@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 ; 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 ; 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 "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 "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 ; 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 , "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 , "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_2091 ; sc:name "Accession" ], [ 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_1528 ; sc:name "Protein isoelectric point" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0942 ; sc:name "2D PAGE image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1528 ; sc:name "Protein isoelectric point" ], [ 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 ; 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. It outputs the imputed data in the same dimension and the same log-transformation.""" ; sc:featureList edam:operation_3435, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "2DImpute" ; sc:url "https://github.com/zky0708/2DImpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0634, edam:topic_3382 ; sc:citation , "pmcid:PMC7011505", "pubmed:32064000" ; sc:description "A toolkit for content-based local image search." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "2DKD" ; sc:url "http://github.com/kiharalab/2DKD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3314, edam:topic_3318 ; sc:citation , "pubmed:36480578" ; sc:description "The 2D semiconductor database (2DSdb) provides an ideal platform for computational modeling and design of new 2D semiconductors and heterostructures in photocatalysis, nanoscale devices, and other applications." ; sc:license "CC-BY-4.0" ; sc:name "2DSdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://materialsdb.cn/2dsdb/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:name "Raw image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_1317 ; sc:citation ; sc:description "A software system designed as a user friendly, platform-independent software package for electron crystallography." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "2DX" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.2dx.unibas.ch/" . 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_3053 ; sc:citation "pubmed:25344498" ; sc:description "Algorithm that searches graphs produced from the de novo assembler cortex." ; sc:featureList edam:operation_0484, edam:operation_2421, edam:operation_3225 ; sc:name "2kplus2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/danmaclean/2kplus2" ; biotools:primaryContact "Team MacLean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0798, edam:topic_3512 ; sc:citation , "pmcid:PMC7549647", "pubmed:32138598" ; sc:description "2lpiRNApred is a 2-layer integrated program for identifying piRNAs in the first layer and determining if piRNAs have the function of instructing target mRNA deadenylation in the second layer." ; sc:featureList edam:operation_3936, edam:operation_3937 ; sc:name "2lpiRNApred" ; sc:url "https://github.com/JianyuanLin/2lpiRNApred" . 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_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing." ; sc:featureList edam:operation_0232, edam:operation_0335, edam:operation_3198, edam:operation_3258, edam:operation_3695 ; sc:license "MIT" ; sc:name "2passtools" ; sc:url "https://github.com/bartongroup/2passtools" . 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, edam:topic_0749, edam:topic_2269, edam:topic_3299 ; sc:citation , "pmcid:PMC7191778", "pubmed:32349677" ; sc:description """2SigFinder implements multiscale statistical algorithm to predict genomic islands from a single genome. It uses small-scale test with large-scale features to score small region deviating from the host and large-scale statistical test with small-scale features to identify multi-window segments for identification of genomic islands. 2SigFinder is a novel prediction method, the first combined use of small-scale and large-scale statistical testing for genomic island detection. 2SigFinder was tested by genomic island boundary detection and identification of genomic islands or functional features of real biological data. 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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. Related to bio.tools/fossilj.""" ; sc:featureList edam:operation_3443 ; sc:name "3DSlicer" ; sc:softwareHelp ; sc:url "https://www.slicer.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3382 ; sc:citation , "pubmed:30886414" ; sc:description "Creates high-quality 3D/4D animations using a natural-language based syntax." ; sc:featureList edam:operation_0250, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "3Dscript" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://imagej.net/3Dscript" ; biotools:primaryContact "Benjamin Schmid" . 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_3768 ; sc:encodingFormat edam:format_3508, edam:format_3603 ; sc:name "Clustered expression profiles" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3751 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3308 ; sc:author , , "Dimitri MEISTERMANN", "Philippe Bordron" ; sc:citation , , , , , , , , , "pmcid:PMC5291739", "pmcid:PMC5676863", "pmcid:PMC5783949", "pmcid:PMC5797797", "pmcid:PMC7284977", "pubmed:28194440", "pubmed:29116112", "pubmed:29367672", "pubmed:29445370", "pubmed:32438566" ; sc:contributor ; sc:description """A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis. This 3’ Digital gene expression sequencing technique allows a precise and low-cost transcriptome profiling. The main steps of the pipeline are: - Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample. - Alignment on refseq reference transcriptome is performed using bwa. - Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix. If secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2. - If DEG are found, annotation is performed using the database GO and KEGG. - A report is provided listing the main quality controls performed and the results found. Cite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1""" ; 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 , "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 , "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 ; 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 ; 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 "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 "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. 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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 "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_1522 ; sc:name "Protein sequence hydropathy plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1520 ; sc:name "Peptide hydrophobic moment" ] ; 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 "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 , "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 , "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_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; 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 ; 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 "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 "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 "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 , "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 "pubmed:20513649" ; sc:description "3DLigandSite is a web server for the prediction of ligand binding sites. 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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 ; 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" ; 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 ; 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 , "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 , , "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 , "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 , "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 , "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 ; 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 ; 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 , "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 ; 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 ; 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 , "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 , "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 , "pmcid:PMC7077848", "pubmed:32134915" ; 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", "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 ; 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 , "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 ; 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 ; 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 ; 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 , "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 , "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 , "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 , "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 , ; 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 , "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 , ; 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 ; 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 , "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 ; 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 , "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 ; 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 ; 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 , "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 ; 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 , "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 ; 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 ; 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 ; 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 , "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 , "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 , "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 , "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_1731 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Ontology concept definition" ], [ 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_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 , "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 ; 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 , , , , ; 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 ; 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. 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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 , "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 , ; 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 , "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 ; 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_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ], [ 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:author ; sc:citation , ; 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 , "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_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 ; 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 ; 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 , "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 ; 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 , "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 , "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_1860 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "QTL map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1288 ; sc:encodingFormat edam:format_1975 ; sc:name "Genome 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 ; 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 , "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 , "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 ; 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_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 ; 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 ; 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 ; 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 , , "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 , "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 , "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 , "pubmed:31691385" ; sc:contributor ; sc:description """An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Clinical Genome & Ancestry Report (CGAR) enables users to identify and prioritize phenotype-associated variants from genome sequencing with a user-friendly and interactive online platform.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3675 ; sc:name "Clinical Genome and Ancestry Report (CGAR)" ; sc:softwareHelp ; sc:url "https://tom.tch.harvard.edu/apps/cgar/" ; biotools:primaryContact "Sek-Won Kong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pubmed:31443042" ; sc:description "Developing the Web Server for CpG Island related Density and LAUPs (Lineage-associated Underrepresented Permutations) Study | WA web server for CpG Island study:CpG Island related density and LAUPs (Lineage-associated Underrepresented Permutations) analysis" ; sc:featureList edam:operation_0430, edam:operation_0440, edam:operation_3431 ; sc:name "CGIDLA" ; sc:url "http://www.combio-lezhang.online/cgidla/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC6700431", "pubmed:31400611" ; sc:description "Genetic Interaction-Based Biomarkers Identification for Drug Resistance and Sensitivity in Cancer Cells | Cancer cells generally harbor hundreds of alterations in the cancer genomes and act as crucial factors in the development and progression of cancer | However, detection of genetic interactions in the cancer genome is a major obstacle in the research of identifying biomarkers for cancer cell drug resistance and sensitivity" ; sc:featureList edam:operation_3501 ; sc:name "CGIdb" ; sc:url "http://www.medsysbio.org/CGIdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0196, edam:topic_3542 ; sc:citation , "pubmed:31860059" ; sc:description "A contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm." ; sc:featureList edam:operation_0476, edam:operation_0481, edam:operation_3454 ; sc:name "CGLFold" ; sc:url "https://github.com/iobio-zjut/CGLFold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:31704313" ; sc:description """Splice sites detection using chaos game representation and neural network. Email: hoangthanhtungvn@gmail.com. Project description: We propose to use chaos game representation and neural network for splice sites detection. DNA sequences are mapped to numerical sequences using chaos game representation. Numerical sequences are used as feature inputs to neural networks for splice sites classification""" ; sc:featureList edam:operation_0232, edam:operation_0446, edam:operation_2871 ; sc:name "CGR" ; sc:url "https://github.com/thoang3/portfolio/tree/SpliceSites_ANN_CGR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3068 ; sc:author "Ramil Nugmanov" ; sc:citation , "pubmed:31063394" ; sc:description "Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing | CGRs, molecules and reactions manipulation." ; sc:featureList edam:operation_0394, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "CGRtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cimm-kzn/CGRtools" ; biotools:primaryContact "Alexandre Varnek", "Ramil Nugmanov", "Timur Madzhidov" . 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_0153 ; sc:citation , , , , "pubmed:18351591", "pubmed:25130509", "pubmed:26631602", "pubmed:30525595" ; sc:description "Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans." ; sc:featureList edam:operation_0417, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CHARMM-GUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.charmm-gui.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199 ; sc:citation , "pmcid:PMC6323790", "pubmed:30616525" ; sc:description "Computing Homozygosity Enriched Regions In genomes to Prioritize Identification of Candidate variants (CHERIPIC) - tools to pick causative mutation from bulks segregant sequencing." ; sc:featureList edam:operation_0524, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CHERIPIC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.2.6" ; sc:url "https://github.com/shyamrallapalli/cheripic" ; biotools:primaryContact "Shyam Rallapalli" . 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 ; sc:description "An integrated database for Cricetulus griseus and CHO cells" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "CHOmine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0.0" ; sc:url "https://chomine.boku.ac.at/chomine" . 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_3173 ; sc:citation ; sc:description "Web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets." ; sc:featureList edam:operation_0438, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CHiCP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.chicp.org/" ; biotools:primaryContact "O. 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 , "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_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1022 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence feature label" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3750 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_3033 ; sc:name "Nucleic acid 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 , "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 , "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 ; 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 , "pubmed:32384242" ; 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 , "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 ; 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 ; 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 ; 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 , "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 , ; 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 ; 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 ; 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 , "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_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" ], [ 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" ] ; 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 , ; 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_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 ; 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 ; 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 ; 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 , "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 , "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 , "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 ; 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 ; 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 , "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 , , "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 ; 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 , "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_3021 ; sc:encodingFormat edam:format_1963 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_1963 ; sc:name "Gene ID" ] ; 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 "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 , , "pmcid:PMC7145505", "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 , "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 , ; 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 , , "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 ; 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 ; 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 ; 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_0906 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein interaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Expression 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_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ], [ 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_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 , ; 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 , "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_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_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 , ; 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_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 ; 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 , "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 , "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 ; 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 ; 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 ; 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 , "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. This includes a GPU-accelerated image processing pipeline (via TensorFlow), CLI tools for batch processing of experimental replicates (often requiring conditional configuration, as things tend go wrong when capturing hundreds of thousands of microscope images over a period of hours or days), and visualization UIs (either Cytokit Explorer or CellProfiler Analyst) | Med Google Cloud Platform kan du oprette, implementere og skalere apps, websites og tjenester på den samme infrastruktur som Google | Fortsæt til Google Cloud Platform | Skriv den tekst, du hører eller ser" ; sc:featureList edam:operation_3552, edam:operation_3629 ; sc:license "Apache-2.0" ; sc:name "Cytokit" ; sc:url "https://github.com/hammerlab/cytokit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382 ; sc:citation , "pubmed:30520559" ; sc:description """Tool for collaborative multimodal imaging and our latest software developments to support next-generation digital pathology bridged to molecular investigations.""" ; sc:featureList edam:operation_0337, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Cytomine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cytomine.be/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite", "Workflow" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3293 ; sc:citation , "pmcid:PMC6717989", "pubmed:31477170" ; sc:description "Cytoscape Automation combines Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio." ; sc:featureList edam:operation_2497, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "Cytoscape Automation" ; sc:url "http://automation.cytoscape.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_0209, edam:topic_0659 ; sc:citation , "pmcid:PMC6779407", "pubmed:31390943" ; sc:description "A comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression" ; sc:featureList edam:operation_2495, edam:operation_3223 ; sc:name "D-lnc" ; sc:url "http://www.jianglab.cn/D-lnc/" . 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_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation ; sc:description "Identification of differentially-expressed genes in single-cell RNA sequencing data." ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "D3E" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.sanger.ac.uk/science/tools/discrete-distributional-differential-expression-d3e" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6933629", "pubmed:31881937" ; sc:description """a data driven dynamic network construction method to infer gene regulatory networks. Gene regulatory network;Dynamic networks construction;Regression;DREAM challenge. 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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 "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_3768 ; sc:encodingFormat edam:format_3508, edam:format_3603 ; sc:name "Clustered expression profiles" ], [ 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" ] ; 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 , , "pubmed:30977188" ; 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 , "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 , "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_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" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3475 ; sc:name "Expression data" ] ; 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: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 , "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 , "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 , "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 , "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 , "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 , "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 ; 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 , "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_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ 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_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 "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_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; 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 , "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_1772 ; sc:encodingFormat edam:format_2330, edam:format_3464 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_4002 ; sc:name "Mathematical model" ] ; 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 , ; 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 , "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 , "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 , ; 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 , "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 , "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 ; 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 ; 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 ; 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 , "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 ; 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 , "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 , "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 , "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 , "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_0842 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Text data" ] ; 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_3736 ; sc:encodingFormat edam:format_2330 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3706 ; sc:name "Biodiversity data" ] ; bsc:output [ 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" ], [ 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" ] ; 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_3736 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2350 ; sc:name "Ecological data" ], [ 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" ] ; bsc:output [ 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_3108 ; sc:encodingFormat edam:format_2332, edam:format_2350 ; sc:name "Experimental measurement" ], [ 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_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" ] ; 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_1274 ; sc:encodingFormat edam:format_2333 ; sc:name "Map" ], [ 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" ] ; 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_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2333, edam:format_2350 ; sc:name "Image" ] ; 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_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" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579 ; sc:name "Image" ] ; 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_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" ] ; 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 ; 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 , "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 , "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 , "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 , "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 , ; 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 ; 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_3768 ; sc:encodingFormat edam:format_3033 ; sc:name "Clustered expression profiles" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3508 ; sc:name "Image" ] ; 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 , , "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 , "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 dat