nalloNallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly, and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional consequences.https://github.com/genomic-medicine-sweden/nallonallobiotools:nallo0.12.0http://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3295EpigeneticsGroovyJavaMITFree of chargehttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2545FASTQ-like format

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_3462CRAMhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3327BAI

https://github.com/genomic-medicine-sweden/nalloRepositoryhttps://genomic-medicine-sweden.github.io/nallo/latest/User manual10.1093/BIOINFORMATICS/BTAG08641712762PMC12988770Lars Feuklars.feuk@igp.uu.sehttps://orcid.org/0000-0003-2355-2919PersonopenbabelOpen Babel is a chemical toolbox designed to speak the many languages of chemical data.http://openbabel.org/openbabelbiotools:openbabelopenbabel-3-2-0http://edamontology.org/topic_3314Chemistryhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_0081Structure analysisRC#ShellPerlCPythonJavaPHPRubyC++ScalaGPL-2.0Maturehttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0883Structure

http://edamontology.org/data_1463Small molecule structure

http://edamontology.org/data_0883Structure

https://github.com/openbabel/openbabel/wikiGeneralhttps://openbabel.org/docs/index.htmlUser manual10.1186/1758-2946-3-3321982300PMC3198950EGAEuropean genome-phenome Archive (EGA) - service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.https://ega-archive.org/egabiotools:egaWeb APIWeb applicationDatabase portalhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0607Laboratory information managementhttp://edamontology.org/topic_3263Data securityhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacJavaRD-connectRare DiseaseMatureFree of chargeOpen accessDataSpainhttp://edamontology.org/operation_3431Depositionhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/data_2383EGA accession

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

https://ega-archive.org/General10.1038/ng.3312PrimaryEMBL-EBI DatabasesInstituteProviderhelpdesk@ega-archive.orgPersonPrimary contactMetaProteomeAnalyzer-CloudThe MetaProteomeAnalyzer Cloud (MPA Cloud) is an intuitive, open-source tool for metaproteomics data analysis and interpretation, designed to analyse comprehensive metaproteomics data from tandem mass spectrometry experiments through a web interface.https://mdoa-tools.bi.denbi.de/mpacloud/mpa-cloudbiotools:mpa-cloudWeb servicehttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_4060Metaproteomicshttp://edamontology.org/topic_0121ProteomicsJavaTypeScriptGPL-3.0MatureFree of chargeOpen accessGermanyhttps://gitlab.com/mdoa-group/mpa-websiteRepositoryhttps://gitlab.com/mdoa-group/mpa-cloud-serverRepositoryhttps://mdoa-tools.bi.denbi.de/mpacloud/documentationUser manualmetaproteomeanalyzerisNewVersionOfmpa_portableisNewVersionOf10.1038/s41596-020-0368-73285998410.3389/fmicb.2019.0188331474963PMC670742510.1021/acs.analchem.7b0354429215871PMC575722010.1021/pr501246w25660940Kay SchallertDaniel KautznerBenjamin J. SaalfeldProf. Dr.-Ing. Robert HeyerLudwig KnocheMalte BöttcherVirtual Imaging PlatformVIP is a web portal for medical imaging applications. It allows users to access scientific applications as a service (directly through the web browser with no installation required), as well as distributed computing resources in a transparent manner. It exploits the resources available in the biomed virtual organization of the EGI e-infrastructure to offer an open service to researchers worldwide.https://vip.creatis.insa-lyon.frvirtual_imaging_platformbiotools:virtual_imaging_platform3.0.14.6.1Bioinformatics portalJavaCECILL-BEUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_2333Binary formathttps://vip.creatis.insa-lyon.fr/Servicehttps://github.com/virtual-imaging-platform/Source code3.0.1https://hub.docker.com/layers/viplatform/vip-portal/4.6.1/images/sha256-5d47d27c3e285dec287506e2b3c436b343e2c1f92818b7c2cbf39afaed46fbb5Container fileVIP Docker image for development or testing (NOT for production)4.6.1https://github.com/virtual-imaging-platform/VIP-portal/wikiOther10.1109/tmi.2012.222015423014715NP-LikenessNatural Product-likeness calculator v-2.1 : calculates natural product-likeness of small molecules based on open-data of natural products.https://github.com/vcnainala/NP-Likenessnp-likenessbiotools:np-likenessCommand-line toolhttp://edamontology.org/topic_0154Small moleculesJavaLGPL-2.0-or-laterFree of charge10.1186/1471-2105-13-10622607271PMC3436723Primary10.1021/ci700286x18034468MethodKalai Vanii Jayaseelankalai@ebi.ac.ukAndreas TruszkowskiPablo MorenoPeter ErtlChristoph Steinbeckchristoph.steinbeck@uni-jena.deEUCAIM ETL toolsetModular toolchain for an extensible and customizable ETL pipeline that extracts, transforms, and loads clinical data and medical imaging metadata, applying dataset-specific mappings to generate outputs compatible with the EUCAIM Common Data Model (CDM). Its design aims to minimize manual data preparation efforts and facilitate customization and integration with other components, such as data quality assurance tools. Containerized, currently supports input datasets in CSV, JSON, XLSX.https://github.com/EUCAIM/etl-toolset/eetl_toolsetbiotools:eetl_toolset0.1.10.1.20.2.1WorkflowLibraryhttp://edamontology.org/topic_3345Data identity and mappinghttp://edamontology.org/topic_0769WorkflowsWindowsLinuxPythonJavaApache-2.0EUCAIMEmergingFree of chargeOpen access (with restrictions)ToolsSpainhttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_0336Format validationhttps://github.com/EUCAIM/etl-toolset/Repositoryhttps://drive.eucaim.cancerimage.eu/s/zXE4xYDm3x3CWtQGeneralTool documentation (updated)tabular_data_curatorusesEUCAIM Wizard ToolThe EUCAIM Wizard Tool performs an analysis of data re-identification risks of imaging and clinical data that follow the EUCAIM CDM. It includes and uses an EUCAIM specific configuration of the ARX Data Anonymization Tool (biotools:arx), by supporting a wide variety of privacy and risk models as well methods for analyzing the usefulness of output data.https://github.com/cbml-forth/eucaim_wizard_tooleucaim_wizard_toolbiotools:eucaim_wizard_toolbeta1.0Desktop applicationhttp://edamontology.org/topic_3384Medical imaginghttp://edamontology.org/topic_4044Data protectionhttp://edamontology.org/topic_2640OncologyMacWindowsLinuxJavaEUPL-1.2EUCAIMEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3283Anonymisationhttps://github.com/cbml-forth/eucaim_wizard_toolRepositoryhttps://drive.eucaim.cancerimage.eu/s/FYwDc66kXqFRebaUser manualarxincludesarxusesComputational BioMedicine Laboratory, Foundation for Research and Technology Hellas (FORTH)https://www.ics.forth.gr/cbml/?lang=enInstituteProviderKnetMinerA comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is used by scientists in academia and industry to accelerate gene-trait discovery research. KnetMiner offers features such as keyword, gene list, genome region search and GWAS Peak Search. Query refinement, gene ranking, gene set enrichment analysis and interactive visualisation of knowledge networks and genomic information are all core app competencies. KnetMiner also has an AI layer, called Graph Chat (https://knetminer.com/news/graph-chat-announcement), for more easily interpreting created knowledge networks.http://knetminer.comknetminerbiotools:knetminerNovaWeb servicehttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_3068Literature and languagehttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3810Agricultural scienceJavaJavaScriptMITMatureCommercialOpen accessUKhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_2421Database searchhttps://app.knetminer.comServicehttp://knetminer.com/Otherhttps://github.com/KnetMiner/Repositoryhttps://github.com/KnetMiner/User manualNavigate through the various KnetMiner repos for individual pieces of documentation.10.1101/2020.04.02.017004Keywan Hassani-Pakkeywan@knetminer.comhttps://orcid.org/0000-0001-9625-0511PersonFounder & CEOArné de Klerkarne@knetminer.comhttps://www.linkedin.com/in/arnedek/https://orcid.org/0000-0002-9525-6820PersonCo-Founder & Product ManagerMarco Brandizimarco@knetminer.comhttps://orcid.org/0000-0002-5427-2496PersonCo-Founder & Senior Software DeveloperBioMercatorBioMercator 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.https://sourcesup.renater.fr/projects/biomercatorBioMercatorbiotools:BioMercator4.2.3Desktop applicationhttp://edamontology.org/topic_3055Quantitative geneticshttp://edamontology.org/topic_0780Plant biologyLinuxWindowsMacJavaGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_2944Physical mappinghttp://edamontology.org/data_1860QTL maphttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1288Genome maphttp://edamontology.org/format_1975GFF3https://sourcesup.renater.fr/frs/?group_id=2301Binaries4.2.310.1093/bioinformatics/bth230150598203KCFtoolsKCFtools is a Java-based toolkit for rapid, alignment-free introgression screening and GWAS using k-mer profiles. It identifies the presence and absence of k-mers in genomic or transcriptomic windows, enabling efficient detection of introgressed or variable regions and facilitating genotype matrix generation for GWAS.https://github.com/sivasubramanics/kcftoolskcftoolsbiotools:kcftoolshttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3923Genome resequencingJavahttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0310Sequence assembly10.1101/2025.11.01.685998SocialVirusesSocialViruses is a Cytoscape app designed to rationally design phage cocktails by integrating quantitative phage-bacteria and phage-phage interaction networks. The tool optimizes cocktail selection based on host range and virulence while minimizing redundancy and antagonism.https://apps.cytoscape.org/apps/SocialVirusesisocialvirusesbiotools:isocialviruseshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_3303MedicineJavahttp://edamontology.org/operation_3461Virulence predictionhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0479Backbone modelling10.1093/BIOADV/VBAF23941103543PMC12527336Felipe Molinafmolina@unex.eshttps://orcid.org/0000-0002-9167-7097PersonBOLD (Barcode of Life Data Systems)BOLD is a data system for DNA barcode information and species delimitation. It facilitates species identification through DNA barcodes and supports a variety of species delimitation algorithms.http://www.boldsystems.orgboldbiotools:boldhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3500Zoologyhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3489Database managementhttp://edamontology.org/topic_0084PhylogenyJavahttp://edamontology.org/operation_0546Phylogenetic inference (minimum distance methods)http://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3200DNA barcodinghttp://edamontology.org/operation_0415Nucleic acid feature detection10.3897/ZOOKEYS.1229.12912340046838PMC11876984Zhijun Zhouzhijunzhou@163.comhttps://orcid.org/0000-0003-2625-6189PersonEpiFusionUtilitiesEpiFusionUtilities is an R package that provides tools for using the EpiFusion Analysis Framework, a workflow for joint phylodynamic and epidemiological analysis of outbreaks. It complements the EpiFusion software and offers utilities for data preparation, result parsing, analysis, and plotting.https://ciarajudge.github.io/EpiFusionUtilities/epifusionutilitiesbiotools:epifusionutilitieshttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_3324Infectious diseasehttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3397Veterinary medicineRJavahttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/operation_3942Tree datinghttp://edamontology.org/operation_0326Phylogenetic tree editinghttps://github.com/ciarajudge/EpiFusion/releasesSoftware package10.12688/F1000RESEARCH.162719.140469802PMC12134729Ciara Judgeciara.judge@lshtm.ac.ukhttps://orcid.org/0000-0001-7923-9898PersondeepImageJdeepImageJ is a Fiji/ImageJ plugin for bioimage analysis that integrates pre-trained convolutional neural networks and supports diverse deep learning frameworks. It facilitates complex pipeline deployments, 3D image analysis, and compatibility with the BioImage Model Zoo, bridging the gap between advanced deep learning models and practical bioimage analysis workflows.https://bioimage.iobioimagebiotools:bioimagehttp://edamontology.org/topic_3383Bioimaginghttp://edamontology.org/topic_0611Electron microscopyhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3474Machine learningJavahttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3435Standardisation and normalisation10.1017/S2633903X2400011439776608PMC11704127Arrate Muñoz-Barrutiamamunozb@ing.uc3m.eshttps://orcid.org/0000-0002-1573-1661PersonBridgeDbBridgeDb is a framework to map identifiers between various databases. It includes a Java library that provides an API to work with identifier-identifier mapping databases and resources.http://bridgedb.github.io/bridgedbbiotools:bridgedb3.0.18Libraryhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_2840ToxicologyMacLinuxWindowsJavaApache-2.0ProteomicsELIXIR-NLBIGCAT-UMBridgeDbRare DiseaseMatureFree of chargeInteroperabilityNetherlandshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1025Gene identifier

http://edamontology.org/data_1025Gene identifier

API for converting gene identifiers (Ensembl, Entrez) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0989Protein identifier

http://edamontology.org/data_0989Protein identifier

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1086Compound identifier

http://edamontology.org/data_1086Compound identifier

API for converting compound identifiers (HMDB, ChEBI, ChemSpider, PubChem, etc) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.https://github.com/bridgedb/BridgeDbRepositoryhttps://github.com/bridgedb/BridgeDb/issuesIssue trackerhttps://fosstodon.org/@bridgedbSocial mediahttps://bridgedb.github.io/pages/docs.htmlGeneralidentifiers.orgusesbioregistryuses10.1186/1471-2105-11-520047655PMC282467810.1007/978-3-319-11964-9_7Primary10.3897/rio.8.e83031PrimaryMaastricht UniversityInstituteProviderVISTAComprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.http://genome.lbl.gov/vista/index.shtmlvistabiotools:vistaWeb applicationDatabase portalhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacJavaRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/operation_0496Global alignmenthttp://genome.lbl.gov/vista/help.shtmlGeneral10.1093/bioinformatics/btg4591503387010.1093/nar/gkm27917488840PMC193319210.1093/bioinformatics/btg10051285543710.1093/bioinformatics/16.11.10461115931810.1101/gr.78980312529311PMC43096710.1101/gr.92660312654723PMC43015810.1093/nar/gkh45815215394PMC44159610.1093/nar/gkl82217130149PMC1716724Vista SupportVista@lbl.govPersonPrimary contactCopySeqA computational approach for the inference of copy-number genotypes from personal genome sequencing data.http://www.embl.de/%7Ekorbel/CopySeq/copyseqbiotools:copyseqCommand-line toolhttp://edamontology.org/topic_3175DNA structural variationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3577Personalised medicinehttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_0080Sequence analysisLinuxMacJavaRMaturehttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_3233Copy number estimationhttp://edamontology.org/operation_3197Genetic variation analysis10.1371/journal.pcbi.100098821085617PMC2978733GWASToolGWASTool is a web pipeline designed for detecting SNP-phenotype associations, offering a unified framework that simplifies GWAS analysis by encapsulating the heterogeneity of various algorithms and providing tools for simulation, detection, visualization, and comparison.http://www.sdu-idea.cn/GWASToolgwastoolbiotools:gwastoolhttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0769WorkflowsJavahttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/operation_3196Genotyping10.1016/J.FMRE.2024.03.00539660349PMC11630686Guoxian Yugxyu@sdu.edu.cnPersonJun Wangkingjun@sdu.edu.cnPersonProteo VisualizerProteo Visualizer is a Cytoscape app designed to retrieve protein interaction networks from STRING using protein groups as input, allowing visualization and network analysis of MS-based proteomics data.https://apps.cytoscape.org/apps/ProteoVisualizerproteo_visualizerbiotools:proteo_visualizerhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0128Protein interactionsJavahttp://edamontology.org/operation_0276Protein interaction network analysishttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_2422Data retrievalhttps://jensenlab.org/training/proteovisualizer/Training material10.1016/J.MCPRO.2024.10087139486590PMC11667155Marie Locard-Pauletmarie.locard-paulet@ipbs.frPersonLars Juhl Jensenlars.juhl.jensen@cpr.ku.dkPersonFunCoup Cytoscape AppFunCoup Cytoscape App integrates the FunCoup web service API with Cytoscape, allowing users to visualize and analyze gene interaction networks for multiple species. It enables users to input gene identifiers and customize search parameters for various network expansions and provides consistent visualizations with the FunCoup website.https://apps.cytoscape.org/funcoup_cytoscape_appbiotools:funcoup_cytoscape_apphttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_0634PathologyJavahttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3926Pathway visualisation10.1101/2024.10.04.616627GVAFGVAF is a command-line software tool designed for generalized and flexible filtering of annotated variant files, eliminating the need for specialized programming skills or software.https://www.sysbiolab.org/gvafgvafbiotools:gvafhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0769WorkflowsJavaBashhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3675Variant filtering10.1007/S13258-024-01580-039395087PMC11604800Sungwon Jungsjung@gachon.ac.krhttps://orcid.org/0000-0001-6002-554XPersonCytoscape CytoHubbaCytoscape CytoHubba is a plugin for Cytoscape that identifies hub genes within a network. It uses topological algorithms to predict and explore important nodes and subnetworks.https://apps.cytoscape.org/apps/cytohubbacytohubbabiotools:cytohubbahttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3474Machine learningJavahttp://edamontology.org/operation_3927Network analysishttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_3435Standardisation and normalisation10.7759/CUREUS.6588639219951PMC11364490Ramya Ramadossdrramya268@gmail.comPersonCatReNetCatReNet is an open-source Java application for interactive analysis of catalytic reaction networks, providing algorithms for computing autocatalytic subnetworks and dynamic visualizations for understanding complex biochemical systems. It's available on GitHub under a GPL3 license and has been published in Bioinformatics.https://github.com/husonlab/catrenetcatrenetbiotools:catrenethttp://edamontology.org/topic_3307Computational biologyJavaGPL-3.0http://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3927Network analysishttp://edamontology.org/operation_3946Ecological modelling10.1093/BIOINFORMATICS/BTAE51539163485PMC11361791Daniel H Husondaniel.huson@uni-tuebingen.dehttps://orcid.org/0000-0002-2961-604XPersonSeqPHASESeqPHASE is a tool for interconverting PHASE input/output files and FASTA sequence alignments, rewritten in Haxe and hosted on GitHub Pages. It addresses security concerns of the original Perl+CGI version and aims to provide a more modern and maintainable solution for sequence phasing.https://eeg-ebe.github.io/SeqPHASEseqphasebiotools:seqphasehttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_4045Cybersecurityhttp://edamontology.org/topic_3372Software engineeringhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3520Proteomics experimentC++PythonPerlJavaJavaScripthttp://edamontology.org/operation_3454Phasinghttp://edamontology.org/operation_0292Sequence alignmenthttps://eeg-ebe.github.io/SeqPHASE/download.htmlDownloads page10.1093/BIB/BBAE36739193916PMC11350380Jean-François Flotjflot@ulb.bePersonScyNetScyNet is a Cytoscape app designed for visualizing community metabolic models, focusing on interactions between community members. It is freely available under an MIT license and provides options for incorporating model state via fluxes or flux ranges.http://apps.cytoscape.org/apps/scynetscynetbiotools:scynethttp://edamontology.org/topic_3407Endocrinology and metabolismhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksJavaMIThttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3660Metabolic network modellinghttp://edamontology.org/operation_2422Data retrieval10.1093/BIOADV/VBAE10439132287PMC11315608Thomas Ratteithomas.rattei@univie.ac.athttps://orcid.org/0000-0002-0592-7791PersonmzQCmzQC is a standard file format for reporting and exchanging data quality information in mass spectrometry. The software provides open-source libraries in Python, R, and Java for processing mzQC data and facilitating data quality control workflows.https://github.com/HUPO-PSI/mzQCmzqcbiotools:mzqchttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3047Molecular biologyPythonRJavaJavaScripthttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_0337Visualisation10.1021/JASMS.4C0017438918936PMC11311537Chris Bielowchris.bielow@bsc.fu-berlin.dehttps://orcid.org/0000-0001-5756-3988PersonMathias Walzerwalzer@ebi.ac.ukhttps://orcid.org/0000-0003-4538-2754PersonSRICATsSRICATs is a Java-based software package for plant miRNA identification from next-generation sequencing (NGS) data, employing convolutional neural network methods. It outperforms other tools and is freely available for non-commercial users.https://sourceforge.net/projects/sricatssricatsbiotools:sricatshttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0203Gene expressionJavahttp://edamontology.org/operation_0463miRNA target predictionhttp://edamontology.org/operation_3792miRNA expression analysis10.3389/FPLS.2024.133085438567128PMC10985208Yun Zhangzhangyun016@gzy.edu.cnPerson123FASTQ123FASTQ is a user-friendly software solution for preprocessing Illumina FASTQ reads, integrating quality control analysis, trimming, and format conversion. It aims to simplify NGS data preprocessing and improve workflow efficiency.https://sourceforge.net/projects/project-123ngs/123fastqbiotools:123fastqhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0091BioinformaticsJavaMIThttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_3219Read pre-processinghttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_0337Visualisation10.1101/2024.03.08.584032ReMASTERReMASTER is a tool for simulating phylogenetic trees and population dynamics within the BEAST 2 platform. It provides efficient methods for specifying and simulating phylogenetic trees under phylodynamic models, supporting various models like birth-death and coalescent.https://tgvaughan.github.io/remasterremasterbiotools:remasterhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_3314Chemistryhttp://edamontology.org/topic_0610EcologyJavaGPL-3.0http://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/operation_0326Phylogenetic tree editing10.1093/BIOINFORMATICS/BTAE01538195927PMC10796175Timothy G Vaughantimothy.vaughan@bsse.ethz.chhttps://orcid.org/0000-0001-6220-2239Personraw2ometiffRaw format to OME-TIFF converterhttps://github.com/glencoesoftware/raw2ometiffraw2ometiffbiotools:raw2ometiffCommand-line toolJavaGPL-2.0bioformats2rawBio-Formats image file format to raw format converterhttps://github.com/glencoesoftware/bioformats2rawbioformats2rawbiotools:bioformats2rawCommand-line toolJavaGPL-2.0The Chemistry Development KitOpen source Java library for bio- and cheminformatics.http://github.com/cdk/cdk/cdkbiotools:cdk1Libraryhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_0091BioinformaticsMacLinuxWindowsJavaLGPL-2.1ELIXIR-NLMatureFree of chargehttp://edamontology.org/operation_0337Visualisationhttp://github.com/cdk/cdk/Repositoryhttps://fosstodon.org/@cdkSocial mediahttps://github.com/cdk/cdk/General10.1186/s13321-017-0220-429086040PMC546123010.1021/ci025584y12653513PMC4901983Primary10.2174/13816120677758527416796559OtherChristoph SteinbeckPersonDeveloperRajarshi GuhaPersonDeveloperJohn MayPersonDeveloperEgon WillighagenPersonDevelopermaastrichtuniversity.nlInstituteProviderhttps://sourceforge.net/p/cdk/mailman/?source=navbarPersonPrimary contactGenetic and Genomic Information System (GnpIS)GnpIS is an integrative and multi-species information system dedicated to plants, including forest trees. It handles various types of data, focusing on genetic resources and phenomics. It allows researchers from the Plant community to access and cross-reference genetic data (accessions, phenotypes, polymorphisms, markers and QTLs) and genomic data (sequences, physical maps, genome annotations) for species of agronomic and forestry interest. Accessible via a public web portal, GnpIS enables different types of data to be managed, browsed and retrieved via specialized search tools and web services. GnpIS is used by the French National Research Institute for Agriculture, Food and Environment (INRAE) and its partners in major national and international projects.https://urgi.versailles.inrae.fr/gnpisgnpisbiotools:gnpis20.2.1doi:10.25504/FAIRsharing.dw22y3doiWeb applicationDatabase portalhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0625Genotype and phenotypeMacLinuxWindowsJavaScriptJavaBSD-3-Clauseelixir-fr-sdp-2019Animal and Crop GenomicsMatureFree of chargeOpen accessToolsFrancehttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/operation_0224Query and retrieval

http://edamontology.org/data_3498Sequence variations

http://edamontology.org/data_0850Sequence set

http://edamontology.org/data_1255Sequence features

http://edamontology.org/data_2044Sequence

http://edamontology.org/data_2353Ontology data

http://edamontology.org/data_2080Database search results

http://edamontology.org/data_0920Genotype/phenotype report

http://edamontology.org/data_0842Identifier

https://forge.inrae.fr/urgi/is/gnpisRepositoryhttps://urgi.versailles.inrae.fr/Data-Services/Data-Access/GnpISGeneralfaidareuseswheatisuseswheatmineincludesoakmineincludesrepetdbincludesgrapemineincludes10.1093/database/bat05823959375PMC3746681Primary10.1007/978-1-4939-6658-5_527987166Primary10.1038/hortres.2016.5627917288PMC5120350Other10.3835/plantgenome2015.06.003827898761Primary10.1186/s13059-018-1491-430115101PMC609728410.34133/2019/167140333313522PMC7718628URGI helpdeskurgi-support@inrae.frDivisionPrimary contactAggreProtAggreProt is a web server to predict and engineer protein aggregation. The tool provides a per-residue numerical aggregation propensity value and an overall protein aggregation propensity profile. Along with the protein solvent accessibility area and its transmembrane propensity, AggreProt predictions aid the users on designing soluble proteins.https://loschmidt.chemi.muni.cz/aggreprot/aggreprotbiotools:aggreprot1.0Web servicehttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacJavaJavaScriptProprietaryMatureFree of chargeOpen accessToolsProteomicsCzech Republic10.1093/nar/gkae420PrimaryJoan Planas-IglesiasDavid BednarJiri DamborskySimeon BorkoAPEAPE (the Automated Pipeline Explorer) as a command-line tool and API for automated composition of scientific workflows. APE is easily configured to a new application domain by providing it with a domain ontology and semantically annotated tools. It can then be used to synthesize purpose-specific workflows based on a specification of the available workflow inputs, desired outputs and possibly additional constraints.https://github.com/sanctuuary/APE/apebiotools:ape2.1.7LibraryWeb APICommand-line toolhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0091BioinformaticsMacWindowsLinuxJavaApache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3429Generationhttp://edamontology.org/data_0949Workflow metadatahttp://edamontology.org/format_3464JSON

http://edamontology.org/data_0949Workflow metadatahttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3857CWLhttp://edamontology.org/format_3603PNG

https://github.com/sanctuuary/apeRepositoryhttps://mvnrepository.com/artifact/io.github.sanctuuary/APE/2.1.7Software packageDownload APE java library or the CLI2.1.7https://ape-framework.readthedocs.io/API documentationPMC7304703Primary10.1021/acs.jproteome.0c0098333720735PMC8041394Benchmarking studyVedran Kasalicavedran.kasalica@health-ri.nlhttps://orcid.org/0000-0002-0097-1056PersonAnna-Lena Lamprechtanna-lena.lamprecht@uni-potsdam.dehttps://orcid.org/0000-0003-1953-5606PersonGrapeMineAn integrated database for grapevine datahttp://urgi.versailles.inra.fr/GrapeMineGrapeMinebiotools:GrapeMine1.0Database portalWeb serviceWeb applicationhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0121ProteomicsMacLinuxJavaRPythonJavaScriptRubyPerlLGPL-2.1LegacyFree of chargehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/data_2353Ontology data

http://edamontology.org/data_3753Over-representation data

http://edamontology.org/data_3786Query script

http://edamontology.org/data_1255Sequence features

https://registry.intermine.orgSoftware cataloguehttp://intermine.orgOtherhttp://intermine.readthedocs.org/en/latest/web-services/API documentationhttps://flymine.readthedocs.io/en/latest/User manual10.1093/bioinformatics/bts57723023984PMC3516146OtherHMDBFreely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.http://www.hmdb.ca/hmdbbiotools:hmdbDatabase portalhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3421Surgeryhttp://edamontology.org/topic_0593NMRhttp://edamontology.org/topic_0621Model organismsWindowsMacLinuxPerlJavaMatureFree of chargeOpen accesshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/data_3035Structure identifierhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/data_0982Molecule identifierhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_0982Molecule identifierhttp://edamontology.org/format_2330Textual format

http://edamontology.org/operation_3431Data depositionhttp://edamontology.org/data_2050Molecular property (general)http://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0982Molecule identifierhttp://edamontology.org/format_2330Textual formathttps://hmdb.ca/Servicehttps://hmdb.ca/downloadsDownloads pagehttp://www.hmdb.ca/helpGeneralhttps://hmdb.ca/simple/apiAPI documentation163029931720216818953024Contact Formhttp://feedback.wishartlab.com/?site=hmdbPersonPrimary contactMSNovelistDe novo structure generation from mass spectra.https://github.com/meowcat/MSNovelistmsnovelistbiotools:msnovelistCommand-line toolhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0153LipidsMacLinuxWindowsPythonJavaAGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_0476Ab initio structure predictionhttp://edamontology.org/operation_3860Spectrum calculationhttp://edamontology.org/operation_3454Phasinghttp://edamontology.org/operation_3431Depositionhttp://edamontology.org/operation_4009Small molecule design10.1038/S41592-022-01486-335637304PMC9262714Nicola Zambonizamboni@imsb.biol.ethz.chhttps://orcid.org/0000-0003-1271-1021PersonSebastian Böckerhttps://orcid.org/0000-0002-9304-8091Kai Dührkophttps://orcid.org/0000-0002-9056-0540Michael A. Stravshttps://orcid.org/0000-0002-1426-8572PeakForestA multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.https://peakforest.orgpeakforestbiotools:peakforestWeb applicationCommand-line toolhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0593NMRhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0219Data submission, annotation and curationMacLinuxWindowsJavaJavaScriptOtherFree of chargeOpen accesshttp://edamontology.org/operation_3803Natural product identificationhttp://edamontology.org/operation_3801Spectral library searchhttp://edamontology.org/operation_3431Depositionhttp://edamontology.org/operation_2422Data retrievalhttps://github.com/peakforestRepository10.1007/S11306-022-01899-335699774PMC9197906Franck GiacomoniFranck.Giacomoni@inrae.frhttps://orcid.org/0000-0001-6063-4214PersonEstelle Pujos-GuillotChristophe JunotFrançois FenailleMetaboAnalystStatistical, functional and integrative analysis of metabolomics data , interpretation, and integration with other omics data.http://www.metaboanalyst.cametaboanalystbiotools:metaboanalyst4.05.0Web applicationhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0154Small moleculesRJavaGPL-3.0http://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2497Pathway or network analysishttp://www.metaboanalyst.ca/faces/docs/Resources.xhtmlSource codehttp://www.metaboanalyst.ca/faces/docs/Faqs.xhtmlGeneralhttp://www.metaboanalyst.ca/faces/docs/Tutorial.xhtmlTraining materialhttp://www.metaboanalyst.ca/faces/docs/Contact.xhtmlGeneral10.1093/nar/gky31029762782PMC603088910.1038/s41596-022-00710-w35715522jeff.xia@mcgill.caPersonPrimary contactThermoRawFileParserOpen-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzMLhttps://github.com/compomics/ThermoRawFileParserThermoRawFileParserbiotools:ThermoRawFileParserCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3172MetabolomicsLinuxMacJavaC#Apache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/operation_3695Filteringhttp://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3712Thermo RAW

http://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3244mzML

https://github.com/compomics/ThermoRawFileParserGUIRepositoryThermoRawFileParserGUIhttps://github.com/compomics/ThermoRawFileParser/releasesSource codehttps://github.com/compomics/ThermoRawFileParser/blob/master/README.mdGeneral10.1101/622852PrimaryComputational Omics and Systems Biology Groupcompomics.list@gmail.comDivisionPrimary contactPeptideShakerPeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics datahttp://compomics.github.io/projects/peptide-shaker.htmlpeptideshakerbiotools:peptideshaker3.0.11Desktop applicationCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0644ProteomeMacLinuxJavaApache-2.0de.NBIProteomicsBioInfra.ProtOpen accesshttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGF

http://edamontology.org/data_2992Protein structure imagehttp://edamontology.org/format_3579JPGhttp://edamontology.org/format_3604SVG

http://edamontology.org/data_3754GO-term enrichment datahttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2969Sequence imagehttp://edamontology.org/format_3547Image format

http://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3475TSV

https://github.com/compomics/peptide-shakerSource codehttp://compomics.github.io/projects/peptide-shaker.html#read-meGeneral10.1038/nbt.310925574629PrimaryBioInfra.ProtInstituteProviderDominik Kopczynskdominik.kopczynski@isas.dehttp://compomics.github.io/projects/peptide-shaker.htmlPersonPrimary contactoncoanalyserOncoanalyser is an nf-core Nextflow implementation of the tools developed by Hartwig Medical Foundation. The workflow is designed to comprehensively detect all variant types (SNV. MNV, InDel, SV, CNV, Fusions, Viral insertions, Telomere length, Genetic Immune Escape, mutational processes) as well as key tumor characteristics (purity, ploidy, TMB, MSI) from data derived from different short read platforms. The tooling is optimised for paired whole genome samples (90x tumor, 30x normal) but can be run on exome or panel (targeted) data. There is support for GRCh37 and GRCh38 human reference genome builds.https://github.com/nf-core/oncoanalyser/tree/devoncoanalyserbiotools:oncoanalyser5.34Workflowhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_3170RNA-SeqLinuxWindowsMacJavaGPL-3.0MatureFree of chargeOpen accesshttps://github.com/nf-core/oncoanalyser/tree/devIssue trackerRepositoryGitHub page for issue tracking of Nextflow workflow implementationhttps://github.com/hartwigmedical/hmftoolsRepositoryIssue trackerGitHub repository of underlying tools with issue trackingXNATXNAT is an open source imaging informatics platform developed by the Neuroinformatics Research Group at Washington University. XNAT was originally developed at Washington University in the Buckner Lab, which is now located at Harvard University. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. Thanks to its extensibility, XNAT can be used to support a wide range of imaging-based projects.https://xnat.orgxnatbiotools:xnatWeb applicationWeb APIhttp://edamontology.org/topic_3384Medical imaginghttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3383Bioimaginghttp://edamontology.org/topic_3452Tomographyhttp://edamontology.org/topic_3071Data managementLinuxWindowsMacJavaBSD-2-ClauseEUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_3802Data sortinghttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3283Anonymisationhttps://groups.google.com/g/xnat_discussion/Discussion forumhttps://bitbucket.org/xnatdev/workspace/repositories/Repositoryhttps://xnat.org/download/Downloads pagehttps://wiki.xnat.org/documentation/User manualhttps://wiki.xnat.org/xnat-api/xnat-rest-api-directoryAPI documentationxnatpyusedByrxnatusedByxnat-picusedBybigr_xnatusedBy10.1385/ni:5:1:1117426351Primary10.1162/jocn.2009.2140719929323PMC2895005UsageDaniel Marcusdmarcus@wustl.eduhttps://profiles.wustl.edu/en/persons/daniel-marcushttps://orcid.org/0000-0001-5662-5358PersonPrimary contactOpenChromOpen source tool for mass spectrometry and chromatography.https://www.openchrom.net/openchrombiotools:openchromDesktop applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3370Analytical chemistryLinuxWindowsMacJavaEPL-1.0ms-utilsMaturehttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/operation_3214Spectral analysishttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/data_0943Mass spectrometry spectrahttp://edamontology.org/format_1637dathttp://edamontology.org/format_3712Thermo RAWhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3650NetCDF

http://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3650NetCDFhttp://edamontology.org/format_3244mzML

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3508PDF

http://ms-utils.orgSoftware cataloguehttps://openchrom.net/downloadDownloads pagehttps://github.com/OpenChrom/openchromSource codehttps://lablicate.com/marketplace/extensions/handbookUser manualhttps://github.com/OpenChrom/openchrom/wiki/faqFAQ10.1186/1471-2105-11-40520673335Philip Wenigphilip.wenig@gmx.netPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorMatthias Mailänderhttps://orcid.org/0000-0001-6114-0304PersonContributorDataDiscoveryDataDiscovery 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.https://urgi.versailles.inrae.fr/data-discovery/DataDiscoverybiotools:DataDiscoveryWeb APIWeb applicationWeb serviceDatabase portalhttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_3071Biological databaseshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3810Agricultural scienceLinuxJavaScriptJavaBashBSD-3-Clauseelixir-fr-sdp-2019URGIEmergingFree of chargeOpen accessDataToolsInteroperabilityFrancehttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3625Relation extractionhttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_3908Information retrievalhttp://edamontology.org/data_0968Keywordhttp://edamontology.org/data_2353Ontology data

http://edamontology.org/data_2080Database search results

http://edamontology.org/data_2093Data reference

http://edamontology.org/data_0842Identifier

https://forgemia.inra.fr/urgi-is/data-discoveryRepositoryGitLab code repository for DataDiscoveryhttps://github.com/gnpis/DataDiscovery/MirrorCode repository mirror link for DataDiscoveryhttps://forgemia.inra.fr/urgi-is/data-discovery/blob/master/LEGAL-MENTIONS.mdTerms of useGeneral terms of usehttps://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#contributeContributions policyHow to contributehttps://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.mdUser manualHow to usehttps://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#setupInstallation instructionsHow to installwheatisusedByRAReusedByPlant_DataDiscoveryusedBy10.3835/plantgenome2015.06.0038Primary1- Spannagl, M., Alaux, M., Lange, M., Bolser, D. M., Bader, K. C., Letellier, T., Kimmel, E., Flores, R.-G., Pommier, C., Kerhornou, A., Walts, B., Nussbaumer, T., Grabmuller, C., Chen, J., Colmsee, C., Beier, S., Mascher, M., Schmutzer, T., Arend, D., Thanki, A., Ramirez-Gonzalez, R., Ayling, M., Ayling, S., Caccamo, M., Mayer, K. F. X., Scholz, U., Steinbach, D., Quesneville, H., Kersey, P. (2016). TransPLANT resources for triticeae genomic data. Plant Genome, 9 (1), 13 p.10.1038/hortres.2016.562- Adam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware, D., Quesneville, H. (2016). Towards an open grapevine information system. Horticulture Research, 3, 8 p. , DOI : 10.1038/hortres.2016.5610.1186/s13059-018-1491-43- Alaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F, Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, 19:111.urgi-supporturgi-support@inrae.frPrimary contactSupportOakMineQuercus robur annotation databasehttps://urgi.versailles.inra.fr/OakMine_PM1NOakMinebiotools:OakMine2.3Web applicationWeb serviceDatabase portalhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0121ProteomicsLinuxMacRRubyJavaPythonJavaScriptPerlLGPL-2.1MatureFree of chargehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/data_2353Ontology data

http://edamontology.org/data_3753Over-representation data

http://edamontology.org/data_3786Query script

http://edamontology.org/data_1255Sequence features

https://registry.intermine.orgSoftware cataloguehttp://intermine.orgOtherhttp://intermine.readthedocs.org/en/latest/web-services/API documentationhttps://flymine.readthedocs.io/en/latest/User manual10.1093/bioinformatics/bts57723023984PMC3516146OtherWheatMineWheat IWGSC RefSeq v1.0https://urgi.versailles.inra.fr/WheatMineWheatMinebiotools:WheatMineWeb applicationWeb serviceDatabase portalhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0121ProteomicsLinuxMacRRubyJavaPythonJavaScriptPerlLGPL-2.1MatureFree of chargehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/data_2353Ontology data

http://edamontology.org/data_3753Over-representation data

http://edamontology.org/data_3786Query script

http://edamontology.org/data_1255Sequence features

https://registry.intermine.orgSoftware cataloguehttp://intermine.orgOtherhttp://intermine.readthedocs.org/en/latest/web-services/API documentationhttps://flymine.readthedocs.io/en/latest/User manual10.1093/bioinformatics/bts57723023984PMC3516146OtherOnline SBML ValidatorCheck the syntax and internal consistency of files in SBML (The Systems Biology Markup Language) format.https://sbml.bioquant.uni-heidelberg.de/validator_servlet/online_sbml_validatorbiotools:online_sbml_validator1Web APIWeb applicationhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_3071Data managementLinuxWindowsMacJavaPythonLGPL-2.0Free of chargeOpen accesshttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0336Format validationhttp://edamontology.org/data_0950Mathematical modelhttp://edamontology.org/format_3686COMBINE OMEXhttp://edamontology.org/format_2585SBMLhttps://sbml.org/facilities/Servicehttps://web.archive.org/web/20210507040418/http://sbml.org/Facilities/Documentation/Validator_Web_APIAPI documentationFrank Bergmannhttps://www.biocatalogue.orgProjectDocumentorFrank Bergmannfrank.bergmann@bioquant.uni-heidelberg.dehttps://orcid.org/0000-0001-5553-4702PersonPrimary contact