcid:PMC8451469", "pubmed:33100132" ; sc:description "AmpliconDesign is an interactive webserver for the design, documentation and analysis of targeted bisulfite sequencing studies." ; sc:featureList edam:operation_0308, edam:operation_3186, edam:operation_3192, edam:operation_3206, edam:operation_3207 ; sc:license "GPL-3.0" ; sc:name "AmpliconDesign" ; sc:url "https://amplicondesign.dkfz.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal." ; sc:featureList edam:operation_0450 ; sc:name "AmpliconNoise" ; sc:url "https://code.google.com/archive/p/ampliconnoise/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC8788131", "pubmed:35078402" ; sc:description "AMPlify is an attentive deep learning model for antimicrobial peptide prediction." ; sc:featureList edam:operation_3192, edam:operation_3461, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AMPlify" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcgsc/AMPlify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description """Automated methylation analysis of amplicons from bisulfite flowgram sequencing. The Roche 454 GS Junior sequencing platform allows locus-specific DNA methylation analysis using deep bisulfite amplicon sequencing. However, bisulfite-converted DNA reads may contain long T homopolymers, and the main sources of errors on pyrosequencing platforms are homopolymer over- and undercalls. Furthermore, existing tools do not always meet the analysis requirements for complex assay designs with multiple regions of interest (ROIs) from multiple samples. We have developed the amplikyzer software package to address the above challenges. It directly aligns the intensity sequences from standard flowgram files (SFF format) to given amplicon reference sequences, without converting to nucleotide FASTA format first, avoiding information loss by rounding flow intensities, and taking special measures to correctly process long homopolymers""" ; sc:featureList edam:operation_3185, edam:operation_3192, edam:operation_3198, edam:operation_3204 ; sc:name "amplikyzer" ; sc:url "https://bitbucket.org/svenrahmann/amplikyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_3168 ; sc:citation , "pmcid:PMC6954648", "pubmed:31350555" ; sc:description "Tool to process and analyze targeted NGS data." ; sc:featureList edam:operation_3192, edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "amplimap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/koelling/amplimap" ; biotools:primaryContact "Nils Koelling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3656, edam:topic_3674 ; sc:citation , "pmcid:PMC5123276", "pubmed:27884103" ; sc:description "Pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons." ; sc:featureList edam:operation_3186, edam:operation_3204 ; sc:license "GPL-3.0" ; sc:name "ampliMethProfiler" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/amplimethprofiler/" ; biotools:primaryContact "Giovanni Scala" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_3168, edam:topic_3519 ; sc:citation ; sc:description "The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq." ; sc:featureList edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "ampliQueso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ampliQueso.html" ; biotools:primaryContact "Michal Okoniewski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation , "pubmed:11807545" ; sc:description "Ampred server predicts the Antimicrobial activity of given sequence. The activity may be antifungal, antiviral and antibacterial .This server works based on Multidimensional signatures of antimicrobial peptides" ; sc:featureList edam:operation_2479 ; sc:name "Ampred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/Antimicrobial/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3307 ; sc:citation , "pubmed:2314284" ; sc:description "Suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures. It also implements flexible pattern matching and database scanning options, and includes functions for running randomisations to estimate the significance of sequence similarities." ; sc:featureList edam:operation_0292, edam:operation_0492 ; sc:name "AMPS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.compbio.dundee.ac.uk/software.html#msa" ; biotools:primaryContact "The Barton Group" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1317 ; sc:citation , "pubmed:21757462" ; sc:description "NMR protein structure refinement. Amber (acronym to Assisted Model Building with Energy Refinement) is a suite of programs 1N3L that allow users to perform molecular dynamics (MD) simulations on biological systems. This web portal makes available the entire functionality of AMBER, in particular (but not only) using NMR-derived information as restraints for MD." ; sc:featureList edam:operation_0320, edam:operation_2476 ; sc:name "AMPS-NMR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CERM" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://py-enmr.cerm.unifi.it/access/index" ; biotools:primaryContact "Antonio Rosato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3050, edam:topic_3679 ; sc:citation , "pmcid:PMC5962104", "pubmed:29742099" ; sc:description "Matlab functions for analysis of patterns in (functions of) parameter values of the Add-my-Pet collection." ; sc:featureList edam:operation_2409, edam:operation_3460 ; sc:name "AmPtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/AmPtool.html" ; biotools:primaryContact "Starrlight Augustine" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_3746 ; sc:name "Biodiversity data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3050 ; sc:citation ; sc:description "ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:license "GPL-2.0" ; sc:name "ampvis" ; sc:softwareHelp ; sc:url "https://github.com/MadsAlbertsen/ampvis2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data" ; sc:featureList edam:operation_3482 ; sc:name "AMR-meta" ; sc:url "https://github.com/smarini/AMR-meta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3324 ; sc:description """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. 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It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis." ; sc:featureList edam:operation_2423 ; sc:license "GPL-2.0" ; sc:name "anamiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/anamiR.html" ; biotools:primaryContact "Ti-Tai Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3169, edam:topic_3512, edam:topic_3517 ; sc:citation , "pmcid:PMC9252736", "pubmed:35446421" ; sc:description "A web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events." ; sc:featureList edam:operation_0484, edam:operation_3501, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ANANASTRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ananastra.autosome.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0637, edam:topic_3056, edam:topic_3697 ; sc:citation , "pmcid:PMC5621509", "pubmed:28966891" ; sc:description "Clustering marker gene data by time-series patterns." ; sc:featureList edam:operation_0313 ; sc:license "MIT" ; sc:name "Ananke" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/beiko-lab/ananke" ; biotools:primaryContact "Michael W. Hall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2229, edam:topic_3169, edam:topic_3512 ; sc:citation ; sc:description "ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to use these GRNs to identify the key transcription factors in cell fate determination." ; sc:featureList edam:operation_0445, edam:operation_2437, edam:operation_3222 ; sc:license "MIT" ; sc:name "ANANSE" ; sc:softwareHelp ; sc:url "https://github.com/vanheeringen-lab/ANANSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3168 ; sc:citation , "pubmed:27502218" ; sc:contributor ; sc:description "The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls." ; sc:featureList edam:operation_3431 ; sc:license "BSD-4-Clause" ; sc:name "Anaquin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Anaquin.html" ; biotools:primaryContact "Ted Wong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2814 ; sc:citation , "pmcid:PMC4708101", "pubmed:26424857" ; sc:description "Tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "ANARCI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3174, edam:topic_3297 ; sc:citation , "pmcid:PMC6543708", "pubmed:31178894" ; sc:description "ANASTASIA (Automated Nucleotide Animoacid Sequences Translational plAtform for Synthetic Interpretation and Analysis) is a metagenomics analysis platform and repository." ; sc:featureList edam:operation_0292, edam:operation_0346, edam:operation_0361, edam:operation_0524, edam:operation_1777, edam:operation_2422, edam:operation_3218, edam:operation_3460 ; sc:name "ANASTASIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://motherbox.chemeng.ntua.gr/anastasia_dev/" ; biotools:primaryContact "Aristotelis Chatziioannou", "Eleftherios Pilalis", "Olga Papadodima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2259, edam:topic_3474 ; sc:citation , "pmcid:PMC8555137", "pubmed:34706638" ; sc:description """ANAT (Advanced Network Analysis Tool) is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models. It is a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. Genome-scale screening studies are gradually accumulating a wealth of data on the putative involvement of hundreds of genes in various cellular responses or functions. A fundamental challenge is to chart out the molecular pathways that underlie these systems. ANAT (Advanced Network Analysis Tool) , is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models. It is a plug-in for Cytoscape.""" ; sc:featureList edam:operation_0276, edam:operation_3925, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ANAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cs.tau.ac.il/~bnet/ANAT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3444 ; sc:description "Matlab functions for flexible plotting of intracranial or fMRI data on 3D brain models" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Anatomical data visualization toolfbox for fMRI ECoG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/71634-anatomical-data-visualization-toolfbox-for-fmri-ecog" ; biotools:primaryContact "Edden M. Gerber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC9712876", "pubmed:35768752" ; sc:description "A medical image segmentation software supporting user interventions and user-defined funtion extention" ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AnatomySketch" ; sc:url "https://github.com/DlutMedimgGroup/AnatomySketch-Software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176 ; sc:citation , "pmcid:PMC5961460", "pubmed:29742397" ; sc:description "A python package with modules to measure anharmonicity in the form of higher-order statistics and its variation as a function of time, output a storyboard representation of the simulations to identify key anharmonic conformational events, and identify putative anharmonic conformational substates and visualization of transitions between these substates." ; sc:featureList edam:operation_2476 ; sc:license "BSD-3-Clause" ; sc:name "ANCA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://csb.pitt.edu/anca/index.html" ; biotools:primaryContact "S. Chakra Chennubhotla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2814, edam:topic_3794 ; sc:citation , "pmcid:PMC7711068", "pubmed:33330622" ; sc:description "A web server for amino acid networks construction and analysis." ; sc:featureList edam:operation_0321, edam:operation_0570, edam:operation_3927 ; sc:name "ANCA" ; sc:url "http://sysbio.suda.edu.cn/anca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , "pubmed:18296746" ; sc:description "AncesHC (ancestral haplotype clustering ) is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome." ; sc:featureList edam:operation_3432 ; sc:name "AncesHC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2009" ; sc:url "http://www.imperial.ac.uk/people/l.coin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3307, edam:topic_3510 ; sc:citation , "pubmed:9071022" ; sc:description "Software which infer ancestral amino acid sequences from a set of homologous amino acid sequences whose phylogenetic relationships are known." ; sc:featureList edam:operation_0253, edam:operation_0540 ; sc:name "Ancestor" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.personal.psu.edu/nxm2/ancestor2.htm" ; biotools:primaryContact "Laboratory of Masatoshi Nei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3293 ; sc:citation ; sc:description "AncestralClust is a tool to cluster divergent sequences. 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The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and others, are highly effective in document search; however, they do not allow knowledge extraction. In contrast to the search engines, text-mining systems provide extraction of knowledge with representations in the form of semantic networks. Of particular interest are tools performing a full cycle of knowledge management and engineering, including automated retrieval, integration, and representation of knowledge in the form of semantic networks, their visualization, and analysis. 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These distances can be used to rapidly infer phylogenies for big sets of genomes. 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It is based on an automated text- and data- mining techniques." ; sc:featureList edam:operation_3660 ; sc:name "ANDSystem" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://pbiosoft.com/en/andsystem" ; biotools:primaryContact "Vladimir A Ivanisenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3416, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC8270840", "pubmed:33507353" ; sc:description "Anduin is a freely available research tool to segment vertebrae in a CT scan, uploaded as NIFTI data. It allows to calculate trabecular vBMD, download the segmentation as NIFTI, and vertebral centroid coordinates as JSON files." ; sc:featureList edam:operation_3799 ; sc:license "CC-BY-SA-4.0" ; sc:name "anduin" ; sc:url "https://anduin.bonescreen.de" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3263, edam:topic_3344 ; sc:citation , "pmcid:PMC8444998", "pubmed:34541525" ; sc:description "A free online citizen science platform." ; sc:featureList edam:operation_3283, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "Anecdata" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.anecdata.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_3382 ; sc:citation , "pubmed:32856793" ; sc:description """A Simple Web-Based Platform to Build Stakeholder Understanding of Groundwater Behavior. This package models simple aquifer and well configurations.""" ; sc:featureList edam:operation_2426 ; sc:name "anem" ; sc:url "http://gopalpenny.shinyapps.io/anem-app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3168 ; sc:citation , "pmcid:PMC4888588", "pubmed:27246460" ; sc:description "This package implements functions for CNV calling, plotting, export and analysis from whole-genome single cell sequencing data." ; sc:featureList edam:operation_3233 ; sc:license "Artistic-2.0" ; sc:name "AneuFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AneuFinder.html" ; biotools:primaryContact , "Aaron Taudt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3390, edam:topic_3794 ; sc:citation ; sc:description "Detection of Cerebral Aneurysm using Modified Hough Circle Transform" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Aneurysm detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63729-jm61288-aneurysm_detection" ; biotools:primaryContact "Jubin Mitra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3308, edam:topic_3335 ; sc:citation , "pubmed:34626395" ; sc:description "anexVis is a transcriptome tool to visualize organ/tissue-specific glycosaminoglycan biosynthetic and catabolic pathways in human health and diseases. anexVis allows one to analyze a large number of genes that are related to biosynthetic and catabolic pathways of all glycosaminoglycans, such as heparan sulfate, chondroitin sulfate, keratan sulfate, and hyaluronic acid, in parallel across various human tissues organs. Such visual analyses have not been accessible to the broad research community despite the accumulation of a large amount of RNA-seq data." ; sc:featureList edam:operation_0314, edam:operation_3463, edam:operation_3926 ; sc:name "anexVis" ; sc:url "https://anexvis.chpc.utah.edu/" ; biotools:primaryContact "Balagurunathan Kuberan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation ; sc:description "This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion." ; sc:featureList edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "ANF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ANF.html" ; biotools:primaryContact "Tianle Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3325, edam:topic_3676 ; sc:citation ; sc:description """An open-source computational platform for the analysis of sequencing data for rare genetic diseases. Anfisa is a Variant Analysis and Curation Tool. Its purpose is to bring together Genetic Research and Clinical settings and provide a medical geneticist with access to research Genome.""" ; sc:featureList edam:operation_3197 ; sc:license "Apache-2.0" ; sc:name "AnFiSA" ; sc:url "https://github.com/ForomePlatform/AnFiSA#public-demo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation , "pmcid:PMC3855653", "pubmed:24324652" ; sc:description "Database of Streptocarpus rexii transcriptome." ; sc:featureList edam:operation_0310, edam:operation_0361, edam:operation_0564 ; sc:license "GPL-3.0" ; sc:name "Angeldust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-MILANO" ; sc:softwareHelp ; sc:url "http://www.beaconlab.it/angeldust" ; biotools:primaryContact "David Horner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8433338", "pubmed:34508124" ; sc:description "A fully automatic method to segment the vessels would eliminate potential subjectivity and provide a quantitative and systematic measurement of diameter reduction. 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LaZerte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0610, edam:topic_3299, edam:topic_3407, edam:topic_3500 ; sc:citation , "pmcid:PMC9163144", "pubmed:35654905" ; sc:description "AnimalTraits is a curated database containing body mass, metabolic rate and brain size measurements across a wide range of terrestrial animal taxa." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3695, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "AnimalTraits" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://animaltraits.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description "Anipose is an open-source toolkit for robust, markerless 3D tracking of animal behavior from multiple camera views. 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Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3047 ; sc:citation ; sc:description "AnnapuRNA is a knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method." ; sc:featureList edam:operation_0478, edam:operation_2489, edam:operation_3893 ; sc:license "GPL-3.0" ; sc:name "AnnapuRNA" ; sc:url "https://github.com/filipspl/AnnapuRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation ; sc:description """From https://anndata.readthedocs.io/en/latest/ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray.\"""" ; sc:license "BSD-3-Clause" ; sc:name "anndata" ; sc:softwareHelp ; sc:url "https://github.com/scverse/anndata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3473 ; sc:citation , "pmcid:PMC7939269", "pubmed:33684153" ; sc:description "Anne O’Tate is a value-added PubMed search engine for analysis and text mining." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3802 ; sc:name "Anne O Tate" ; sc:url "http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1775 ; sc:citation , "pmcid:PMC2703921", "pubmed:19389726" ; sc:description "ANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer." ; sc:featureList edam:operation_0267, edam:operation_1777, edam:operation_2479, edam:operation_3092 ; sc:name "ANNIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://annie.bii.a-star.edu.sg" ; biotools:primaryContact "Singapore Bioinformatics institute" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2031 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2330 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0092 ; sc:citation , "pmcid:PMC2238884", "pubmed:17932061" ; sc:description "Provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl." ; sc:featureList edam:operation_0361 ; sc:license "GPL-2.0" ; sc:name "annmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/annmap.html" ; biotools:primaryContact "Chris Wirth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation , "pubmed:20195257" ; sc:description "Annotation browsing 2.0." ; sc:featureList edam:operation_0524, edam:operation_3208, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Anno-J" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dandelion.liveholonics.com/dart/annoj.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0114, edam:topic_0203, edam:topic_2640, edam:topic_3170 ; sc:citation ; sc:description """an R Package to annotate and prioritize putative oncogenic RNA fusions. Filter and prioritize fusion calls. Using annoFuse, users can filter out fusions known to be artifactual and retained high-quality fusion calls using support of at least one junction read and remove false calls if there is disproportionate spanning fragment support of more than 10 reads compared to the junction read count. For prioritization, users can capture known as well as putative driver fusions reported in TCGA, or fusions containing gene partners that are known oncogenes, tumor suppressor genes, or COSMIC genes. Finally, users can also determine recurrent fusions across the cohort and recurrently-fused genes within each histology. By providing a standardized filtering and annotation method from multiple callers (STAR-Fusion and Arriba) users are able to merge, filter and prioritize putative oncogenic fusions across the PBTA""" ; sc:featureList edam:operation_2436, edam:operation_3695 ; sc:name "annoFuse" ; sc:url "https://github.com/d3b-center/annoFuse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:25701574" ; sc:description "Pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission" ; sc:featureList edam:operation_0361, edam:operation_3258 ; sc:name "Annocript" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/frankMusacchia/Annocript" ; biotools:primaryContact "Frank Musacchia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0749 ; sc:citation , "pmcid:PMC7203733", "pubmed:31930398" ; sc:description "AnnoGen is a toolkit for annotating three pragmatic genomic features for the GRCh38 genome in enormous base-wise quantities. The three features are chemical binding Energy, sequence information Entropy, and Homology Score. The Homology Score is an exceptional feature that captures the genome-wide homology through single-base-offset tiling windows of 100 continual nucleotide bases." ; sc:featureList edam:operation_0337, edam:operation_0362, edam:operation_2422 ; sc:license "MIT" ; sc:name "AnnoGen" ; sc:url "https://github.com/shengqh/annogen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640 ; sc:description "Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest." ; sc:featureList edam:operation_2421 ; sc:name "Annokey" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bjpop.github.io/annokey/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_2815 ; sc:citation , "pmcid:PMC5112684", "pubmed:27852242" ; sc:description "A web server for systematically annotating novel human lncRNAs." ; sc:featureList edam:operation_0361 ; sc:name "AnnoLnc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://annolnc.cbi.pku.edu.cn/index.jsp" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0659, edam:topic_2885, edam:topic_3794 ; sc:citation , "pmcid:PMC7319567", "pubmed:32406920" ; sc:description "AnnoLnc2 is a web server for integratively annotating novel human and mouse lncRNAs" ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3661 ; sc:name "AnnoLnc2" ; sc:softwareHelp ; sc:url "http://annolnc.gao-lab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3173, edam:topic_3308 ; sc:citation ; sc:description "AnnoMiner is a web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators." ; sc:featureList edam:operation_0362, edam:operation_3222, edam:operation_3223, edam:operation_3501, edam:operation_3672 ; sc:name "AnnoMiner" ; sc:softwareHelp ; sc:url "http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0621, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "Automatic preparation of annotated DNA sequences for bulk submissions to ENA." ; sc:featureList edam:operation_0260, edam:operation_0361, edam:operation_3200, edam:operation_3431 ; sc:license "BSD-2-Clause" ; sc:name "annonex2embl" ; sc:url "https://github.com/michaelgruenstaeudl/annonex2embl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_0602, edam:topic_0621, edam:topic_3053 ; sc:citation , "pmcid:PMC9252745", "pubmed:35640593" ; sc:description "The Annotation Query (AnnoQ) is an integrated functional annotation platform for large-scale genetic variant annotation." ; sc:featureList edam:operation_0224, edam:operation_0361, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "AnnoQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://annoq.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622, edam:topic_0659, edam:topic_0769, edam:topic_0780 ; sc:citation , "pmcid:PMC8825457", "pubmed:34792587" ; sc:description "AnnoSINE is a SINE annotation tool for plant genomes. The program is designed to generate high-quality non-redundant SINE libraries for genome annotation. It uses the manually curated SINE library in the Oryza sativa genome to benchmark the annotation performance." ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_0525 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AnnoSINE" ; sc:url "https://github.com/yangli557/AnnoSINE" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0769, edam:topic_3170, edam:topic_3922 ; sc:citation , "pmcid:PMC9723129", "pubmed:36482896" ; sc:description "An integrated tool to annotate eukaryotic proteins using multi-omics data." ; sc:featureList edam:operation_0362, edam:operation_1812, edam:operation_3216, edam:operation_3631, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "AnnotaPipeline" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/bioinformatics-ufsc/AnnotaPipeline" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_1920, edam:format_2332 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "Using R enviroments for annotation." ; sc:featureList edam:operation_0361, edam:operation_2421 ; sc:license "Artistic-2.0" ; sc:name "annotate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.52.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/annotate.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC9724561", "pubmed:36472574" ; sc:description "annotate_my_genomes is a pipeline that aims to annotate genome-guided transcriptome assemblies from StringTie, coming from long read RNA-Seq alignments in vertebrate genomes (i.e. PacBio technology)" ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3192, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "annotate_my_genomes" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/cfarkas/annotate_my_genomes" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3169 ; sc:citation , , "pmcid:PMC4987906", "pubmed:27137889" ; sc:description "This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution." ; sc:featureList edam:operation_3222 ; sc:name "annotategenes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/annotategenes/annotateGenes/1.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0622 ; sc:citation , "pmcid:PMC4015944", "pubmed:24564446" ; sc:description "Web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations." ; sc:featureList edam:operation_0362 ; sc:name "AnnotateGenomicRegions" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cru.genomics.iit.it/AnnotateGenomicRegions/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here." ; sc:featureList edam:operation_0226 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "annotatemyids" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fannotatemyids%2Fannotatemyids%2F3.12.0%2Bgalaxy1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169 ; sc:citation , , "pmcid:PMC4987906", "pubmed:27137889" ; sc:description "This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution." ; sc:featureList edam:operation_0362 ; sc:name "annotatepeaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/annotatepeaks/annotatePeaks/1.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_3621 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_1920 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3366 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "Provides user interface and database connection code for annotation data packages using SQLite data storage." ; sc:featureList edam:operation_0361, edam:operation_2421 ; sc:license "Artistic-2.0" ; sc:name "AnnotationDbi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0219 ; sc:description "It provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages." ; sc:featureList edam:operation_0226 ; sc:license "Artistic-2.0" ; sc:name "AnnotationFilter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AnnotationFilter.html" ; biotools:primaryContact "Bioconductor Maintainer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2031, edam:format_2195 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2031, edam:format_2195 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_3621 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3366, edam:topic_3489 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi." ; sc:featureList edam:operation_2421, edam:operation_3436 ; sc:license "Artistic-2.0" ; sc:name "AnnotationForge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AnnotationForge.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2091 ; sc:encodingFormat edam:format_2330 ; sc:name "Accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2091 ; sc:encodingFormat edam:format_2330 ; sc:name "Accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3366 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "Functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. org.Bt.eg.db)." ; sc:featureList edam:operation_3282 ; sc:license "GPL-2.0" ; sc:name "AnnotationFuncs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AnnotationFuncs.html" ; biotools:primaryContact "Stefan McKinnon Edwards" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0622, edam:topic_3489 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "This package provides a client for the BioConductor corresponding web resource, which provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. 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Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:32770192" ; sc:description "AntiCP 2.0 is an updated version of AntiCP, developed to predict and design anticancer peptides with high accuracy" ; sc:featureList edam:operation_2997 ; sc:name "anticp2" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/anticp2/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9205309", "pubmed:35722269" ; sc:description "The AntiDMPpred tool is a predictor that can be used to foretell if the query peptides might be anti-diabetic bioactive peptides." ; sc:featureList edam:operation_0224, edam:operation_3631, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AntiDMPpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://i.uestc.edu.cn/AntiDMPpred/cgi-bin/AntiDMPpred.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC5834480", "pubmed:29535692" ; sc:description "Antifp is an in silico method, which is developed to predict and design antifungal peptides. 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AOCD delivers a comprehensive resource on botanicals isolated from plant source(s) and its classification. It also includes compounds derived from Marine seaweeds; Microbial source that are found to have potent source of inhibition targeting obesity." ; sc:featureList edam:operation_0224, edam:operation_3216, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "AOCD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aocd.swmd.co.in/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3047, edam:topic_3335, edam:topic_3390 ; sc:citation , "pubmed:37001349" ; sc:description "A comprehensive database for antioxidants including small molecules, peptides and proteins." ; sc:featureList edam:operation_0418, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "AODB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aodb.idruglab.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0121 ; sc:citation , "pubmed:26345449" ; sc:description "This tool was developed to identify antioxidant proteins based on the sequence information." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "AodPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/AntioxiPred" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0749, edam:topic_0769, edam:topic_3520 ; sc:citation , "pubmed:32812285" ; sc:description "A web application for DNA/RNA tandem mass spectrometry data interpretation." ; sc:featureList edam:operation_3629, edam:operation_3643, edam:operation_3644, edam:operation_3767 ; sc:name "Aom2S" ; sc:url "https://mstools.epfl.ch/am2s/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0160, edam:topic_0769, edam:topic_3474 ; sc:citation , "pmcid:PMC10196667", "pubmed:37158576" ; sc:description "Genome mining for anti-CRISPR operons using machine learning." ; sc:featureList edam:operation_0303, edam:operation_0435, edam:operation_0579, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:name "AOminer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://aca.unl.edu/AOminer/AOminer_APP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3375, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC10840476", "pubmed:38322350" ; sc:description "Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application." ; sc:featureList edam:operation_3216, edam:operation_3454, edam:operation_3660, edam:operation_3929, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "AOMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aomp.alphama.com.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3068, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC8796376", "pubmed:34718414" ; sc:description "AOP-helpFinder is a web tool for identification and extraction of associations between stressors and biological events at various level of the biological organization (molecular initiating event (MIE), key event (KE), and adverse outcome (AO)). AOP-helpFinder is a hybrid tool, combining text mining and graph theory. Currently, AOP-helpFinder screens all the >30 millions of abstracts available from the PubMed database, to decipher co-mentioned terms (e.g. a stressor and a MIE)." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_1812 ; sc:license "CECILL-2.1" ; sc:name "AOP-helpFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://aop-helpfinder.u-paris-sciences.fr/index.php" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:encodingFormat edam:format_3790 ; sc:name "Query script" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2332, edam:format_3255, edam:format_3464, edam:format_3475, edam:format_3752 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "SPARQL endpoint", "Web application" ; sc:applicationSubCategory edam:topic_2840 ; sc:citation , "pmcid:PMC8978481", "pubmed:35388368" ; sc:description "SPARQL interface for AOP-Wiki data" ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "AOP-Wiki RDF" ; sc:url "https://aopwiki.rdf.bigcat-bioinformatics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_2840, edam:topic_3305, edam:topic_3407 ; sc:citation , "pmcid:PMC7520043", "pubmed:32467965" ; sc:description "The AOP4EUpest webserver is a resource for annotated pesticides-biological events involved in Adverse Outcome Pathways (AOPs)." ; sc:featureList edam:operation_0306, edam:operation_0533, edam:operation_2421 ; sc:name "AOP4EUpest" ; sc:url "http://www.biomedicale.parisdescartes.fr/aop4EUpest/home.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC7203727", "pubmed:31971579" ; sc:description "Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest." ; sc:featureList edam:operation_0269, edam:operation_3659, edam:operation_3925 ; sc:name "AOPEDF" ; sc:url "https://github.com/ChengF-Lab/AOPEDF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """APA-Scan detects the potential Alternative Polyadenylation (APA) events in the downstream 3'-UTR of a gene among two different biological conditions. APA-Scan is a python tool which can be downloaded directly from github. Python (version 3.0 or higher) is required to be installed on users machine to run APA-Scan. It can work on Windows, Linux and Mac platform.""" ; sc:featureList edam:operation_0337, edam:operation_0428, edam:operation_3800 ; sc:name "APA-Scan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/compbiolabucf/APA-Scan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web API", "Web application", "Web service", "Workbench" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0202, edam:topic_2258, edam:topic_3071, edam:topic_3473 ; sc:author "Apache Taverna community" ; sc:citation , "pmcid:PMC3692062", "pubmed:23640334" ; sc:description "Open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation." ; sc:featureList edam:operation_0224, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Apache Taverna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Apache Software Foundation", "cs.manchester.ac.uk" ; sc:softwareHelp , ; sc:softwareVersion "3" ; sc:url "http://taverna.incubator.apache.org/" ; biotools:primaryContact "Apache Taverna community", "Apache Taverna mailing lists" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Trino is a distributed SQL query engine designed to query large data sets distributed over one or more heterogeneous data sources. Trino is a tool designed to efficiently query vast amounts of data using distributed queries. If you work with terabytes or petabytes of data, you are likely using tools that interact with Hadoop and HDFS. Trino was designed as an alternative to tools that query HDFS using pipelines of MapReduce jobs, such as Hive or Pig, but Trino is not limited to accessing HDFS. Trino can be and has been extended to operate over different kinds of data sources, including traditional relational databases and other data sources such as Cassandra. Trino was designed to handle data warehousing and analytics: data analysis, aggregating large amounts of data and producing reports. These workloads are often classified as Online Analytical Processing (OLAP).""" ; sc:featureList edam:operation_0224 ; sc:license "Apache-2.0" ; sc:name "Apache Trino" ; sc:softwareHelp , ; sc:softwareVersion "Release 406 (25 Jan 2023)" ; sc:url "https://trino.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description """Web-based notebook that enables data-driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more.""" ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Apache Zeppelin" ; sc:softwareHelp ; sc:softwareVersion "0.10.1" ; sc:url "https://zeppelin.apache.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3583 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC10234309", "pubmed:37117035" ; sc:description "Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ." ; sc:featureList edam:operation_0428, edam:operation_3435, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APAIQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://anaconda.org/joshuachou/apaiq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7320624", "pubmed:32321166" ; sc:description "A R bioinformatics package for analysis of alternative polyadenylation isoforms. Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data." ; sc:featureList edam:operation_3680 ; sc:license "LGPL-3.0" ; sc:name "APAlyzer" ; sc:url "https://bioconductor.org/packages/release/bioc/html/APAlyzer.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0820, edam:topic_3314, edam:topic_3382 ; sc:citation , "pubmed:34085265" ; sc:description "Open source software tool for fast and light-weight data analysis and data conversion from platereaders and images to formats of more powerful analysis software such as MATLAB, GraphPad Prism and SBToolbox2 (IQMTools)." ; sc:featureList edam:operation_0269, edam:operation_2995, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Aparecium" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gpcr.ut.ee/aparecium.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC9411867", "pubmed:36035147" ; sc:description "A web-based platform for alternative polyadenylation analyses in hematological cancers." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APAview" ; sc:url "https://github.com/Wu-xjtu/APAview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2275, edam:topic_3318 ; sc:citation , "pubmed:33052694" ; sc:description "Atom Pair-Based Scoring function (APBScore) is a physical-based scoring function, which includes pairwise van der Waals (VDW), electrostatic interaction, and hydrogen bond energies between the receptor and ligand." ; sc:featureList edam:operation_0387, edam:operation_0394, edam:operation_3938 ; sc:license "GPL-3.0" ; sc:name "APBScore" ; sc:url "https://github.com/BaoJingxiao/APBScore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2640, edam:topic_3301 ; sc:citation , "pmcid:PMC7332564", "pubmed:32339223" ; sc:description "A R package and Shiny app for covariate adjusted principal coordinates analysis." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "aPCoA" ; sc:url "https://biostatistics.mdanderson.org/shinyapps/aPCoA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1317, edam:topic_2814, edam:topic_3520 ; sc:citation , "pubmed:15998662" ; sc:description "Functions to estimate a bipartite graph of protein complex membership using AP-MS data." ; sc:featureList edam:operation_0320 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "apComplex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/apComplex.html" ; biotools:primaryContact "Denise Scholtens" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0949 ; sc:encodingFormat edam:format_3464 ; sc:name "Workflow metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0949 ; sc:encodingFormat edam:format_3603, edam:format_3604, edam:format_3857 ; sc:name "Workflow metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web API" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0769 ; sc:citation , "pmcid:PMC7304703", "pmcid:PMC8041394", "pubmed:33720735" ; sc:description "APE (the Automated Pipeline Explorer) as a command-line tool and API for automated composition of scientific workflows. APE is easily configured to a new application domain by providing it with a domain ontology and semantically annotated tools. It can then be used to synthesize purpose-specific workflows based on a specification of the available workflow inputs, desired outputs and possibly additional constraints." ; sc:featureList edam:operation_3429 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "APE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.7" ; sc:url "https://github.com/sanctuuary/APE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_2885, edam:topic_3125, edam:topic_3168 ; sc:citation , "pmcid:PMC9580900", "pubmed:36304290" ; sc:description "A plasmid Editor (ApE) is a free, multi-platform application for visualizing, designing, and presenting biologically relevant DNA sequences. ApE provides a flexible framework for annotating a sequence manually or using a user-defined library of features. ApE can be used in designing plasmids and other constructs via in silico simulation of cloning methods such as PCR, Gibson assembly, restriction-ligation assembly and Golden Gate assembly." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_0365, edam:operation_0564, edam:operation_0578 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ApE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://jorgensen.biology.utah.edu/wayned/ape/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520, edam:topic_3524 ; sc:citation , "pubmed:20836568" ; sc:description "Proteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC." ; sc:featureList edam:operation_2426, edam:operation_3627 ; sc:name "APECS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://trac.nbic.nl/apecs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "It provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients." ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "apeglm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/apeglm.html" ; biotools:primaryContact "Anqi Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3168, edam:topic_3175, edam:topic_3512 ; sc:citation ; sc:description """Aperture is a new alignment-free SV caller designed for cfDNA dataset. Aperture applies a unique strategy of k-mer based searching, fast breakpoint detection using binary labels and candidates clustering to detect SVs and viral integrations in high sensitivity, especially when junctions span repetitive regions, followed by a barcode based filter to ensure specificity. Aperture takes paired-end reads in fastq format as inputs and reports all SVs and viral integrations in VCF 4.2 format.""" ; sc:featureList edam:operation_3192, edam:operation_3228, edam:operation_3472, edam:operation_3695 ; sc:license "Apache-2.0" ; sc:name "Aperture" ; sc:url "https://github.com/liuhc8/Aperture" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0108, edam:topic_0121, edam:topic_3474 ; sc:citation , "pubmed:17187058" ; sc:description "Absolute protein expression Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which favor or hinder detection. A sample data set and descriptive tutorial help to acquaint users with the operation of the tool." ; sc:featureList edam:operation_2423, edam:operation_3630, edam:operation_3637 ; sc:name "APEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0" ; sc:url "http://sourceforge.net/projects/apexqpt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3365 ; sc:citation , "pmcid:PMC5215480", "pubmed:27417145" ; sc:description "apex is an R package that can be used for phylogenetic studies. It implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data." ; sc:featureList edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "apex" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.3" ; sc:url "https://cran.r-project.org/web/packages/apex/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3293 ; sc:citation , "pubmed:30840059" ; sc:description "R package designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis." ; sc:featureList edam:operation_0296, edam:operation_0499, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "aphid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.3" ; sc:url "https://cran.r-project.org/package=aphid" ; biotools:primaryContact "Shaun Wilkinson" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "An aphid genome database." ; sc:featureList edam:operation_0258 ; sc:isAccessibleForFree true ; sc:name "AphidBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:url "http://aphidbase.com/" ; biotools:primaryContact "BIPAA platform" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "Automated Pipeline for Infants Continuous EEG (APICE) is a fully automated, flexible, and modular. Artifacts are detected using multiple algorithms and adaptive thresholds, making it suitable to different age groups and testing procedures without redefining parameters" ; sc:featureList edam:operation_3435 ; sc:name "APICE" ; sc:url "https://github.com/neurokidslab/eeg_preprocessing" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "APICURON is an open resource that tracks and credits the work of biocurators across multiple participating knowledgebases. Biocuration is essential to extract knowledge from research data and make it available in a structured and standardized way to the scientific community. However, processing biological data - mainly from literature - requires a huge effort which is difficult to quantify and acknowledge. APICURON collects biocuration events from third party resources and aggregates this information, spotlighting biocurator contributions. APICURON promotes biocurator engagement implementing gamification concepts like badges, medals and leaderboards and at the same time provides a monitoring service for registered resources. APICURON adopts a data model that is flexible enough to represent and track the majority of biocuration activities." ; sc:featureList edam:operation_3436 ; sc:name "APICURON" ; sc:softwareHelp ; sc:url "http://apicuron.org" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2764 ; sc:encodingFormat edam:format_1963 ; sc:name "Protein name (UniProt)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602 ; sc:author ; sc:citation , , "pmcid:PMC4987915", "pmcid:PMC6354026", "pubmed:27131791", "pubmed:30715274" ; sc:description """APID Interactomes provides a comprehensive collection of protein interactomes for more than 500 organisms based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. APID also includes a data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions reliability of the "edges") and a mapping of the functional environment of the proteins (functional annotations of the "nodes").""" ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "APID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:url "http://apid.dep.usal.es" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2764 ; sc:encodingFormat edam:format_1963 ; sc:name "Protein name (UniProt)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602 ; sc:author ; sc:citation , , "pmcid:PMC4987915", "pmcid:PMC6354026", "pubmed:27131791", "pubmed:30715274" ; sc:description """APID Interactomes provides a comprehensive collection of protein interactomes for more than 500 organisms based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. APID also includes a data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions reliability of the "edges") and a mapping of the functional environment of the proteins (functional annotations of the "nodes").""" ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "APID Interactomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:url "http://apid.dep.usal.es" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC6929291", "pubmed:31870282" ; sc:description """Antimicrobial peptide identification using multi-scale convolutional network. BACKGROUND:Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine learning methods have been commonly used. More recently, some deep learning methods have also been applied to this problem. RESULTS:In this paper, we designed a deep learning model to identify AMP sequences. We employed the embedding layer and the multi-scale convolutional network in our model. The multi-scale convolutional network, which contains multiple convolutional layers of varying filter lengths, could utilize all latent features captured by the multiple convolutional layers. To further improve the performance, we also incorporated additional information into the designed model and proposed a fusion model""" ; sc:featureList edam:operation_3092, edam:operation_3631, edam:operation_3695 ; sc:name "APIN" ; sc:url "https://github.com/zhanglabNKU/APIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2640, edam:topic_3336, edam:topic_3542 ; sc:citation , "pmcid:PMC9734560", "pubmed:36494486" ; sc:description "A database of apoptosis-inducing anticancer peptides." ; sc:featureList edam:operation_0250, edam:operation_0267, edam:operation_3646 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ApInAPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinf.modares.ac.ir/software/ApInAPDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description "APIR: flexible and powerful FDR-control framework for aggregating peptides identified by multiple database search algorithms from mass spectrometry data." ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3436, edam:operation_3631 ; sc:name "APIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yiling0210/APIR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3071, edam:topic_3382 ; sc:citation ; sc:description """Collection of wing images for conservation of honey bees (Apis mellifera) biodiversity in Europe. We provide 26,481 forewing images of honey bee workers. They represent 1,725 samples from 13 European countries. The shape of the wings was described using the coordinates for 19 landmarks at wing veins’ intersections. The whole dataset, including the wing images, landmark coordinates, geographic coordinates of sampling locations, and other data, is available on the Zenodo website under a Public Domain licence.""" ; sc:featureList edam:operation_2238 ; sc:license "CC0-1.0" ; sc:name "Apis-wings-EU" ; sc:url "https://zenodo.org/record/7244070" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3796 ; sc:citation , "pubmed:16877866" ; sc:description "The Association in the Presence of Linkage tool provides a novel test for association in the presence of linkage using general pedigree data." ; sc:featureList edam:operation_0324 ; sc:name "APL" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://hihg.med.miami.edu/software-download/apl-version-1.1" ; biotools:primaryContact "John P. Hussman Institute for Human Genomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0820, edam:topic_2229 ; sc:citation , "pubmed:36752505" ; sc:description "APL@VORO is a software designed to aid in analyzing membrane simulations made with GROMACS." ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_2476 ; sc:license "Other" ; sc:name "APL_voro" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://aplvoro.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC7431853", "pubmed:32807888" ; sc:description """The R package apLCMS is designed for the processing of LC/MS based metabolomics data. It starts with a group of LC/MS files in the same folder, and generates a table with features in the rows and intensities in the columns. There are two major routes of data analysis. The first, which we call unsupervised analysis, doesn't use existing knowledge. It detects peaks de novo from the data based on the data itself. The second, which we call hybrid analysis, combines de novo peak detection with existing knowledge. The existing knowledge can come from two sources - known metabolites and historically detected features from the same machinery.""" ; sc:featureList edam:operation_3215, edam:operation_3435, edam:operation_3799 ; sc:name "apLCMS" ; sc:url "https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3714 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3651 ; sc:name "Peptide mass fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Converts MaxQuant APL (Andromeda peak lists) to MGF." ; sc:featureList edam:operation_0335 ; sc:name "APLToMGFConverter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.wehi.edu.au/people/andrew-webb/1298/apl-mgf-converter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation "pubmed:26861916" ; sc:description "ApoCanD: Database of Human Apoptotic Proteins in the context of cancer" ; sc:featureList edam:operation_2945 ; sc:name "apocand" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/apocand/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_3538 ; sc:citation , "pmcid:PMC7773485", "pubmed:33381830" ; sc:description "APOD (Accurate Predictor Of Disordered flexible linkers) is an accurate sequence-based predictor of disordered flexible linkers. It utilizes both local- and protein-level inputs that quantify propensity for disorder, sequence composition, sequence conservation and selected putative structural properties." ; sc:featureList edam:operation_0267, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "APOD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yanglab.nankai.edu.cn/APOD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0659, edam:topic_3172, edam:topic_3308 ; sc:citation ; sc:description "Analysis of Pan-Omics Data in Human Interactome Network (APODHIN) is a platform where users can upload and map multiple types of 'omics' data such as genomics, transcriptomics, proteomics, metabolomics, etc. in human cellular interaction networks. User can filter the interactions (protein-protein, gene regulatory, etc.) based on the status of the omics data. This filtered network of interaction can be used to identify topologically important nodes (TINs), namely hubs, central nodes and bottleneck nodes." ; sc:featureList edam:operation_0276, edam:operation_0533, edam:operation_1781, edam:operation_3660, edam:operation_3925 ; sc:name "APODHIN" ; sc:url "http://www.hpppi.iicb.res.in/APODHIN/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0219, edam:topic_0602, edam:topic_0622, edam:topic_3512 ; sc:citation "pubmed:12537571" ; sc:description "Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment." ; sc:featureList edam:operation_0361, edam:operation_0362, edam:operation_3096 ; sc:name "Apollo Genome Annotation and Curation Tool" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://apollo.berkeleybop.org" ; biotools:primaryContact "Apollo team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pubmed:32167530" ; sc:description "Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size." ; sc:featureList edam:operation_0232, edam:operation_0310, edam:operation_3198, edam:operation_3359, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "Apollo" ; sc:url "https://github.com/CMU-SAFARI/Apollo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0176 ; sc:citation , "pmcid:PMC10185404", "pubmed:37115636" ; sc:description "Predicting allosteric pockets in protein biological assemblages." ; sc:featureList edam:operation_2476, edam:operation_3897, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APOP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://apop.bb.iastate.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0820, edam:topic_3474 ; sc:citation , "pmcid:PMC7820372", "pubmed:33490085" ; sc:description "ApoPred is a tool for odentification of apolipoproteins and their subfamilies with multifarious features." ; sc:featureList edam:operation_1777, edam:operation_3936, edam:operation_3937 ; sc:name "ApoPred" ; sc:url "http://tang-biolab.com/server/ApoPred/service.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:description "Tool to automate the process of creating standalone, model-exploration apps for SimBiology model" ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "App Builder for SimBiology Models" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/43832-app-builder-for-simbiology-models" ; biotools:primaryContact "Fulden Buyukozturk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC6396488", "pubmed:30819089" ; sc:description "R package for accurate SNP-based parentage analysis in the absence of guiding information." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "apparent" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://cran.r-project.org/package=apparent" ; biotools:primaryContact "Arthur Melo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3416 ; sc:citation , "pmcid:PMC7780701", "pubmed:33424481" ; sc:description "APPECO (Applying Evidence with Confidence) is a tool that aims to help you find and use the best evidence for the rehabilitation of patients with Multiple Sclerosis." ; sc:featureList edam:operation_2422 ; sc:name "APPECO" ; sc:url "http://www.appeco.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0203, edam:topic_2640 ; sc:citation , "pubmed:25091586" ; sc:description "Web-based platform to perform survival analysis, particularly, to support identifying molecular signatures significantly associated with cancer patients’ outcome. It provides various analysis methods to discover genes or any other molecules associated with survival of cancer patients." ; sc:featureList edam:operation_0415, edam:operation_2478 ; sc:name "APPEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.appex.kr/appex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3360 ; sc:citation , "pubmed:37159410" ; sc:description "Web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "AppIndels" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://AppIndels.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_3047, edam:topic_3957 ; sc:citation , "pmcid:PMC9639416", "pubmed:36353604" ; sc:description "An R package for building and computational analysis of protein-protein interaction networks." ; sc:featureList edam:operation_2949, edam:operation_3359, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "APPINetwork" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://forgemia.inra.fr/GNet/appinetwork" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3293 ; sc:citation , , "pmcid:PMC4613772", "pubmed:23110901", "pubmed:26482678" ; sc:description "Set of tools to analyse promoter sequences on a genome-wide scale." ; sc:featureList edam:operation_0253 ; sc:license "GPL-3.0" ; sc:name "APPLES" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cyverseuk.org/applications/warwick/analysis-of-plant-promoter-linked-elements/" ; biotools:primaryContact "Eran Tauber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3293 ; sc:citation , "pmcid:PMC7164367", "pubmed:31545363" ; sc:description "Scalable Distance-based Phylogenetic Placement with or without Alignments | distance based phylogenetic placement | APPLES stands for Accurate Phylogenetic Placement with LEast Squares and addresses the problem of phylogenetic placement of DNA and protein sequences into an already existing reference tree. APPLES is a command-line tool and it can run on Linux, Mac OSX, and Windows" ; sc:featureList edam:operation_0545, edam:operation_0547, edam:operation_3478 ; sc:license "MIT" ; sc:name "APPLES" ; sc:url "http://github.com/balabanmetin/apples" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3474 ; sc:citation ; sc:description "The Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED)." ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "APPLESEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mhpuglia/APPLESEED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3320, edam:topic_3512 ; sc:author "Jose Rodriguez" ; sc:citation , , , , "pmcid:PMC3531113", "pmcid:PMC4489225", "pmcid:PMC5753224", "pmcid:PMC8728124", "pubmed:23161672", "pubmed:25990727", "pubmed:29069475", "pubmed:34755885" ; sc:contributor "ISCIII" ; sc:description "Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation." ; sc:featureList edam:operation_0361, edam:operation_0362, edam:operation_3672 ; sc:funder "ISCIII" ; sc:name "APPRIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BU_CNIO", "CNIO", "INB" ; sc:softwareHelp , ; sc:softwareVersion "2022_07.v47" ; sc:url "https://appris.bioinfo.cnio.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_2275, edam:topic_3534 ; sc:citation , "pubmed:21557747" ; sc:description "Computational tool that predicts the interaction of a PPR (pentatricopeptide repeat) with its RNA binding site." ; sc:featureList edam:operation_0245, edam:operation_0420 ; sc:name "aPPRove" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cs.colostate.edu/~approve/" ; biotools:primaryContact "Thomas Harrison" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:citation , "pmcid:PMC7195136", "pubmed:32362697" ; sc:description "ApproximantCoefficientsSIR is a MATLAB tool that computes the the coefficients of an approximate analytic solution to the SIR epidemic model." ; sc:isAccessibleForFree true ; sc:name "ApproximantCoefficientsSIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75131-approximantcoefficientssir" ; biotools:primaryContact "Nathaniel Barlow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176 ; sc:citation ; sc:description "APPTEST is an innovative new method for the automatic prediction of peptide tertiary structures." ; sc:featureList edam:operation_0471, edam:operation_0474, edam:operation_2476, edam:operation_3454, edam:operation_4009 ; sc:name "APPTEST" ; sc:url "https://research.timmons.eu/apptest" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3474, edam:topic_3794 ; sc:citation , "pmcid:PMC7961182", "pubmed:33748796" ; sc:description "Appyters are standalone applications for generating jupyter notebooks, the appyter catalog features many bioinformatics related appyters. Appyters turn Jupyter Notebooks into fully functional standalone web-based bioinformatics applications. Appyters present to users an entry form enabling them to upload their data and set various parameters for a multitude of data analysis workflows." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2436, edam:operation_3891, edam:operation_3935 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Appyters" ; sc:url "https://appyters.maayanlab.cloud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_3474 ; sc:citation , "pubmed:32821925" ; sc:description "aPRBind is a convolutional neural network (CNN)-based ab-initio method for RNA-binding residue prediction. aPRBind is trained with sequence features and structural ones (particularly including residue dynamics information and residue-nucleotide propensity developed by us) that are extracted from the predicted structures by I-TASSER" ; sc:featureList edam:operation_0476, edam:operation_3901, edam:operation_3902 ; sc:name "aPRBind" ; sc:url "https://github.com/ChunhuaLiLab/aPRbind" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0659 ; sc:citation , "pmcid:PMC5499795", "pubmed:28334975" ; sc:description "Integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins." ; sc:featureList edam:operation_1777 ; sc:name "APRICOT" ; sc:url "https://pypi.org/project/bio-apricot/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3070, edam:topic_3316, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC7746519", "pubmed:32777825" ; sc:description """APRICOT (Advanced Platform for Reproducible Infrastructures in the Cloud via Open Tools) is an open-source extension to support customised virtual infrastructure deployment and usage from Jupyter notebooks. Scientific publications are meant to exchange knowledge among researchers but the inability to properly reproduce computational experiments limits the quality of scientific research. Furthermore, bibliography shows that irreproducible preclinical research exceeds 50%, which produces a huge waste of resources on nonprofitable research at Life Sciences field. As a consequence, scientific reproducibility is being fostered to promote Open Science through open databases and software tools that are typically deployed on existing computational resources. However, some computational experiments require complex virtual infrastructures, such as elastic clusters of PCs, that can be dynamically provided from multiple clouds""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "APRICOT" ; sc:url "https://github.com/grycap/apricot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3050 ; sc:citation , "pmcid:PMC9563694", "pubmed:36029248" ; sc:description "Apscale is a metabarcoding pipeline that handles the most common tasks in metabarcoding pipelines like paired-end merging, primer trimming, quality filtering, otu clustering and denoising as well as an otu filtering step." ; sc:featureList edam:operation_0232, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APSCALE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DominikBuchner/apscale" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation , "pubmed:28880292" ; sc:description "This search engine recommends PubMed articles relevant to a given article. It automatically extracts keywords from the title and abstract indexed in PubMed to generate recommendations. The database contains all PubMed records, providing up to 60 recommendations per searched article. Researchers were invited to annotate degrees of relevance for provided recommendations. All evaluations received will be curated into a benchmark dataset to be made available for free download and redistribution." ; sc:featureList edam:operation_0305 ; sc:isAccessibleForFree true ; sc:name "Article-based PubMed Search Engine (APSE)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pubmed.ict.griffith.edu.au/" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This server allow to predict the secondary structure of protein's from their amino acid sequence" ; sc:featureList edam:operation_2945 ; sc:name "apssp" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/apssp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3542 ; sc:description "APSSP2 allows to predict the secondary structure of protein’s from their amino acid sequence." ; sc:featureList edam:operation_0267, edam:operation_0271, edam:operation_2423, edam:operation_2479, edam:operation_2488 ; sc:name "APSSP2" ; sc:url "https://webs.iiitd.edu.in/raghava/apssp2/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3003 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1317, edam:topic_3295 ; sc:citation , "pmcid:PMC5942889", "pubmed:29702633" ; sc:description "A tool for designing primers and identifying accurate normalization controls for ATAC-qPCR." ; sc:featureList edam:operation_2419, edam:operation_2480 ; sc:isAccessibleForFree true ; sc:name "ATAC Primer Tool (APT)" ; sc:softwareHelp ; sc:url "https://github.com/ChangLab/ATACPrimerTool" ; biotools:primaryContact "Howard Y Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3374 ; sc:citation , "pmcid:PMC6144873", "pubmed:29986050" ; sc:description "Design RNA complexes that hybridize via sticky bridges." ; sc:featureList edam:operation_0310 ; sc:name "AptaBlocks" ; sc:url "https://github.com/wyjhxq/AptaBlocks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071, edam:topic_3316 ; sc:citation , "pmcid:PMC4281958", "pubmed:25558474" ; sc:description "Allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets." ; sc:featureList edam:operation_3432 ; sc:name "AptaCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#aptatools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3071, edam:topic_3370 ; sc:citation , "pubmed:38164624" ; sc:description "AptaDB is an online database that integrated comprehensive information on aptamers. It collects thousands of aptamers obtained from SELEX-based screening in the literature and and other databases, which may facilitate biologists to develop novel aptamers and accelerate aptamer-related researches." ; sc:featureList edam:operation_2419, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "AptaDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lmmd.ecust.edu.cn/aptadb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_0654 ; sc:citation , "pmcid:PMC9805580", "pubmed:36440922" ; sc:description "AptaMat is a simple script which aims to measure differences between DNA or RNA secondary structures. The method is based on the comparison of the matrices representing the two secondary structures to analyze, assimilable to dotplots." ; sc:featureList edam:operation_0278, edam:operation_0483, edam:operation_0502, edam:operation_2488, edam:operation_2518 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AptaMat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GEC-git/AptaMat.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3511 ; sc:citation , "pubmed:26395772" ; sc:description "Computational tool to identify target-specific aptamers from HT-SELEX data and secondary structure information." ; sc:featureList edam:operation_0415, edam:operation_2441 ; sc:name "APTANI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://aptani.unimore.it/" ; biotools:primaryContact "Silvio Bicciato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC7955126", "pubmed:33712618" ; sc:description "Aptardi (Alternative Polyadenylation Trascriptome Analysis from RNA sequencing and DNA sequencing Information) predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence." ; sc:featureList edam:operation_0314, edam:operation_0428, edam:operation_3192, edam:operation_3258, edam:operation_3800 ; sc:license "MIT" ; sc:name "aptardi" ; sc:url "https://github.com/luskry/aptardi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_3299 ; sc:citation , "pmcid:PMC8524629", "pubmed:31999328" ; sc:description "A method for optimized de novo motif discovery of RNA aptamers via HTS-SELEX." ; sc:featureList edam:operation_0238, edam:operation_0278 ; sc:name "AptCompare" ; sc:url "https://bitbucket.org/shiehk/aptcompare" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3393 ; sc:citation , "pubmed:33715568" ; sc:description "The Automated Phonetic Transcription (APT) Comparison Tool (APTct) is an online tool that facilitates the comparison of phonetic transcriptions for a variety of clinical and research purposes." ; sc:featureList edam:operation_3096, edam:operation_3799 ; sc:name "APTct" ; sc:url "https://aptct.auburn.edu" ; biotools:primaryContact "Dallin J. Bailey" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1856 ; sc:name "PDB insertion code" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0153, edam:topic_0154, edam:topic_0601 ; sc:citation , "pmcid:PMC10503417", "pubmed:37596782" ; sc:description "A web server that identifies weak molecular interactions in protein structures." ; sc:featureList edam:operation_0417, edam:operation_0477, edam:operation_1839 ; sc:isAccessibleForFree true ; sc:name "AQcalc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aqcalcbiocomputing.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "The AQMM was developed to perform absolute quantification of multiple metagenomes and it's parallel metatranscriptome. In order to use this algorithm, the experiment should be designed with both metagenome and metatranscriptome data. From the initial stage, the molecular experimental data should be recorded to help on estimating the overall DNA or RNA of a unit (ml/gram) of the sample. The AQMM was demonstrated to obtain better results of differential expression genes identification in comparative metatranscriptomic studies." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "aqmm" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/biofuture/aqmm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0593, edam:topic_2814 ; sc:citation , "pubmed:9008363" ; sc:description "Suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy." ; sc:featureList edam:operation_1844 ; sc:name "AQUA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://code.google.com/archive/p/aquad/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3173, edam:topic_3179 ; sc:citation , "pmcid:PMC10763690", "pubmed:32051612" ; sc:description """Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP). Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data. Induced chromatin interactions anchored with protein contacts will be readily differentiated using AQuA-HiChIP, but with normalizing by total interactive paired-end tags (PETs), differential interaction frequencies may produce false positives or false negatives.""" ; sc:featureList edam:operation_3222, edam:operation_3435, edam:operation_3799 ; sc:name "AQuA-HiChIP" ; sc:url "https://github.com/GryderArt/AQuA-HiChIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3361, edam:topic_3398, edam:topic_3474 ; sc:citation ; sc:description "AQUA (Advanced QUery Architecture for the SPARC Portal) is an application that aims at improving the search capabilities of the SPARC Portal." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AQUA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SPARC-FAIR-Codeathon/aqua" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_3500, edam:topic_3810 ; sc:citation , "pmcid:PMC9342733", "pubmed:35913974" ; sc:description "A tool to assist aquaculture production design based on abiotic requirements of animal species." ; sc:featureList edam:operation_3960 ; sc:license "Not licensed" ; sc:name "AquaDesign" ; sc:url "https://github.com/GregoireButruille/AquaDesign" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1869 ; sc:encodingFormat edam:format_2330 ; sc:name "Organism identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1063 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1096 ; sc:encodingFormat edam:format_1963 ; sc:name "Sequence accession (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0893 ; sc:encodingFormat edam:format_3464 ; sc:name "Sequence-structure alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3510 ; sc:author "Andrea Schafferhans", "Christian Stolte", "Kenneth S Sabir", "Seán I O'Donoghue" ; sc:citation , "pubmed:25633501" ; sc:contributor "Alexander von Humboldt Foundation", "Benjamin Wellmann", "Burkhard Rost", "CSIRO's OCE Science Leader program and its Computational and Simulation Sciences platform", "Fabian A Buske", "Julian Heinrich", "Manfred Roos", "Maria Kalemanov", "Nelson Perdigão", "Vivian Ho" ; sc:description "Simplifying the generation of insight from protein structures through structure visualisation, annotated with protein features; loads sequence-to-structure alignments from the PSSH2 database, sequence features from UniProt and Interpro and user defined features on demand from JSON files; there is also a WebAPI (see ...)." ; sc:featureList edam:operation_0338, edam:operation_0339, edam:operation_0474, edam:operation_0564, edam:operation_0570 ; sc:funder "Alexander von Humboldt Foundation", "CSIRO's OCE Science Leader program and its Computational and Simulation Sciences platform" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Aquaria" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Department for Bioinformatics and Computational Biology, Technische Universität München", "Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney", "Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney", "RostLab", "School of Molecular Bioscience, The University of Sydney" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://aquaria.ws" ; biotools:primaryContact "Andrea Schafferhans", "Seán O'Donoghue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3068, edam:topic_3382, edam:topic_3810 ; sc:citation , "pmcid:PMC8209617", "pubmed:34151028" ; sc:description "Open-source laboratory software for design, execution and data management. Build reproducible experimental workflows, manage samples, store data, and share know-how." ; sc:featureList edam:operation_2409, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Aquarium" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.aquarium.bio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3050, edam:topic_3500 ; sc:citation ; sc:description """Expanding our understanding of the trade in aquatic marine wildlife. Marine Aquarium Biodiversity and Trade Flow. Aquariumtradedata.org is a commitment to understanding the diversity and magnitude of the marine aquarium trade by illuminating and evaluating the global shipping pathways of the trade. You will be logged off in seconds due to inactivity. Click here to continue using this web page. Clownfish, or anemonefish (family Pomacentridae), are some of the most iconic fish species on tropical coral reefs, where they live symbiotically with giant sea anemones. Read more about the global trade of clownfish by RET TALBOT""" ; sc:featureList edam:operation_2422, edam:operation_3436 ; sc:name "aquarium trade date data" ; sc:url "https://www.aquariumtradedata.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2828 ; sc:citation , "pmcid:PMC3125794", "pubmed:21665925" ; sc:description "AquaSAXS is a web server for computation of and fitting of small angle x-ray scattering (SAXS) profiles with non-uniformally hydrated atomic models." ; sc:featureList edam:operation_3453 ; sc:name "AquaSAXS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lorentz.dynstr.pasteur.fr/aquasaxs.php" ; biotools:primaryContact "Poitevin F." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_3263, edam:topic_3308 ; sc:citation , "pmcid:PMC9825501", "pubmed:36243967" ; sc:description "A spatial omics database and analysis platform." ; sc:featureList edam:operation_0247, edam:operation_0314, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Aquila" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://aquila.cheunglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3384 ; sc:citation ; sc:description "Novel automatic muscle artifact reduction method for ictal EEG interpretation." ; sc:featureList edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "AR2" ; sc:url "https://github.com/shennanw/AR2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0602 ; sc:citation , "pubmed:15094041" ; sc:description "Predicts the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_2492, edam:operation_3439 ; sc:name "Ar_NHPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/ar_nhpred" ; biotools:primaryContact "Dr. G. P. S. Raghava" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_3345 ; sc:author ; sc:contributor "Maciej Szymanski" ; sc:description "An automatic pipeline for exploration of SRA datasets with sequences as a query" ; sc:featureList edam:operation_0253, edam:operation_0292, edam:operation_0338, edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ARA (Automated Record Analysis)" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "https://github.com/maurya-anand/ARA" ; biotools:primaryContact "Wojciech Karlowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3518 ; sc:citation , "pmcid:PMC1934936", "pubmed:17684564" ; sc:description "An \"\"Electronic Fluorescent Pictograph\"\" browser for exploring and analyzing large-scale biological data sets (using example of Arabidopsis). Explores microarray and other data for hypothesis generation. eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets." ; sc:featureList edam:operation_3429 ; sc:name "Arabidopsis eFP Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi" ; biotools:primaryContact "Nicholas Provart" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780 ; sc:citation , "pmcid:PMC4664945", "pubmed:26620795" ; sc:description "Integrated network of Arabidopsis growth regulators." ; sc:featureList edam:operation_3562 ; sc:name "Arabidopsis growth regulators network" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/supplementary_data/ehsab/gene_prioritization/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC155255", "pubmed:11779843" ; sc:description "Program for assembling data from whole genome shotgun sequencing experiments." ; sc:featureList edam:operation_0310 ; sc:name "Arachne" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.broadinstitute.org/computational-rd/computational-research-and-development" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3626 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2013 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3334 ; sc:citation , "pmcid:PMC5393895", "pubmed:28362877" ; sc:description "A simulation environment with simple user interface for analyzing neural and neuroglial networks organisation, optimisation and execution." ; sc:featureList edam:operation_2497, edam:operation_3562, edam:operation_3664 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ARACHNE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/LeonidSavtchenko/Arachne" ; biotools:primaryContact "Leonid Savtchenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0154, edam:topic_3500 ; sc:citation , , "pmcid:PMC2907703", "pmcid:PMC3013666", "pubmed:19674480", "pubmed:21036864" ; sc:description "ArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface." ; sc:featureList edam:operation_0245, edam:operation_0346, edam:operation_3092 ; sc:name "ArachnoServer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.arachnoserver.org" ; biotools:primaryContact "ArachnoServer Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis." ; sc:featureList edam:operation_2945, edam:operation_3629 ; sc:name "ARACNE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE?" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579, edam:format_3603 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3752 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_0780, edam:topic_3298, edam:topic_3382 ; sc:citation , , "pmcid:PMC7721323", "pubmed:33037149" ; sc:description "ARADEEPOPSIS is a software tool that enables plant researchers to non-invasively score plant growth, biomass accumulation and senescence from image data in a highly parallelized, high throughput, yet easy to use manner." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ARADEEPOPSIS" ; sc:softwareHelp ; sc:softwareVersion "1.0", "1.1", "1.2", "1.2.1", "1.3", "1.3.1" ; sc:url "https://github.com/Gregor-Mendel-Institute/aradeepopsis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659 ; sc:citation , "pmcid:PMC373265", "pubmed:14704338" ; sc:description "ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes" ; sc:featureList edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "aragorn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.ansikte.se/ARAGORN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3050 ; sc:citation ; sc:description "arakno is an R package for effective spider nomenclature, distribution and trait data retrieval from online resources. Online open databases are increasing in number, usefulness, and ease of use. There are currently two main global databases exclusive for spiders, the World Spider Catalogue (WSC) and the World Spider Trait (WST) database. Both are regularly used by thousands of researchers. Computational tools that allow effective processing of large data are now part of the workflow of any researcher and R is becoming a de facto standard for data manipulation, analysis, and presentation. Here we present an R package, arakno , that allows interface with the two databases. Implemented tools include checking species names against nomenclature of the WSC, obtaining and mapping data on distribution of species from both WST and the Global Biodiversity Information Facility (GBIF), and downloading trait data from the WST." ; sc:featureList edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "arakno" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=arakno" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1895 ; sc:name "Locus ID (AGI)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_0820 ; sc:citation , "pubmed:12529511" ; sc:description "Plant membrane proteins." ; sc:featureList edam:operation_0224 ; sc:name "ARAMEMNON database of plant membrane proteins" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Botanical Institute University of Cologne" ; sc:softwareHelp ; sc:url "http://aramemnon.botanik.uni-koeln.de/" ; biotools:primaryContact "Rainer Schwacke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0196, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC8574707", "pubmed:34013348" ; sc:description "Accurate long-Reads Assembly correction Method for Indel errorS (ARAMIS) is a NGS long-reads indels correction pipeline that combines several correction software in just one step using accurate short reads. As a proof OF concept, six organisms were selected based on their different GC content, size and genome complexity, and their PacBio-assembled genomes were corrected thoroughly by this pipeline." ; sc:featureList edam:operation_0452, edam:operation_0524, edam:operation_0525, edam:operation_3195 ; sc:name "ARAMIS" ; sc:url "https://github.com/genomics-ngsCBMSO/ARAMIS.git" ; biotools:primaryContact "B Aguado" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0780, edam:topic_3170, edam:topic_3517 ; sc:citation , "pubmed:31642487" ; sc:description "A major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. AraPheno is a public database collection of Arabidopsis thaliana phenotypes." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3283, edam:operation_3431, edam:operation_3557 ; sc:license "MIT" ; sc:name "AraPheno" ; sc:softwareHelp , , , ; sc:url "https://arapheno.1001genomes.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625 ; sc:citation , "pubmed:27862469" ; sc:description "Resource for Arabidopsis thaliana genomics. Araport offers gene and protein reports with orthology, expression, interactions and the latest annotation, plus analysis tools, community apps, and web services" ; sc:featureList edam:operation_0224, edam:operation_0227 ; sc:license "Not licensed" ; sc:name "Araport" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.araport.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3360, edam:topic_3517 ; sc:author ; sc:citation , "pubmed:27995664" ; sc:description """AraQTL is the A.thaliana workbench and database for eQTL analysis. It allows easy access to the data of all published Arabidopsis thaliana genetical genomics experiments.""" ; sc:featureList edam:operation_0224, edam:operation_0282, edam:operation_3232 ; sc:name "AraQTL" ; sc:softwareVersion "1.0" ; sc:url "https://www.bioinformatics.nl/AraQTL" ; biotools:primaryContact "Basten L. Snoek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0769 ; sc:citation , "pmcid:PMC10027432", "pubmed:36752514" ; sc:description "A graph-based modular reasoning tool for translational biomedicine." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "ARAX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://arax.rtx.ai" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084 ; sc:citation , , "pmcid:PMC390282", "pubmed:14985472" ; sc:description "The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria" ; sc:featureList edam:operation_0259, edam:operation_0260, edam:operation_0278, edam:operation_0287, edam:operation_0289, edam:operation_0291, edam:operation_0294, edam:operation_0326, edam:operation_0346, edam:operation_0349, edam:operation_0368, edam:operation_0371, edam:operation_0492, edam:operation_0496, edam:operation_0558, edam:operation_0567, edam:operation_3080, edam:operation_3081 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "ARB" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "6.0.6" ; sc:url "http://arb-home.de" ; biotools:primaryContact "ARB Users Mailing List" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "ARBic is an All-Round Biclustering Algorithm for Analyzing Gene Expression Data. Identifying significant biclusters of genes with specific expression patterns is an effective approach to reveal functionally correlated genes in gene expression data. However, existing algorithms are limited to finding either broad or narrow biclusters but both due to failure of balancing between effectiveness and efficiency. ARBic can accurately identify any meaningful biclusters of shape no matter broad or narrow in a large scale gene expression data matrix, even when the values in the biclusters to be identified have the same distribution as that the background data has. ARBic is developed by integrating column-based and row-based strategies into biclustering procedure. The column-based strategy borrowed from ReBic, a recently published biclustering tool, prefers to narrow bicluters." ; sc:featureList edam:operation_3463, edam:operation_3501 ; sc:license "MIT" ; sc:name "ARBic" ; sc:url "https://github.com/holyzews/ARBic" ; biotools:primaryContact "Guojun Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation , , "pmcid:PMC8352505", "pubmed:33216122" ; sc:description "ARBitR is an overlap aware genome assembly scaffolder for linked sequencing reads. It is used for merging and scaffolding an existing genome assembly. It takes a position sorted read alignment file in the bam/sam format with 10X Chromium barcodes in the BX tag, and if additionally provided with the genome fasta file used for mapping, it will sort and merge the provided contigs into scaffolds. A key functionality is the possibility to resolve links between contigs by overlap-layout-consensus (OLC) instead of indiscriminately inserting a gap between them." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "ARBitR" ; sc:url "https://github.com/markhilt/ARBitR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation , "pubmed:24990605" ; sc:description "Pipeline for automated retrieval of all sequences for a specified gene from GenBank." ; sc:featureList edam:operation_0349, edam:operation_2422 ; sc:name "ARBitrator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.jzehrlab.com/nifh" ; biotools:primaryContact "Jonathan P. Zehr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation , "pubmed:30445495" ; sc:description """efficient and scalable inference of gene regulatory networks. Usage Example — arboreto 0.1.5 documentation. Free document hosting provided by Read the Docs.""" ; sc:featureList edam:operation_2437 ; sc:license "BSD-3-Clause" ; sc:name "Arboreto" ; sc:softwareHelp ; sc:softwareVersion "0.1.5" ; sc:url "http://arboreto.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3056 ; sc:citation , "pmcid:PMC3668358", "pubmed:23640720" ; sc:description "Scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories." ; sc:featureList edam:operation_0324, edam:operation_2495 ; sc:name "Arboretum" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://pages.discovery.wisc.edu/~sroy/arboretum/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "ARC is a pipeline which facilitates iterative, reference guided de novo assemblies." ; sc:featureList edam:operation_0310 ; sc:name "ARC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.4-beta" ; sc:url "http://ibest.github.io/ARC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3068, edam:topic_3318, edam:topic_3393 ; sc:citation , "pmcid:PMC7921781", "pubmed:33665184" ; sc:description "Academic Resources Platform for COVID-19 The Academic Resources for COVID-19 (ARC) is an online platform to match equipment, consumables, reagents and other critical resources needed by Swiss diagnostic laboratories involved in combating the Sars-CoV-2 virus with Swiss academic groups who are able and willing to provide them." ; sc:featureList edam:operation_2421, edam:operation_2428, edam:operation_3799 ; sc:name "ARC" ; sc:url "http://arc.epfl.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation , "pmcid:PMC2872004", "pubmed:20453003" ; sc:description "Light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.It is a viewer, not an editor: this means a simpler interface, offering multiple perspectives on the same data, with a focus on navigation. It translates text-based descriptions of biological networks into standardized diagrams. 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sc:citation , "pmcid:PMC3606041", "pubmed:23519672" ; sc:description "A program for building macromolecular models from crystallograpgic data. 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Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3179, edam:topic_3365, edam:topic_3518 ; sc:citation , "pmcid:PMC441584", "pubmed:15215429" ; sc:description "ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. 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One and two color array platforms are supported." ; sc:featureList edam:operation_2428 ; sc:license "GPL-2.0" ; sc:name "arrayQualityMetrics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/arrayQualityMetrics.html" ; biotools:primaryContact "Audrey Kauffmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0199, edam:topic_0203, edam:topic_0622 ; sc:citation , "pmcid:PMC3436589", "pubmed:22722935" ; sc:description "An application for gene expression and variant analysis. It enables analyzing a variety of experimental data." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2495, edam:operation_3197, edam:operation_3352 ; sc:name "ArrayStar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dnastar.com/t-sub-products-genomics-arraystar.aspx" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3572 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "This package is designed to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. It generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases." ; sc:featureList edam:operation_0313 ; sc:license "GPL-2.0" ; sc:name "ArrayTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ArrayTools.html" ; biotools:primaryContact "Arthur Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0208, edam:topic_2840, edam:topic_3518 ; sc:citation "pubmed:14630514" ; sc:description "This tool provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. Specifically, it is MIAME (Minimum Information About A Microarray Experiment)-supportive for storing both microarray data and experiment parameters associated with a pharmacogenomics or toxicogenomics study." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3431 ; sc:name "ArrayTrack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/" ; biotools:primaryContact "Weida Tong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3516, edam:topic_3572 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "Wave correction for genotyping and copy number arrays." ; sc:featureList edam:operation_2428 ; sc:license "GPL-2.0" ; sc:name "ArrayTV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ArrayTV.html" ; biotools:primaryContact "Eitan Halper-Stromberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3518 ; sc:citation "pubmed:15215430", "pubmed:15980549" ; sc:description "Web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams." ; sc:featureList edam:operation_0335, edam:operation_2497, edam:operation_3432 ; sc:name "ArrayXPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.snubi.org/software/ArrayXPath/" ; biotools:primaryContact "Ju Han Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0804, edam:topic_3511 ; sc:citation , "pubmed:26249808" ; sc:description "This tool is designed to enable a deep understanding of antigen receptor sequences with a cascade of algorithms and databases." ; sc:featureList edam:operation_0415, edam:operation_2575 ; sc:name "ARResT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.bat.infspire.org/arrest/assignsubsets/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_2814, edam:topic_3047, edam:topic_3307 ; sc:description "ArrestinDb is dedicated to arrestin proteins, which like G proteins, are major GPCR transducers but also have their own highly active research community." ; sc:isAccessibleForFree true ; sc:name "ArrestinDb" ; sc:url "https://arrestindb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3168, edam:topic_3295 ; sc:citation , "pmcid:PMC4283580", "pubmed:25599564" ; sc:description "Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay." ; sc:featureList edam:operation_3435 ; sc:license "Artistic-2.0" ; sc:name "ARRmNormalization" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ARRmNormalization.html" ; biotools:primaryContact "Jean-Philippe Fortin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3307 ; sc:citation , "pmcid:PMC3233989", "pubmed:22060410" ; sc:description "This software calculates asymptotic and robust regressions corresponding to the constant and linear asymptotic regression models." ; sc:featureList edam:operation_3659 ; sc:name "ARRP" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/software/program.html?uid=3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2275, edam:topic_3542 ; sc:citation , "pubmed:21887824" ; sc:description "Method of calculating side-chain aromatic chemical shifts from protein structures." ; sc:featureList edam:operation_0267, edam:operation_2479 ; sc:name "ArShift" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-sidechain.ch.cam.ac.uk/ArShift/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pmcid:PMC3278762", "pubmed:22199392" ; sc:description "ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD" ; sc:featureList edam:operation_3434 ; sc:license "GPL-3.0" ; sc:name "ART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3421 ; sc:citation , "pubmed:33611053" ; sc:description "ART-Net (Augmented Reality Tool Network) is a integrated lightweight framework for tool detection, segmentation, and 3D pose estimation from a laparoscopic image." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3553 ; sc:name "ART-Net" ; sc:url "https://github.com/kamruleee51/ART-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3295, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC7249449", "pubmed:32456667" ; sc:description "ARTDeco is a pipeline for analyzing and characterizing transcriptional readthrough. ARTDeco functions to process a set of BAM files such that transcriptional readthrough can be quantified via a variety of measures including read-in levels, readthrough levels, downstream of gene (DoG) transcript detection, and inference of read-in genes. ARTDeco can also correct gene expression values by using read-in levels to deconvolute native gene expression and contribution from upstream readthrough transcription. ARTDeco works on both single-end and paired-end data, stranded and unstranded data, and forward and reverse strand oriented data." ; sc:featureList edam:operation_2495, edam:operation_3222, edam:operation_3223, edam:operation_3629, edam:operation_3799 ; sc:license "MIT" ; sc:name "ARTDeco" ; sc:url "https://github.com/sjroth/ARTDeco" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1465 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "RNA structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1493 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "RNA structure alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0097, edam:topic_0099, edam:topic_0654, edam:topic_0659, edam:topic_3307, edam:topic_3511 ; sc:author "Davyd Bohdan" ; sc:citation , , "pmcid:PMC10484739", "pubmed:37471030" ; sc:description """ARTEM is a tool for the superposition of two arbitrary RNA 3D structure fragments. ARTEM doesn’t rely on sequence similarity, annotated interactions, or backbone topology. Instead, ARTEM assumes at least one residue-residue match has a close-to-zero RMSD in the ideal superposition. Then, ARTEM tries all N*M single-residue matches and derives a subset of mutually closest residues as the matches for each of the single-residue-based superpositions. Finally, ARTEM returns the superpositions ordered by their size, letting the user choose the best one based on any specific requirements. ARTEM can read/write both PDB and mmCIF format.""" ; sc:featureList edam:operation_0503, edam:operation_0509 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ARTEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "version 2.0" ; sc:url "https://github.com/david-bogdan-r/ARTEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation , , , , "pmcid:PMC2606163", "pmcid:PMC3278759", "pubmed:11120685", "pubmed:12846394", "pubmed:18845581", "pubmed:22199388" ; sc:description "Free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation." ; sc:featureList edam:operation_3208 ; sc:name "Artemis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sanger.ac.uk/science/tools/artemis" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1459 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Nucleic acid structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1459 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Nucleic acid structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1459 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Nucleic acid structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0888 ; sc:encodingFormat edam:format_2330 ; sc:name "Structure similarity score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1482 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid structure alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0097, edam:topic_0099, edam:topic_0102, edam:topic_0654, edam:topic_3307, edam:topic_3511 ; sc:citation , , "pmcid:PMC11472068", "pubmed:39258540" ; sc:description "a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment" ; sc:featureList edam:operation_0503, edam:operation_2518 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ARTEMIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "version 1.5" ; sc:url "https://github.com/david-bogdan-r/ARTEMIS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:name "Database metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "The Arthropoda Assembly Assessment Catalogue is a database of metadata and assembly quality metrics for all Arthropod assemblies on the NCBI" ; sc:featureList edam:operation_0310 ; sc:name "Arthropoda Assembly Assessment Catalogue" ; sc:url "https://evofunvm.dcsr.unil.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0611, edam:topic_3452 ; sc:citation , "pmcid:PMC9667824", "pubmed:36251681" ; sc:description "An Electron Tomography Toolbox for the Interactive Handling of Sub-Tomograms in UCSF ChimeraX." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ArtiaX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FrangakisLab/ArtiaX" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2182 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author , ; sc:description "A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore" ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ARTIC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.1.0-rc2" ; sc:url "https://github.com/artic-network/fieldbioinformatics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC9202890", "pubmed:35709137" ; sc:description "Artifact3-D offers a suite of functions for analysing 3D scans of archaeological artifacts. These functions are repeatable, objective, precise, and customizable." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Artifact3-D" ; sc:operatingSystem "Windows" ; sc:url "https://sourceforge.net/projects/artifact3-d/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3299, edam:topic_3474 ; sc:description "New Artificial Landscape for Single-Objective Problems" ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "New Artificial Landscape for Single-Objective Problems" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/65130-new-artificial-landscape-for-single-objective-problems" ; biotools:primaryContact "Seyed Muhammad Hossein Mousavi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3315, edam:topic_3382 ; sc:citation ; sc:description "Artistoo (Artificial Tissue Toolbox, formerly called CPMjs) is a framework that lets you build interactive, explorable simulation models of cells and tissues in the web browser." ; sc:featureList edam:operation_2426, edam:operation_3802 ; sc:license "MIT" ; sc:name "Artistoo" ; sc:url "https://artistoo.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , "pmcid:PMC3492150", "pubmed:23145042" ; sc:description "The Analysis of Replication Timing and Organization tool uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. It takes raw time of replication (ToR) measurement signals as input and outputs for each genomic location an estimate of its ToR and an association to CTR (constant ToR region) or TTR (Temporal Transition Region)." ; sc:featureList edam:operation_2403 ; sc:name "ARTO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:citation , "pmcid:PMC2907250", "pubmed:20460509" ; sc:description "Adaptive Rank Truncated Product is an R package for analyzing pre-defined genetic pathway based on a genetic association study." ; sc:featureList edam:operation_2497 ; sc:name "ARTP2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://dceg.cancer.gov/tools/analysis/artp" ; biotools:primaryContact "Division of Cancer Epidemiology and Genetics (DCEG), NCI", "Han Zhang", "Kai Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2885 ; sc:citation , , "pmcid:PMC1538835", "pubmed:16204124", "pubmed:16845038" ; sc:description "ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_2422, edam:operation_3196 ; sc:name "ARTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/ARTS/" ; biotools:primaryContact "ARTS team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3293, edam:topic_3336 ; sc:citation , "pmcid:PMC8728217", "pubmed:34718689" ; sc:description "ARTS-DB is an online repository of precomputed results of Antibiotic Resistant Target Seeker (ARTS), a rapid genome mining tool for the exploration of antibiotics with interesting and novel targets. ARTS-DB supports two main searching functionalities." ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3482 ; sc:name "ARTS-DB" ; sc:softwareHelp ; sc:url "https://arts-db.ziemertlab.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0780 ; sc:citation , "pmcid:PMC5570205", "pubmed:28472505" ; sc:description "Antibiotic Resistant Target Seeker. Specific and efficient genome mining for antibiotics with interesting and novel targets. Automate the screening of large amounts of sequence data and to focus on the most promising strains that produce antibiotics with new modes of action. It integrates target directed genome mining methods, antibiotic gene cluster predictions and ‘essential gene screening’ to provide an interactive page for rapid identification of known and putative targets in BGCs." ; sc:featureList edam:operation_0224, edam:operation_3482 ; sc:license "GPL-3.0" ; sc:name "ARTS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "https://arts.ziemertlab.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC8329541", "pubmed:34330087" ; sc:description "ARTS is a fully automated biomarker that outputs a score linked to the likelihood a person suffers from arteriolosclerosis based on brain MRI data (3D T1w, T2w FLAIR, DTI data) and basic demographic information (age at MRI, sex). The higher the ARTS score, the higher the likelihood of arteriolosclerosis." ; sc:featureList edam:operation_2238, edam:operation_2421, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "ARTS" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://www.nitrc.org/projects/arts/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0781, edam:topic_2830, edam:topic_3948, edam:topic_3966 ; sc:author "ICMR-National Institute of Virology" ; sc:citation ; sc:description "ArVirInd is a knowledge-base of Arbo-Viral proteins from India and its neighbourhood. his is a annotated database, which acts as a repository of Protein sequences for arbo-viruses along with antigenic information. Users can search for protein sequences by virus / protein name or by country of origin (India and countries of the Indian subcontinent: Nepal, Bhutan, Bangladesh, SriLanka, Pakistan) and year of collection (that is, the year of outbreak which defines the origin of the strain)." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "ArVirInd" ; sc:url "http://www.arvirind.co.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3342, edam:topic_3473 ; sc:citation , , "pmcid:PMC7729909", "pubmed:33303746" ; sc:contributor ; sc:description """ARX is a comprehensive open source software for anonymizing sensitive personal data. It supports a wide variety of (1) privacy and risk models, (2) methods for transforming data and (3) methods for analyzing the usefulness of output data. The software has been used in a variety of contexts, including commercial big data analytics platforms, research projects, clinical trial data sharing and for training purposes. 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ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. 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The pipeline first extracts germline, CDR canonical structure, isoelectric point and frequent positional motifs features from sequences and creates an antibody feature fingerprint. Machine-learning and statistical significance testing are applied to antibody sequences and feature fingerprints to identify distinguishing feature values and combinations thereof. 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sc:citation , "pubmed:12354655" ; sc:description "Discriminates aa substitutions with high and low probabilities of occurrence." ; sc:featureList edam:operation_2451 ; sc:name "ASaturA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/ASaturA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3168, edam:topic_3308 ; sc:citation "pubmed:21080965" ; sc:description "Empirical Bayes method to detect differential expression based on sequencing technology." ; sc:featureList edam:operation_2238, edam:operation_3695, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "ASC" ; sc:softwareHelp ; sc:url "http://www.stat.brown.edu/Zwu/research.aspx" ; biotools:primaryContact "Bethany D Jenkins", "LeAnn P Whitney", "Mak A Saito", "Melissa Mercier", "Sonya T Dyhrman", "Tatiana A Rynearson", "Zhijin Wu" . a sc:SoftwareApplication ; 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sc:license "Not licensed" ; sc:name "ASC-G4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://tiny.cc/ASC-G4" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_2885, edam:topic_3421, edam:topic_3519 ; sc:citation , "pmcid:PMC7188954", "pubmed:32391349" ; sc:description "AScall is a web tool providing automatic processing of allele specific real-time PCR experiments: variation conducted real-time whereis each allele is detected by independent reaction separated into individual wells. The positive outcome of the reaction for a particular allele is judged by the increase in the fluorescent signal." ; sc:featureList edam:operation_0308, edam:operation_0337, edam:operation_0484, edam:operation_3196 ; sc:license "MIT" ; sc:name "AScall" ; sc:url "http://shtest.evrogen.net/AScall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:33508309" ; sc:description "aScan is a software tool for the determination of allele-specific-expression at the single individual level from matched RNA-Seq and genomic data." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "aScan" ; sc:url "https://github.com/Federico77z/aScan/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_2640, edam:topic_3320 ; sc:citation , "pmcid:PMC9825479", "pubmed:36318242" ; sc:description "A comprehensive knowledgebase of alternative splicing in human cancers." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-3.0" ; sc:name "ASCancer Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/ascancer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0634, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC10562615", "pubmed:37822561" ; sc:description "Positional feature annotation and protein structure-based representation of single amino acid variations." ; sc:featureList edam:operation_0331 ; sc:isAccessibleForFree true ; sc:name "ASCARIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://huggingface.co/spaces/HUBioDataLab/ASCARIS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:encodingFormat edam:format_2333 ; sc:name "Raw microarray data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_3574 ; sc:citation , "pmcid:PMC2947907", "pubmed:20837533" ; sc:description "Tool for accurate dissection of genome-wide allele-specific copy number in tumors. It accounts for normal cell admixture and tumor aneuploidy in the analysis of SNP array data from cancer samples. It allows analysis of Illumina and Affymetrix SNP array data of tumor samples (with or without matching germline samples)." ; sc:featureList edam:operation_3208, edam:operation_3233 ; sc:name "ASCAT" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "UiO" ; sc:softwareHelp , ; sc:softwareVersion "2.4" ; sc:url "https://www.crick.ac.uk/peter-van-loo/software/ASCAT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation , , "pmcid:PMC6735844", "pubmed:31505654" ; sc:description "scRNA-seq analysis toolkit (R package) for quality control, normalization, dimensionality reduction, clustering and differential expression." ; sc:featureList edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ascend" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/IMB-Computational-Genomics-Lab/ascend" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3067, edam:topic_3306, edam:topic_3379 ; sc:citation , "pmcid:PMC8423288", "pubmed:34492004" ; sc:description "ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds). A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves." ; sc:featureList edam:operation_2426, edam:operation_2428, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ASCENT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wmglab-duke/ascent" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3398 ; sc:citation , "pmcid:PMC9617685", "pubmed:36325307" ; sc:description "Automated Selection of Changepoints using Empirical P-values and Trimming (ASCEPT), to select an optimal set of changepoints in mobile health data" ; sc:featureList edam:operation_3192, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ASCEPT" ; sc:url "https://github.com/matthewquinn1/changepointSelect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation ; sc:description "ASCoVPred is a machine learning-based platform for quantitative prediction of anti-SARS-CoV-2 activity and human cell toxicity of molecules. ASCoVPred is a collection of compounds descriptors / fingerprints (FPs) calculator tool (PaDEL v2.21) and different machine learning (ML) algorithms (implemented in Weka v3.8.2) that are used to build the ML-based quantitative structure-activity relationship (QSAR) prediction models. These QSAR models can be used for ML-assisted prediction of anti-SARS-CoV-2 activity and human cell toxicity of compounds." ; sc:featureList edam:operation_3799 ; sc:name "ASCoVPred" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://14.139.62.220/ascovpred/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0154, edam:topic_0209, edam:topic_0634 ; sc:citation , "pmcid:PMC3013650", "pubmed:21051350" ; sc:description "AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area." ; sc:featureList edam:operation_0224, edam:operation_0250, edam:operation_2414 ; sc:name "ASD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mdl.shsmu.edu.cn/ASD/" ; biotools:primaryContact "ASD Support", "Jian Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3474 ; sc:citation , "pmcid:PMC10311404", "pubmed:37387128" ; sc:description "Genome-wide scans for selective sweeps using convolutional neural networks." ; sc:featureList edam:operation_0451, edam:operation_1812, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "ASDEC" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/pephco/ASDEC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workbench" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3407, edam:topic_3512 ; sc:citation , "pmcid:PMC7591752", "pubmed:33173536" ; sc:description "ASDmiR is a step-wise method to uncover miRNA regulation related to autism spectrum disorder. MiRNAs (miRNAs) are involved in nervous system developmental, and have potential to cause ASD. However, the miRNA regulation mechanism in ASD is largely unclear. In this work, we present a novel framework, ASDmiR, to identify miRNA-target networks and modules, miRNA sponge networks and modules for uncovering the pathogenesis of ASD, as well as conduct enrichment analysis." ; sc:featureList edam:operation_0463, edam:operation_1781, edam:operation_2436, edam:operation_3792 ; sc:license "GPL-3.0" ; sc:name "ASDmiR" ; sc:url "https://github.com/chenchenxiong/ASDmiR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384 ; sc:citation , "pubmed:36449588" ; sc:description "Semi-supervised medical image segmentation using adversarial consistency learning and dynamic convolution network." ; sc:featureList edam:operation_3927 ; sc:license "Not licensed" ; sc:name "ASE-Net" ; sc:url "https://github.com/SUST-reynole/ASE-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation , "pmcid:PMC3394258", "pubmed:22600735" ; sc:description "R package to predict lysine sites that can be acetylated by a specific KAT-family." ; sc:featureList edam:operation_0417 ; sc:license "GPL-3.0" ; sc:name "ASEB" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ASEB.html" ; biotools:primaryContact "Likun Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3168, edam:topic_3320 ; sc:citation , "pmcid:PMC1160168", "pubmed:15980562" ; sc:description "Tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs." ; sc:featureList edam:operation_0264, edam:operation_2499 ; sc:name "ASePCR" ; sc:url "http://genome.ewha.ac.kr/ASePCR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_3170, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description "Animal Sex Reversal database." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0544, edam:operation_3223 ; sc:name "ASER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://aser.ihb.ac.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_3168, edam:topic_3305, edam:topic_3810 ; sc:citation , "pmcid:PMC6935939", "pubmed:31694969" ; sc:description """Rapid Sequence-Based Characterization of African Swine Fever Virus by Use of the Oxford Nanopore MinION Sequence Sensing Device and a Companion Analysis Software Tool. https://www.ncbi.nlm.nih.gov/pubmed/?term=31694969. O'Donnell VK, Grau FR, Mayr GA, Sturgill Samayoa, Dodd KA, Barrette RW., RAPID SEQUENCE-BASED CHARACTERIZATION OF AFRICAN SWINE FEVER VIRUS USING THE OXFORD NANOPORE MINION SEQUENCE SENSING DEVICE AND A COMPANION ANALYSIS SOFTWARE TOOL. J Clin Microbiol. 2019 Nov 6. pii: JCM.01104-19. doi: 10.1128/JCM.01104-19. Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Plum Island Animal Disease Center, New York.""" ; sc:featureList edam:operation_0310, edam:operation_3185, edam:operation_3200, edam:operation_3211 ; sc:license "MIT" ; sc:name "ASF-FAST" ; sc:url "https://github.com/rwbarrette/ASFV_MinION_RapidAssembler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0160, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:34133282" ; sc:description "Protein Fold Recognition based on Evolutionary Features with Variable Parameters using Full Connected Neural Network." ; sc:featureList edam:operation_0303, edam:operation_3936, edam:operation_3937 ; sc:name "ASFold-DNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Bioinformatics-Laboratory/project/tree/master/ASFold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation ; sc:description "A web server for the development of customized scoring functions in the field of protein docking." ; sc:featureList edam:operation_3891, edam:operation_3899, edam:operation_3938 ; sc:name "ASFP" ; sc:softwareHelp ; sc:url "http://cadd.zju.edu.cn/asfp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0199, edam:topic_3056, edam:topic_3796 ; sc:citation , "pmcid:PMC7159030", "pubmed:32294195" ; sc:description "The African Swine Fever Virus Database (ASFVdb) is an integrative resource for genomic and proteomic analyses of African swine fever virus." ; sc:featureList edam:operation_2421, edam:operation_2489, edam:operation_3208 ; sc:name "ASFVdb" ; sc:url "http://asfvdb.popgenetics.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3336, edam:topic_3373, edam:topic_3379, edam:topic_3577 ; sc:citation , "pmcid:PMC9945835", "pubmed:36813801" ; sc:description "Using scRNA-seq data, Asgard repurposes drugs and predicts personalized drug combinations to address the cellular heterogeneity of patients." ; sc:featureList edam:operation_3223, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ASGARD" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/lanagarmire/ASGARD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053 ; sc:citation , "pubmed:25558046" ; sc:description "The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA)." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "ASGSCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ASGSCA.html" ; biotools:primaryContact "Hela Romdhani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3169, edam:topic_3940 ; sc:citation , , "pmcid:PMC7708071", "pubmed:33074315" ; sc:description "A method for allele-specific modeling of diploid Hi-C data (chromatin contacts and structures) using hierarchical Bayesian modeling." ; sc:featureList edam:operation_0487, edam:operation_3435, edam:operation_3557 ; sc:name "ASHIC" ; sc:url "https://github.com/wmalab/ASHIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , "pmcid:PMC8504637", "pubmed:33792647" ; sc:description "Automated Selection of High quality Libraries for the Extensive analYsis of Strandseq data (ASHLEYS) is an automated quality control for single-cell Strand-seq data." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_0487, edam:operation_2428 ; sc:license "MIT" ; sc:name "ASHLEYS" ; sc:url "http://github.com/friendsofstrandseq/ashleys-qc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0623, edam:topic_0659 ; sc:citation , , , , "pmcid:PMC1160207", "pubmed:11751222", "pubmed:11847076", "pubmed:15130931", "pubmed:15980557" ; sc:description "Server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_1781, edam:operation_2495, edam:operation_3659 ; sc:name "ASIAN" ; sc:url "http://eureka.cbrc.jp/asian/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3172 ; sc:citation ; sc:description "Automatic Statistical Identification in Complex Spectra quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty." ; sc:featureList edam:operation_3214, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "ASICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ASICS.html" ; biotools:primaryContact "Gaëlle Lefort" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC2447810", "pubmed:18480122" ; sc:description "Design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. 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The alternative splicing in livestock animals database (ASlive.org) is a collection of alternative splicing events across tissues in livestock animal speceis in including cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa), chickens (Gallus gallus) and horses (Equus Caballus).""" ; sc:featureList edam:operation_0264, edam:operation_2421, edam:operation_3799 ; sc:name "ASlive" ; sc:url "http://ASlive.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3300, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:37000299" ; sc:description "Novel computational tool for prediction of abiotic stress-responsive long non-coding RNAs in plants." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "ASLncR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://iasri-sg.icar.gov.in/aslncr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "ASLPrep is a robust preprocessing pipeline for Arterial Spin Labeling data. ASLPrep is a Arterial Spin Labeling (ASL) data preprocessing and Cerebral Blood FLow (CBF) computation pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "ASLPrep" ; sc:softwareHelp ; sc:url "https://pennlinc.github.io/aslprep_paper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3401, edam:topic_3444 ; sc:citation , "pmcid:PMC6690842", "pubmed:31406952" ; sc:description "Imaging Clinically Relevant Pain States Using Arterial Spin Labeling | The Center for Functional Neuroimaging at the University of Pennsylvania provides unification for currently distributed medical center efforts in physiological and clinical brain imaging and advance the general interests of the brain imaging community through targeted methods development, symposia and colloquia, handling of regulatory issues, and fund-raising efforts | Updated manual, ASL MoCo code, and asl_perf_subtract.m. Major new features include: | asl_perf_subtract.m has been updated with new parameters (T1b, T2wm, Rwm-blood) from the latest literature. CBF quantification for PASL using voxelwise M0 value has been updated. Please see the document therein for the details | Made a new version for SPM12. Major new features include: | 1) wraper functors for most of the processing steps," ; sc:featureList edam:operation_3799 ; sc:name "ASLtbx" ; sc:softwareHelp ; sc:url "https://cfn.upenn.edu/~zewang/ASLtbx.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "Cconverts the Celera ASM assembly format to the Consed ACE or the CAF file format." ; sc:featureList edam:operation_0310, edam:operation_0335 ; sc:name "asm2ace" ; sc:operatingSystem "Linux" ; sc:softwareVersion "0.6" ; sc:url "http://sourceforge.net/projects/asm2ace/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_0634, edam:topic_3172, edam:topic_3360 ; sc:citation , "pmcid:PMC10218045", "pubmed:37239321" ; sc:description "Integrative method for identifying key biomarkers from multi-omics data." ; sc:featureList edam:operation_0314, edam:operation_3891, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "asmbPLS-DA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RunzhiZ/asmbPLS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640, edam:topic_3170, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC8728259", "pubmed:34664666" ; sc:description "Allele-Specific DNA Methylation Databases (ASMdb) is a comprehensive database for allele-specific DNA methylation in diverse organisms. ASMdb is aiming to provide a comprehensive resource and a web tool for showing the DNA methylation level and differential DNA methylation in diverse organisms." ; sc:featureList edam:operation_3186, edam:operation_3192, edam:operation_3206, edam:operation_3207, edam:operation_3919 ; sc:name "ASMdb" ; sc:url "http://www.dna-asmdb.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3300, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:36939943" ; sc:description "Machine learning framework for prediction of abiotic stress-specific miRNAs in plants." ; sc:featureList edam:operation_0463, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "ASmiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://iasri-sg.icar.gov.in/asmir/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_2815, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC441542", "pubmed:15215376" ; sc:description "Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes." ; sc:featureList edam:operation_0310, edam:operation_0477, edam:operation_0526, edam:operation_2499 ; sc:name "ASmodeler" ; sc:url "http://genome.ewha.ac.kr/ECgene/ASmodeler/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3516 ; sc:citation , "pmcid:PMC4690232", "pubmed:26705468" ; sc:description "Software for discovery, genotyping and characterization of structural variants." ; sc:featureList edam:operation_3202 ; sc:name "AsmVar" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bioinformatics-centre.github.io/AsmVar/" ; biotools:primaryContact "Shujia Huang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC4609008", "pubmed:25028722" ; sc:description "An ASP-based method for finding attractors in genetic regulatory networks." ; sc:featureList edam:operation_1781 ; sc:name "ASP-G" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Musthofa_2014/asp-g.zip" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:name "Mathematical model" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2585 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3071 ; sc:citation , "pmcid:PMC5315406", "pubmed:28158307" ; sc:description "A toolkit for constructing statistical models for biological processes. 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It takes as input a list of composite parts described in terms of their basic part composition." ; sc:featureList edam:operation_0310 ; sc:name "assemblyManager" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://andersonlab.qb3.berkeley.edu/#/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "This series of scripts calculates various metrics on an input FASTA file. 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It employs a Bayesian factor analysis approach to adapt predetermined pathway signatures derived from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. 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SNPs may be called using the Atlas-SNP2 application and indels may be called using the Atlas-Indel2 application." ; sc:featureList edam:operation_3227 ; sc:license "BSD-3-Clause" ; sc:name "Atlas Suite" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.hgsc.bcm.edu/software/atlas-2" ; biotools:primaryContact "Fuli Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3304, edam:topic_3384 ; sc:citation , "pubmed:31491525" ; sc:description "Construction of a rat spinal cord atlas of axon morphometry | Scripts to generate a microstructure atlas of the rat spinal cord | Pipeline for generating spinal cord atlas from electron microscopy | This pipeline is designed to generate an atlas of the spinal cord based on electron microscopy images. The output is a 4D nifti volume containing metrics obtained from scanning electron microscopy | One slice corresponds to one spinal level: C1, C2, ... C8, T1, ...T13, L1, ... L6, S1, ... 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sc:name "B-NEM" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MartinFXP/B-NEM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """The bio2byte tools server (b2btools) offers the following single protein sequence based predictions: - Backbone and sidechain dynamics (DynaMine) - Helix, sheet, coil and polyproline-II propensity - Early folding propensity (EFoldMine) - Disorder (DisoMine) - Beta-sheet aggregation (Agmata) In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA""" ; sc:featureList edam:operation_0267, edam:operation_3092, edam:operation_3904 ; sc:name "b2bTools" ; sc:url "https://www.bio2byte.be/b2btools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3047, edam:topic_3332, edam:topic_3374 ; sc:citation , "pmcid:PMC8556334", "pubmed:34716354" ; sc:description "Blood-Brain Barrier Database (B3DB) is a curated diverse molecular database of blood-brain barrier permeability with chemical descriptors." ; sc:featureList edam:operation_3431, edam:operation_3659, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "B3DB" ; sc:url "https://github.com/theochem/B3DB" ; biotools:primaryContact "Paul W. Ayers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3304, edam:topic_3334, edam:topic_3374, edam:topic_3930 ; sc:citation , "pubmed:34269889" ; sc:description "B3Pdb: a database of blood-brain barrier-penetrating peptides." ; sc:featureList edam:operation_0224, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "B3Pdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://webs.iiitd.edu.in/raghava/b3pdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0804, edam:topic_3304, edam:topic_3374, edam:topic_3474 ; sc:citation ; sc:description "In silico tool for predicting and designing Blood-Brain Barrier Penetrating Peptides." ; sc:featureList edam:operation_3631 ; sc:name "B3pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://webs.iiitd.edu.in/raghava/b3pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3292 ; sc:citation , "pmcid:PMC2748086", "pubmed:19723314" ; sc:description "A tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families." ; sc:featureList edam:operation_2990 ; sc:name "The B6 Database (B6DB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PARMA" ; sc:softwareHelp ; sc:url "http://bioinformatics.unipr.it/B6db" ; biotools:primaryContact "Riccardo Percudani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0611, edam:topic_3315 ; sc:citation , "pmcid:PMC7232674", "pubmed:31486672" ; sc:description "A Novel Bayesian Network Structural Learning Algorithm and Its Comprehensive Performance Evaluation Against Open-Source Software | Structural learning of Bayesian networks (BNs) from observational data has gained increasing applied use and attention from various scientific and industrial areas. The mathematical theory of BNs and their optimization is well developed. Although there are several open-source BN learners in the public domain, none of them are able to handle both small and large feature space data and recover network structures with acceptable accuracy. bAIcis® is a novel BN learning and simulation software from BERG. It was developed with the goal of learning BNs from \"Big Data\" in health care, often exceeding hundreds of thousands features when research is conducted in genomics or multi-omics. This article provides a comprehensive performance evaluation of bAIcis and its comparison with the open-source BN learners" ; sc:name "bAIcis" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31486672" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pmcid:PMC5408793", "pubmed:27694198" ; sc:description "Tool for the prediction of promoters in cyanobacteria and Escherichia coli." ; sc:featureList edam:operation_0440 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "bTSSfinder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.cbrc.kaust.edu.sa/btssfinder" ; biotools:primaryContact "Ilham Ayub Shahmuradov", "Vladimir B. Bajic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0625, edam:topic_2269 ; sc:citation , "pubmed:31647543" ; sc:description "An R package that enables users to efficient fit and cross-validate Bayesian and likelihood whole-genome regression methods." ; sc:featureList edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "bWGR" ; sc:url "https://cran.r-project.org/package=bWGR" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pubmed:34058399" ; sc:description "A web tool for generating Bland-Altman plots and constructing limits of agreement." ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BA-plotteR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://huygens.science.uva.nl/BA-plotteR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3169, edam:topic_3572 ; sc:citation , "pmcid:PMC5326502", "pubmed:28235418" ; sc:description "This package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele-specific events. It is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples." ; sc:featureList edam:operation_2478 ; sc:license "Artistic-2.0" ; sc:name "BaalChIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BaalChIP.html" ; biotools:primaryContact "Ines de Santiago" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3954 ; sc:citation , "pubmed:37155375" ; sc:description "An open-source application for prospective modeling of transcranial focused ultrasound for neuromodulation applications." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "BabelBrain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://proteusmrighifu.github.io/BabelBrain" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:name "ID list" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:name "Raw microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:name "Ontology" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_2259, edam:topic_3071, edam:topic_3172, edam:topic_3308, edam:topic_3517 ; sc:citation , "pmcid:PMC4489263", "pubmed:25897133" ; sc:description "Integrative platform for the analysis of Transcriptomics, Proteomics and Genomics data with advanced functional profiling. It integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods." ; sc:featureList edam:operation_0277, edam:operation_0313, edam:operation_2495, edam:operation_3463, edam:operation_3501, edam:operation_3559 ; sc:name "Babelomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Computational Genomics Department. Prince Felipe Research Center (CIPF)", "cipf.es", "http://bioinfo.cipf.es" ; sc:softwareHelp , ; sc:softwareVersion "5" ; sc:url "http://babelomics.bioinfo.cipf.es/" ; biotools:primaryContact "babelomics@cipf.es (Francisco García)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3125, edam:topic_3169 ; sc:citation , "pubmed:17888037" ; sc:description "This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments." ; sc:featureList edam:operation_3501 ; sc:license "Artistic-2.0" ; sc:name "BAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BAC.html" ; biotools:primaryContact "Raphael Gottardo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0203, edam:topic_3168 ; sc:citation , "pmcid:PMC4377007", "pubmed:25652236" ; sc:description "R-based graphical tool to concisely visualise and compare biological annotations queried from the DAVID web service." ; sc:featureList edam:operation_0361, edam:operation_2451 ; sc:license "GPL-3.0" ; sc:name "BACA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/BACA/" ; biotools:primaryContact "Vittorio Fortino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0798, edam:topic_3305, edam:topic_3673 ; sc:citation ; sc:description "BacAnt is a consolidation tool for finding the Resistance genes, Insertion elements and Transposon regions from genome sequences. It provide curated database for transfer elements search and annotation." ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3482 ; sc:name "BacAnt" ; sc:softwareHelp ; sc:url "http://bacant.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3524 ; sc:citation , "pmcid:PMC5460873", "pubmed:28531184" ; sc:description "Modeling framework for cellular communities in their environments. Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques." ; sc:featureList edam:operation_3660 ; sc:name "BacArena" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cran.r-project.org/web/packages/BacArena/index.html" ; biotools:primaryContact "Johannes Zimmermann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_3168, edam:topic_3174, edam:topic_3301 ; sc:citation ; sc:description "A Comprehensive and Interactive Web-Resource to Discern Antibiotic Resistance Gene Diversity in –Omics Datasets." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "BacARscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://proteininformatics.org/mkumar/bacarscan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3379 ; sc:citation , "pmcid:PMC7033354", "pubmed:32095660" ; sc:description "An online platform for clinical back-averaging. The back-average technique is very useful to study the relation between the activity in the cortex and the muscles." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "BacAv" ; sc:url "https://electrophysiology.shinyapps.io/BacAv/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:encodingFormat edam:format_3464 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2912 ; sc:encodingFormat edam:format_1964 ; sc:name "Strain accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_2376, edam:format_3464 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3720 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Geographic location" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0912 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Nucleic acid property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "NCBI taxonomy ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3719 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Biosafety classification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3718 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Pathogenicity report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1872 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Taxonomic classification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3721 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Isolation source" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Data reference" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3723 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Morphology parameter" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2912 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Strain accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3722 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Physiology parameter" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Molecular property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1097 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "Sequence accession (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3050, edam:topic_3301, edam:topic_3339 ; sc:citation , , , , , , "pmcid:PMC3965005", "pmcid:PMC4702946", "pubmed:24214959", "pubmed:26424852", "pubmed:28487186" ; sc:description "Provides strain-linked information about bacterial and archaeal biodiversity. The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. 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BacDive is the Bacterial Diversity Metadatabase and provides strain-linked information about bacterial and archaeal biodiversity. The web-service offers several possibilities to query detailed strain information. It allows the retrieval by genus, species and/or subspecies, a given culture collection number or an INSDC accession number." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "BacDive WS" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH", "bacdive" ; sc:softwareHelp , ; sc:url "http://bacdive.dsmz.de/api/bacdive/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Plug-in", "Script", "Web service" ; sc:applicationSubCategory edam:topic_3301 ; sc:citation ; sc:description "The DSMZ's Bacterial Diversity Metadatabase (BacDive) focuses on providing organism-linked information covering the multifarious aspects of bacterial biodiversity: taxonomic classification, morphology, physiology, cultivation, origin natural habitat and more, both for bacterial and archaeal strains. BacDiveR helps you investigate this data offline, and semi-automatically in R." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BacDiveR: A Programmatic Interface For BacDive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , ; sc:softwareVersion "0.7.0" ; sc:url "https://tibhannover.github.io/BacDiveR/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0623, edam:topic_0821, edam:topic_3301 ; sc:citation , "pmcid:PMC7283322", "pubmed:32518231" ; sc:description "BacEffluxPred is a SVM based 2-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins and their sub-families." ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_3482 ; sc:isAccessibleForFree true ; 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biotools:primaryContact , "Andrea Pierleoni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation ; sc:description "This server allows to use the BACHSCORE tool with the aim of discriminating the best model of a protein (the native state or a structure very similar to it) among a large set of alternative conformations." ; sc:featureList edam:operation_2406 ; sc:license "GPL-3.0" ; sc:name "BACH Bayesian Analysis Conformation Hunt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://bachserver.pd.infn.it/" ; biotools:primaryContact "Antonio Trovato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0637, edam:topic_3174, edam:topic_3300, edam:topic_3944 ; 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BAlaS is interactive and intuitive to use. Results are displayed directly in the browser for the structure being interrogated enabling their rapid inspection. BAlaS has broad applications in areas, such as drug discovery and protein-interface design." ; sc:featureList edam:operation_0248, edam:operation_0321, edam:operation_3907 ; sc:license "MIT" ; sc:name "BAlaS" ; sc:url "https://balas.app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_1317 ; sc:citation , "pmcid:PMC2394813", "pubmed:18094476" ; sc:description "A system for solving protein structures using x-ray crystallographic data." ; sc:featureList edam:operation_0322 ; sc:isAccessibleForFree true ; sc:name "BALBES" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/balbes/balbes.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0219, edam:topic_3321 ; sc:citation "pubmed:18831786" ; sc:description "An ORF (Open Reading Frame) annotation approach, in which classifiers are constructed from the class specific expression patterns discovered by bicluster analysis. 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BALDR includes protein, gene and disease data from major public repositories, text-mining data and human and mouse experimental data from the IMI2 RHAPSODY consortium. These data are provided as easy-to-read figures and tables enabling direct comparison of up to 20 biomarker candidates for diabetes." ; sc:featureList edam:operation_0306, edam:operation_2436, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "BALDR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://baldr.cpr.ku.dk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2182 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_2330 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3170 ; sc:citation ; sc:description "Pipeline for reconstructing human or rhesus macaque immunoglobulin(Ig)/B cell receptor(BCR) sequences from single cell RNA-Seq data generated by Illumina sequencing" ; sc:featureList edam:operation_0524 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BALDR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bosingerlab.com/baldr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293 ; sc:citation , , , , "pmcid:PMC1853084", "pmcid:PMC4155473", "pubmed:16012107", "pubmed:16679334", "pubmed:17359539", "pubmed:24866534" ; sc:description "Markov chain Monte Carlo software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters). 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It enables the assessment of multiple non-synonymous single nucleotide polymorphisms (nsSNPs) in a single protein by visualizing the mutated residues within the wild type structure, collecting available pathogenicity information from different databases, predicting binding pockets, protein stability changes and pathogenicity, as well as performing a cluster analysis on comprised amino acid substitutions." ; sc:featureList edam:operation_2487 ; sc:name "BALL-SNPgp" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.ccb.uni-saarland.de/?page_id=1127" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0091, edam:topic_0769, edam:topic_2275, edam:topic_3307 ; sc:citation , , "pubmed:25183489" ; sc:description "Galaxy-based workflow toolkit for structural bioinformatics." ; sc:featureList edam:operation_3431, edam:operation_3760 ; sc:name "ballaxy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ball-project.org/ballaxy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC4792117", "pubmed:25748911" ; sc:description "Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation." ; sc:featureList edam:operation_2238, edam:operation_3258 ; sc:license "Artistic-2.0" ; sc:name "ballgown" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ballgown.html" ; biotools:primaryContact "Jack Fu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0203, edam:topic_0621, edam:topic_3125, edam:topic_3174 ; sc:citation ; sc:description "Balrog is a prokaryotic gene finder based on a Temporal Convolutional Network." ; sc:featureList edam:operation_0362, edam:operation_0477, edam:operation_2454 ; sc:license "MIT" ; sc:name "Balrog" ; sc:url "https://github.com/salzberg-lab/Balrog" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2534 ; sc:name "Sequence attribute" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Extract and plot Lorenz and Coverage stats directly derived from bam files" ; sc:featureList edam:operation_0258 ; sc:name "bam-lorenz-coverage" ; sc:softwareVersion "v2.3.0" ; sc:url "https://github.com/yhoogstrate/bam-lorenz-coverage" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2572 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """The purpose of this program is to generate metrics at single nucleotide positions. 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sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Convert BAM format to SAM format." ; sc:featureList edam:operation_0335 ; sc:name "bam_to_sam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.3" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , ; sc:description "Converts a list of BAM format files to SAM format." ; sc:featureList edam:operation_0335 ; sc:name "bam_to_sam_parallel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0199 ; sc:citation , "pmcid:PMC3051333", "pubmed:21278191" ; sc:description "Variant detector and graphical alignment viewer for SAM/BAM format data." ; sc:featureList edam:operation_0361, edam:operation_2421, edam:operation_3184, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Bambino" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/NCIP/cgr-bambino" ; biotools:primaryContact "National Cancer Institute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC314292", "pubmed:14707177" ; sc:description "An algorithm for scaffolding genome assemblies. It enables the use of linking data and allows the user to control the scaffolding parameters." ; sc:featureList edam:operation_0292, edam:operation_3216, edam:operation_3436 ; sc:name "Bambus" ; sc:operatingSystem "Linux" ; sc:softwareVersion "Bambus 2" ; sc:url "http://www.cbcb.umd.edu/software/bambus/" ; biotools:primaryContact "Info CBCB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3407 ; sc:citation , "pmcid:PMC6612884", "pubmed:31510676" ; sc:description "Bayesian metabolic flux analysis reveals intracellular flux couplings | Bayesian metabolic flux analysis | Bayesian Metabolic Flux Analysis MATLAB package by Markus Heinonen, Maria Osmala, Henrik Mannerström, Juho Rousu, Samuel Kaski and Harri Lähdesmäki from the CSB research group of Aalto University" ; sc:featureList edam:operation_2238, edam:operation_2940, edam:operation_3660 ; sc:name "BaMFA" ; sc:url "http://github.com/markusheinonen/bamfa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3071, edam:topic_3572 ; sc:citation , "pubmed:26363028" ; sc:description "Checksum program for verifying the integrity of sequence data." ; sc:featureList edam:operation_2409 ; sc:name "BamHash" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/DecodeGenetics/BamHash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Bamkit is a collection of tools for common BAM file manipulations" ; sc:featureList edam:operation_2409 ; sc:license "MIT" ; sc:name "bamkit" ; sc:url "https://github.com/hall-lab/bamkit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3169 ; sc:citation , "pmcid:PMC6030882", "pubmed:29846656" ; sc:description """de-novo motif discovery and regulatory sequence analysis. Discovery of regulatory motifs with higher-order Bayesian Markov Models (BaMMs)""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_3501 ; sc:license "AGPL-3.0" ; sc:name "BaMM" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "https://bammmotif.mpibpc.mpg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3056 ; sc:citation , "pmcid:PMC4184259", "pubmed:24974206" ; sc:description "Software that allows to create a multidimensional scaling (MDS) plot of populations for genetic data." ; sc:featureList edam:operation_0337 ; sc:name "bammds" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://dna.ku.dk/~sapfo/bammds.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0749, edam:topic_0769 ; sc:author ; sc:citation , "pmcid:PMC8087283", "pubmed:33936358" ; sc:description "BaMORC (Bayesian Model Optimized Reference Correction) is designed to facilitate protein NMR research with an easy-to-use tool that detects and corrects 13C referencing errors before and after the protein resonance assignment step." ; sc:featureList edam:operation_3215 ; sc:license "BSD-3-Clause" ; sc:name "BaMORC" ; sc:softwareHelp , ; sc:url "https://moseleybioinformaticslab.github.io/BaMORC/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3170, edam:topic_3922, edam:topic_3930 ; sc:citation , "pmcid:PMC10426134", "pubmed:37582761" ; sc:description "Proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens." ; sc:featureList edam:operation_0252, edam:operation_3223, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BamQuery" ; sc:url "http://bamquery.iric.ca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3169, edam:topic_3170, edam:topic_3295 ; sc:citation , , "pmcid:PMC7175505", "pubmed:32321568" ; sc:description "BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3222, edam:operation_3435, edam:operation_3799 ; sc:name "BAMscale" ; sc:url "https://github.com/ncbi/BAMscale" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:description "Large file viewer for BAM and SAM alignment files." ; sc:featureList edam:operation_0564 ; sc:license "GPL-3.0" ; sc:name "BAMseek" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://code.google.com/archive/p/bamseek/" ; biotools:primaryContact "Bamseek issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3574 ; sc:citation , "pmcid:PMC6019789", "pubmed:29940842" ; sc:description "The BAM Search Infrastructure - is a tool for extracting data from the 1000 Genomes phase 3 set of mapped reads (BAM files). It is a filtering tool - subsets of the ~60TB data can be specied and downloaded via the browser, with no need to download the entire data set." ; sc:featureList edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "BAMSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bamsi.research.it.uu.se/" ; biotools:primaryContact "Carl Nettelblad" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_1921 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data." ; sc:featureList edam:operation_2478 ; sc:license "GPL-2.0" ; sc:name "bamsignals" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/bamsignals.html" ; biotools:primaryContact "Alessandro Mammana" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC8055225", "pubmed:33416869" ; sc:description "BamSnap is a lightweight command-based visualization tool for sequencing reads in BAM files." ; sc:featureList edam:operation_0337, edam:operation_0564, edam:operation_3198 ; sc:license "MIT" ; sc:name "BamSnap" ; sc:softwareHelp ; sc:url "https://github.com/parklab/bamsnap" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; 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sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC6003146", "pubmed:29902968" ; sc:description "Dynamic programming in a band is well suited to the problem of aligning long reads between themselves and can be used as a core component of methods for obtaining a consensus sequence from the long reads alone." ; sc:featureList edam:operation_0496, edam:operation_3195 ; sc:name "BAND_DYN_PROG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://forgemia.inra.fr/jean-francois.gibrat/BAND_DYN_PROG" ; biotools:primaryContact "Jean-François Gibrat" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:author "Ryan Wick" ; sc:citation , "pmcid:PMC4595904", "pubmed:26099265" ; sc:contributor "Elmar Pruesse", "Justin Zobel", "Kathryn Holt", "Mark Schultz", "Rayan Chikhi" ; 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Sayers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3308 ; sc:citation , "pubmed:38413725" ; sc:description "A Spatial Omics Algorithm that Unifies Cell Type Clustering and Tissue Domain Segmentation." ; sc:featureList edam:operation_3223, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "BANKSY" ; sc:url "https://github.com/prabhakarlab/Banksy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3337, edam:topic_3474, edam:topic_3517 ; sc:citation ; sc:description "Biologically Annotated Neural Networks (BANNs), a novel probabilistic framework that makes machine learning fully amenable for GWA applications. 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With BAR 3.0 and a sequence you can annotate when possible: function, structure, protein domains. Also if your sequence falls into a cluster with a structural/some structural template/s we provide an alignment towards the template/templates based on the Cluster-HMM that allows you to directly compute your 3D model. 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Sequence annotation is derived from UniProtKB, GO, Pfam and PDB. 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BAR-Seq pipeline is a strategy for clonal tracking of cells harboring homology-directed targeted integration of a barcoding cassette.BAR-Seq can be applied to most editing strategies." ; sc:featureList edam:operation_3096, edam:operation_3695, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "BAR-Seq" ; sc:softwareHelp ; sc:url "http://www.bioinfotiget.it/barseq" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:name "Resource metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation , "pmcid:PMC4463510", "pubmed:25407005" ; sc:description "A freely available catalogue describing expertise and molecular analysis resources available at centers and companies in Sweden for analysis of biobanked samples." ; sc:featureList edam:operation_2421 ; sc:name "BARC" ; sc:provider "bils.se" ; sc:url "http://barcdb.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_3293 ; sc:citation "pubmed:7882153" ; sc:description "Encodes a multiple alignment according to the method developed by Véronique Barriel (C.R.Acad.Sci.III 317(7):693-701).From a an existing alignment (which will not be changed) BARCOD builds a character matrix suitable for use in phylogeny recontstruction programs. The method allows to encode each insertion/deletion event as one single event (whatever the number of nucleotides involved), while retaining any indel common to two or more taxa as a possibly shared character." ; sc:featureList edam:operation_0492 ; sc:name "BARCOD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://wwwabi.snv.jussieu.fr/public/Barcod/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3168, edam:topic_3345 ; sc:description "The program generates barcodes for sequences suitable for Illumina sequencing." ; sc:featureList edam:operation_0231, edam:operation_0364, edam:operation_2403, edam:operation_3200 ; sc:name "Barcode generator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://comailab.genomecenter.ucdavis.edu/index.php/Barcode_generator" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3452, edam:topic_3511 ; sc:citation ; sc:description "A tool to generate unique, orthogonal genetic tags for qPCR detection. barCoder is a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode “modules” that consist of binding sites for primers and probes and appropriate spacer sequences." ; sc:featureList edam:operation_0308, edam:operation_3200, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "barCoder" ; sc:url "https://github.com/ECBCgit/Barcoder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3168, edam:topic_3421, edam:topic_3500 ; sc:citation ; sc:description "barcodetrackR is an R package developed for the analysis and visualization of clonal tracking data from cellular barcoding experiments." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799, edam:operation_3891 ; sc:license "CC0-1.0" ; sc:name "barcodetrackR" ; sc:url "https://dunbarlabNIH.github.io/barcodetrackR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC6034344", "pubmed:29976145" ; sc:description "It is a web tool for selecting an optimal set of barcode sequences. User must provide a set of candidate barcodes from which the defined number of barcodes is selected." ; sc:featureList edam:operation_2425 ; sc:name "BARCOSEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ekhidna2.biocenter.helsinki.fi/barcosel/" ; biotools:primaryContact "Panu Somervuo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_3168 ; sc:citation , "pmcid:PMC2777893", "pubmed:19874596" ; sc:description "Design of barcoded primers, for multiplexed high-throughput sequencing." ; sc:featureList edam:operation_0227, edam:operation_2409, edam:operation_3200, edam:operation_3237 ; sc:license "GPL-3.0" ; sc:name "Barcrawl Bartab" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.phyloware.com/Phyloware/XSTK.html" ; biotools:primaryContact "Daniel N. Frank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3382, edam:topic_3512 ; sc:citation ; sc:description "The bardensr (barcode dexmixing through non-negative spatial regression) package is a collection of tools for modeling linearly multiplexed observations. 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Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. 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Using these tools you can perform several common tasks such as doing BLAST alignments, getting the open reading frames of the sequences in a Fasta file or changing the format of a Fasta file. All these task make use of several known tools such as EMBOSS, bedtools, and NCBI's BLAST, Splign and Compart." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BLAST DataBase Manager" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0.2" ; sc:url "http://www.sing-group.org/BDBM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3168, edam:topic_3360, edam:topic_3518 ; sc:citation ; sc:description "BDdb is a comprehensive database associated with birth-defect-related diseases. 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Lun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0622, edam:topic_0797, edam:topic_3301 ; sc:citation , "pmcid:PMC4539851", "pubmed:26283419" ; sc:description "Automated tool for Bacterial GEnome Annotation ComparisON." ; sc:featureList edam:operation_0362, edam:operation_3209 ; sc:name "BEACON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbrc.kaust.edu.sa/BEACON/" ; biotools:primaryContact "Contact list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0632 ; sc:description "Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. 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It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. It uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. It includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results." ; sc:featureList edam:operation_0551, edam:operation_3478 ; sc:name "BEAST 2" ; sc:softwareHelp ; sc:softwareVersion "2.5.1" ; sc:url "http://www.beast2.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3293, edam:topic_3316 ; sc:citation ; sc:description "Beastiary is designed for visualising and analysing MCMC trace files generated from Bayesian phylogenetic analyses. Beastiary works in real-time and on remote servers (e.g. a HPC). Its goal is to be a beautiful and simple yet powerful tool for Bayesian phylogenetic inference." ; sc:featureList edam:operation_0323, edam:operation_0337 ; sc:name "Beastiary" ; sc:softwareHelp ; sc:url "https://github.com/Wytamma/beastiary" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293 ; sc:citation , "pmcid:PMC5552126", "pubmed:28796784" ; sc:description "Open source software tool designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform." ; sc:featureList edam:operation_0324 ; sc:name "BEASTling" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/glottobank/BEASTling_paper" ; biotools:primaryContact "Luke Maurits" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2548 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3295 ; sc:citation , "pmcid:PMC4509590", "pubmed:25633503" ; sc:description "Model-based analysis of single-cell methylation data." ; sc:featureList edam:operation_3204 ; sc:license "GPL-3.0" ; sc:name "BEAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BEAT.html" ; biotools:primaryContact "Kemal Akman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_2533 ; sc:citation "pubmed:23723246" ; sc:description "This program evaluates the change in binding affinity between proteins (or protein chains) caused by single-site mutations in their sequence." ; sc:featureList edam:operation_2464, edam:operation_2479 ; sc:name "BeAtMuSiC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://babylone.ulb.ac.be/beatmusic" ; biotools:primaryContact "Dimitri Gilis", "Jean Marc Kwasigroch", "Marianne Rooman", "Yves Dehouck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation , , , "pmcid:PMC3065679", "pmcid:PMC3163573", "pubmed:21278367", "pubmed:21824423" ; sc:description "Software to understand the molecular mechanisms of infectious disease and to identify therapeutic and diagnostic targets via NGS data." ; sc:featureList edam:operation_0337 ; sc:name "BeatsonLab-MicrobialGenomics" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University of Queensland" ; sc:softwareHelp ; sc:url "https://github.com/BeatsonLab-MicrobialGenomics" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC7260831", "pubmed:32471392" ; sc:description "A browser-based tool for the exploration and visualization of RNA-seq data. 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It helps researchers, healthcare professionals and developers in the identification of over 1,200,000 biomedical concepts in text and PubMed abstracts." ; sc:featureList edam:operation_0226 ; sc:name "BECAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ua.pt/software/becas/" ; biotools:primaryContact "José Luis Oliveira" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2548 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3572 ; sc:citation , "pmcid:PMC4999208", "pubmed:27559732" ; sc:description "This tool provides some functions to detect and correct for batch effects in DNA methylation data. Its core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers." ; sc:featureList edam:operation_2425, edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "BEclear" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BEclear.html" ; biotools:primaryContact "Markus Merl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2815, edam:topic_3304 ; sc:citation , "pmcid:PMC5611738", "pubmed:28763057" ; sc:description "Interpreting DNA methylation findings from blood in the context of brain." ; sc:featureList edam:operation_3204 ; sc:name "BECon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://redgar598.shinyapps.io/BECon/" ; biotools:primaryContact "M S Kobor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3345 ; sc:citation ; sc:description "Biological Entity Dictionary. Get and explore mapping between identifiers of biological entities. 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Barrett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068 ; sc:description "Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP)." ; sc:featureList edam:operation_3434 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "bed to protein map" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Convert bedGraph to bigWig file." ; sc:featureList edam:operation_0335 ; sc:name "bedGraphToBigWig" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.encodeproject.org/software/bedgraphtobigwig/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0160 ; sc:citation , "pmcid:PMC3389768", "pubmed:22576172" ; sc:description "BEDOPS is an open-source command-line toolkit that performs efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. 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The end coordinate is computed by inspecting the CIGAR string. 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sc:description "Count the number of intervals in a BAM or BED file (the source) that overlap another BED file (the target)." ; sc:featureList edam:operation_0335 ; sc:name "bedtools_coveragebed_counts" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/arq5x/bedtools3" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_3003 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3168 ; sc:citation , , "pmcid:PMC4213956", "pubmed:25199790" ; sc:description "Calculate a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format." ; 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sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v2.10.0" ; sc:url "https://github.com/arq5x/bedtools6" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , "pmcid:PMC4213956", "pubmed:25199790" ; sc:description "Create a new BAM alignment file based on alignments that overlap (or optionally, those that do not overlap) intervals in another BED file. Example usage would be to cull a BAM file from an exome capture experiment to include on the \"on-target\" alignments." ; sc:featureList edam:operation_0292 ; sc:name "bedtools_intersectbed_bam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/arq5x/bedtools5" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation , , , "pmcid:PMC2832824", "pmcid:PMC4987906", "pubmed:20110278", "pubmed:27137889" ; sc:description "Merge multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files." ; sc:featureList edam:operation_0232 ; sc:name "bedtools_mergebedgraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/arq5x/bedtools7" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , , "pmcid:PMC2832824", "pmcid:PMC4987906", "pubmed:20110278", "pubmed:27137889" ; sc:description "Identify common intervals among multiple, sorted BED files." ; sc:featureList edam:operation_0415 ; sc:name "bedtools_multiintersectbed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/arq5x/bedtools8" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3174, edam:topic_3372 ; sc:citation , "pmcid:PMC6941791", "pubmed:31903447" ; sc:description "BedtoolsR is an R package that provides a convenient wrapper for bedtools functions allowing for the documentation and use of them from within the R programming environment, using standard R data types. It uses the version of bedtools installed on your system, rather than its own version, such that you should be able to use it interchangeably from the command line or within R. It also includes additional functionality including the ability to provide either file paths or R objects as inputs and outputs. 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It is capable of installing sequence databanks, such as: Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl, Fasta and Silva, as well as any files using these formats. In addition, BeeDeeM can install major biological classifications (ontologies), such as NCBI Taxonomy, Gene Ontology, Enzyme and Intepro. BeeDeeM can be used from the command-line or from a graphical user interface. It is cluster ready: use of a job scheduler (e.g. PBS, SLURM), smooth use of cluster structures (e.g. data downloading from Internet-connected nodes vs. data processing on network-isolated nodes). 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Raghava", "Harpreet Kaur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:11934756" ; sc:description "Beta Turn predictions in proteins" ; sc:featureList edam:operation_2945 ; sc:name "betatpred3" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/betatpred3/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_2814 ; sc:citation , "pubmed:15145798" ; sc:description "This software predicts the beta turns and their types in a protein from its amino acid sequence." ; sc:featureList edam:operation_0267 ; sc:name "Betaturns" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/betaturns/" ; biotools:primaryContact "Dr. G.P.S. 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BETS uses elastic net regression and stability selection from bootstrapped samples to infer causal relationships among genes. 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