HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 233,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=220&ordering=citations",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=180&ordering=citations",
"results": [
{
"id": 95,
"name": "RSAT oligo-analysis",
"description": "Compute k-mer frequencies (oligonucleotides or oligopeptides) and various statistics to discover exceptional motifs (over-represented or under-represented). Typical applications include discovery of transcription factor binding motifs, restriction sites in bacterial genomes, RNA termination and polyadenylation signals, detection of motifs associated with replication origins, analysis of oligopeptide frequencies in protein sequences.",
"homepage": "http://teaching.rsat.eu/oligo-analysis_form.cgi",
"biotoolsID": "oligo-analysis",
"biotoolsCURIE": "biotools:oligo-analysis",
"tool_type": [
"Web service",
"Web application",
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"FR",
"Regulatory Sequence Analysis Tools (RSAT)"
],
"scientific_topics": [
"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_0749"
],
"primary_publication": [
"10.1006/jmbi.1998.1947"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "RSAT",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Jacques van Helden",
"email": "Jacques.van-Helden@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Jacques van Helden",
"email": "Jacques.van-Helden@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "AFL-3.0",
"documentation": "http://rsat.eu/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:23.505699Z",
"teams": [],
"source_repository": null
},
{
"id": 110,
"name": "RSAT retrieve-ensembl-seq",
"description": "Returns upstream, downstream, intronic, exonic, UTR, transcript, mRNA, CDS or gene sequences for a list of genes from the EnsEMBL database.\nMulti-genome queries are supported: automatic retrieval of sequences for all the orthologs of the query genes, at a given taxonomical level.",
"homepage": "http://rsat.sb-roscoff.fr/retrieve-ensembl-seq_form.cgi",
"biotoolsID": "rsat-retrieve-ensembl-seq",
"biotoolsCURIE": "biotools:rsat-retrieve-ensembl-seq",
"tool_type": [
"Web service",
"Web application",
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"FR",
"Regulatory Sequence Analysis Tools (RSAT)"
],
"scientific_topics": [
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_0749"
],
"primary_publication": [
"10.1093/bioinformatics/btp519"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Developer",
"Documentor",
"Maintainer",
"Support"
],
"name": "Olivier Sand",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-1465-1640",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Morgane Thomas-Chollier",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-2608-476X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Université Libre de Bruxelles",
"email": null,
"url": "https://www.ulb.be/",
"orcidid": null,
"gridid": "grid.4989.c",
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "AFL-3.0",
"documentation": "https://rsat-doc.github.io/using-RSAT/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [],
"source_repository": "https://github.com/rsat-doc"
},
{
"id": 142,
"name": "SeaView",
"description": "Multiplatform graphical user interface designed to facilitate alignment and phylogenic tree building from molecular sequences.",
"homepage": "http://doua.prabi.fr/software/seaview",
"biotoolsID": "seaview",
"biotoolsCURIE": "biotools:seaview",
"tool_type": [
"Command-line tool",
"Desktop application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0084",
"http://edamontology.org/topic_0092",
"http://edamontology.org/topic_0080"
],
"primary_publication": [
"10.1093/molbev/msp259"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "IFB ELIXIR-FR",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Manolo Gouy",
"email": "mgouy@biomserv.uni-lyon1.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://doua.prabi.fr/main/index",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:49:59.006607Z",
"teams": [
"PRABI-Lyon-Grenoble"
],
"source_repository": null
},
{
"id": 137,
"name": "SHAMAN",
"description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].",
"homepage": "http://shaman.c3bi.pasteur.fr/",
"biotoolsID": "shaman",
"biotoolsCURIE": "biotools:shaman",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3174"
],
"primary_publication": [
"10.1073/pnas.1523899113"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Stevenn Volant",
"email": null,
"url": "https://research.pasteur.fr/en/member/stevenn-volant/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "C3BI",
"email": null,
"url": "https://research.pasteur.fr/en/center/c3bi/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Hugo Varet",
"email": null,
"url": "https://research.pasteur.fr/en/member/hugo-varet/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Pierre Lechat",
"email": null,
"url": "https://research.pasteur.fr/en/member/pierre-lechat/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "https://research.pasteur.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Amine Ghozlane",
"email": null,
"url": "https://research.pasteur.fr/en/member/amine-ghozlane/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "SHAMAN team",
"email": "shaman@pasteur.fr",
"url": "https://research.pasteur.fr/en/software/shaman-shiny-application-for-metagenomic-analysis/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Bioinformatics and Biostatistics Hub",
"email": null,
"url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://shaman.c3bi.pasteur.fr/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 742,
"citations": null,
"annual_visits": 1855,
"last_update": "2025-10-23T10:46:59.953305Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://github.com/aghozlane/shaman"
},
{
"id": 182,
"name": "S-MART",
"description": "This tool manages your RNA-Seq and ChIP-seq data.",
"homepage": "http://urgi.versailles.inra.fr/Tools/S-MART",
"biotoolsID": "s-mart",
"biotoolsCURIE": "biotools:s-mart",
"tool_type": [
"Suite"
],
"collection": [
"S-MART"
],
"scientific_topics": [
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_3169",
"http://edamontology.org/topic_0092"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Matthias Zytnicki",
"email": "matthias.zytnicki@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://urgi.versailles.inra.fr/download/s-mart/doc.pdf",
"maturity": "Mature",
"cost": null,
"unique_visits": 267,
"citations": null,
"annual_visits": 474,
"last_update": "2024-11-25T14:22:04.089851Z",
"teams": [],
"source_repository": null
},
{
"id": 240,
"name": "SMS",
"description": "Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection.",
"homepage": "http://www.atgc-montpellier.fr/sms/",
"biotoolsID": "PhyMLSMS",
"biotoolsCURIE": "biotools:PhyMLSMS",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [
"PhyML"
],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_2269"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/download/papers/sms-HowItWorks.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:18.380055Z",
"teams": [],
"source_repository": null
},
{
"id": 147,
"name": "SortMeRNA",
"description": "Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.",
"homepage": "https://bioinfo.cristal.univ-lille.fr/RNA/sortmerna/",
"biotoolsID": "sortmerna",
"biotoolsCURIE": "biotools:sortmerna",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [
"ELIXIR Trainer Tools"
],
"scientific_topics": [
"http://edamontology.org/topic_3941",
"http://edamontology.org/topic_3174",
"http://edamontology.org/topic_3308"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://github.com/sortmerna/sortmerna/issues",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://github.com/biocore/sortmerna/issues",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/sortmerna/sortmerna/wiki/User-manual-v4.3.2",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:49:42.747317Z",
"teams": [
"Bilille"
],
"source_repository": null
},
{
"id": 118,
"name": "SouthGreen_Galaxy Not found.",
"description": "A Galaxy instance focused on agriculture, food, biodiversity and environment, from the Agropolis campus in France.",
"homepage": "http://galaxy.southgreen.fr/galaxy",
"biotoolsID": "SouthGreen_Galaxy",
"biotoolsCURIE": "biotools:SouthGreen_Galaxy",
"tool_type": [
"Workbench"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3810"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": "https://southgreen.fr/content/galaxy-tool",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-01-24T09:53:10Z",
"teams": [],
"source_repository": null
},
{
"id": 14,
"name": "UMD-Predictor",
"description": "A tool that provides a combinatorial approach to identify potential pathogenic variations, that associates the following data: localization within the protein, conservation, biochemical properties of the mutant and wild-type residues, and the potential impact of the variation on mRNA.",
"homepage": "http://umd-predictor.eu",
"biotoolsID": "umd-predictor",
"biotoolsCURIE": "biotools:umd-predictor",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_3574",
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_0199"
],
"primary_publication": [
"10.1002/humu.22965"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Christophe Beroud",
"email": "christophe.beroud@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2019-07-24T20:06:47Z",
"teams": [],
"source_repository": null
},
{
"id": 94,
"name": "VarAFT",
"description": "VarAFT (Variant Analysis and Filtration Tool) is a standalone and multiplatform tool for annotation and prioritization of potential disease causing genes. With this tool users can annotate variant (VCF) files, combine multiple samples from various individuals, prioritize list of variants by multi-filtering parameters. Additionally, users can perform a coverage analysis and quality check from any BAM file.",
"homepage": "http://varaft.eu",
"biotoolsID": "varaft",
"biotoolsCURIE": "biotools:varaft",
"tool_type": [
"Desktop application"
],
"collection": [
"elixir-fr-sdp-2019",
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_3063"
],
"primary_publication": [
"10.1093/nar/gky471"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact form",
"email": null,
"url": "http://varaft.eu/#contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Jean-Pierre Desvignes",
"email": "jean-pierre.desvignes@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "Other",
"documentation": "http://varaft.eu/download_files/VarAFT_Documentation_V2.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-04-02T21:35:23.173094Z",
"teams": [
"MMG-GBIT"
],
"source_repository": null
},
{
"id": 69,
"name": "WheatIS",
"description": "This project aims at building an International Wheat Information System (WheatIS) to support the wheat research community. The main objective is to provide a single-access web based system to access to the available data resources and bioinformatics tools. The web portal indexes and makes findable any kind of data from wheat related species. \nThe WheatIS search is an implementation of DataDiscovery.",
"homepage": "https://urgi.versailles.inrae.fr/wheatis/",
"biotoolsID": "WheatIS",
"biotoolsCURIE": "biotools:WheatIS",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3810"
],
"primary_publication": [
"10.1186/s13059-018-1491-4"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"name": "Support service",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://urgi.versailles.inra.fr/wheatis/about",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-02-15T15:54:13Z",
"teams": [
"URGI"
],
"source_repository": null
},
{
"id": 89,
"name": "Workflow4Metabolomics",
"description": "First fully open-source and collaborative online platform for computational metabolomics. It includes preprocessing, normalization, quality control, statistical analysis of LC/MS, FIA-MS, GC/MS and NMR data.",
"homepage": "https://workflow4metabolomics.org/",
"biotoolsID": "workflow4metabolomics",
"biotoolsCURIE": "biotools:workflow4metabolomics",
"tool_type": [
"Bioinformatics portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3307",
"http://edamontology.org/topic_3172",
"http://edamontology.org/topic_2259"
],
"primary_publication": [
"10.1093/bioinformatics/btu813"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "MetaboHUB - National infrastructure in metabolomics & fluxomics",
"email": null,
"url": "https://www.metabohub.fr/home.html",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Christophe Caron",
"email": null,
"url": "http://abims.sb-roscoff.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Christophe Duperier",
"email": null,
"url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Franck Giacomoni",
"email": "franck.giacomoni@inrae.fr",
"url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse",
"orcidid": "https://orcid.org/0000-0001-6063-4214",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Gildas Le Corguillé",
"email": "lecorguille@sb-roscoff.fr",
"url": "http://abims.sb-roscoff.fr",
"orcidid": "https://orcid.org/0000-0003-1742-9711",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Marie Tremblay-Franco",
"email": null,
"url": "https://www6.toulouse.inrae.fr/axiomm",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Jean-François Martin",
"email": null,
"url": "https://www6.toulouse.inrae.fr/axiomm",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Pierrick Roger-Melee",
"email": null,
"url": "http://www-list.cea.fr/index.php/en/",
"orcidid": "https://orcid.org/0000-0001-8177-4873",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Yann Guitton",
"email": null,
"url": "https://www.laberca.org/plateforme-analytique/presentation/",
"orcidid": "https://orcid.org/0000-0002-4479-0636",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Documentor"
],
"name": "Cécile Canlet",
"email": null,
"url": "https://www6.toulouse.inrae.fr/axiomm",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Misharl Monsoor",
"email": null,
"url": "http://abims.sb-roscoff.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Etienne A. Thévenot",
"email": null,
"url": "http://www-list.cea.fr/index.php/en/",
"orcidid": "https://orcid.org/0000-0003-1019-4577",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Mélanie Pétéra",
"email": null,
"url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Workflow4Metabolomics Team",
"email": "contact@workflow4metabolomics.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Marion Landi",
"email": null,
"url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "IFB - Institut Français de Bioinformatique",
"email": null,
"url": "https://www.france-bioinformatique.fr/en",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Pierre Pericard",
"email": null,
"url": "http://abims.sb-roscoff.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Alexis Delabrière",
"email": null,
"url": "http://www-list.cea.fr/index.php/en/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Sophie Goulitquer",
"email": null,
"url": "http://www.sb-roscoff.fr/en/research-and-training-centre-marine-biology-and-oceanography/services/technological-core-facilities/mass-spectrometry-core-facility",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://workflow4metabolomics.org/howto",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-12-16T14:17:30Z",
"teams": [
"ABiMS"
],
"source_repository": "https://github.com/workflow4metabolomics"
},
{
"id": 153,
"name": "xHeinz",
"description": "Software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions. Active subnetwork modules are sets of genes, one for each species, which: - induce a connected subnetwork in a species-specific interaction network, - show overall differential behavior, and - contain a large number of orthologous genes.",
"homepage": "https://github.com/ls-cwi/xheinz",
"biotoolsID": "xheinz",
"biotoolsCURIE": "biotools:xheinz",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602"
],
"primary_publication": [
"10.1093/bioinformatics/btv316"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Tobias Müller",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://github.com/ls-cwi/xheinz",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Hayssam Soueidan",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Marcus Dittrich",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Mohammed El-Kebir",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Thomas Hume",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Daniela Beisser",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Macha Nikolski",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Lodewyk F. A. Wessels",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Jaap Heringa",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Gunnar W. Klau",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "u-bordeaux.fr",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Guillaume Blin",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Bordeaux University, CBiB, France",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "The Netherlands",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Würzburg University, Germany",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "University Duisburg-Essen",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "The Netherlands Cancer Institute, Amsterdam",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Univ. Bordeaux, CNRS/LaBRI, 33405 Talence, France,",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "MIT",
"documentation": "https://github.com/ls-cwi/xheinz",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2019-03-12T14:52:11Z",
"teams": [
"CBiB"
],
"source_repository": "https://software.cwi.nl/software/xheinz/releases/1.0"
},
{
"id": 283,
"name": "3SRP",
"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.\n\nThe main steps of the pipeline are:\n- Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample.\n- Alignment on refseq reference transcriptome is performed using bwa.\n- Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix.\nIf secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2.\n- If DEG are found, annotation is performed using the database GO and KEGG.\n- A report is provided listing the main quality controls performed and the results found.\n\nCite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1",
"homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline",
"biotoolsID": "3SRP",
"biotoolsCURIE": "biotools:3SRP",
"tool_type": [
"Workflow"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3308"
],
"primary_publication": [
"10.1038/s41598-017-14892-x"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Dimitri MEISTERMANN",
"email": "dimitri.meistermann@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Philippe Bordron",
"email": "philippe.bordron@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider",
"Support"
],
"name": "BiRD bioinformatics facility",
"email": "pf-bird@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Primary contact",
"Developer",
"Support"
],
"name": "Eric Charpentier",
"email": "eric.charpentier@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/about-us/members/",
"orcidid": "https://orcid.org/0000-0002-8571-7603",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Broad Institute",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": "Some scripts of the pipeline regarding sample demultiplexing and UMI counting have been adapated and modified from this paper:\nXiong, Y., Soumillon, M., Wu, J. et al. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries. Sci Rep 7, 14626 (2017)."
},
{
"type_role": [
"Developer"
],
"name": "Solenne Dumont",
"email": "solenne.dumont@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
"orcidid": "https://orcid.org/0000-0003-3237-7382",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact",
"Contributor"
],
"name": "Audrey Bihouée",
"email": "audrey.bihouee@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-8689-2083",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/wikis/home",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:40:06.421826Z",
"teams": [
"BiRD"
],
"source_repository": null
},
{
"id": 5,
"name": "AgroLD",
"description": "The RDF Knowledge-based Database for plant molecular networks.",
"homepage": "http://agrold.southgreen.fr/agrold/",
"biotoolsID": "AgroLD",
"biotoolsCURIE": "biotools:AgroLD",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_3810"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2019-11-05T14:52:28Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 104,
"name": "ANISEED",
"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: \ni) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; \nii) A multispecies genomic browser; \niii) a Genomicus gene synteny browser.",
"homepage": "https://www.aniseed.fr",
"biotoolsID": "ANISEED",
"biotoolsCURIE": "biotools:ANISEED",
"tool_type": [
"Database portal",
"Web API",
"Web application",
"Ontology"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3065",
"http://edamontology.org/topic_3383",
"http://edamontology.org/topic_3679",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_0084",
"http://edamontology.org/topic_0219",
"http://edamontology.org/topic_2229",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3064",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_3308"
],
"primary_publication": [
"10.1016/j.cub.2005.12.044",
"10.1093/nar/gkz955",
"10.1093/nar/gkx1108",
"10.1101/gr.108175.110",
"10.1093/nar/gkv966"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "contact@aniseed.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Support"
],
"name": null,
"email": "contact@aniseed.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Patrick Lemaire",
"email": "patrick.lemaire@crbm.cnrs.fr",
"url": "http://www.crbm.cnrs.fr/en/team/lemaire/",
"orcidid": "https://orcid.org/0000-0003-4925-2009",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Christelle Dantec",
"email": "christelle.dantec@crbm.cnrs.fr",
"url": "http://www.crbm.cnrs.fr/en/team/lemaire/",
"orcidid": "https://orcid.org/0000-0001-7247-6460",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "https://www.aniseed.fr/api",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2023-09-25T14:25:18.910230Z",
"teams": [],
"source_repository": null
},
{
"id": 86,
"name": "BIII (BioImage Informatics Index, biii.eu)",
"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.",
"homepage": "https://biii.eu",
"biotoolsID": "BISE",
"biotoolsCURIE": "biotools:BISE",
"tool_type": [
"Database portal",
"Bioinformatics portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"NEUBIAS"
],
"scientific_topics": [
"http://edamontology.org/topic_3298",
"http://edamontology.org/topic_0769",
"http://edamontology.org/topic_3382",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_0091"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "NEUBIAS Network of Bioimage Analysts",
"email": null,
"url": "https://neubias.eu",
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": "COST action having supported the creation and curation of this database"
},
{
"type_role": [
"Primary contact"
],
"name": "Perrine Paul-Gilloteaux",
"email": "perrine.paul-gilloteaux@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-4822-165X",
"gridid": null,
"typeEntity": "Person",
"note": "Leader of the project"
},
{
"type_role": [
"Contributor"
],
"name": "Kota Miura",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-6926-191X",
"gridid": null,
"typeEntity": "Person",
"note": "Main technical support and one of the founders of the project"
},
{
"type_role": [
"Contributor"
],
"name": "Chong Zhang",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": "Co-leader of the developement"
},
{
"type_role": [
"Contributor"
],
"name": "Alban Gaignard",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-3597-8557",
"gridid": null,
"typeEntity": "Person",
"note": "Developed the core ontology (data model) and enabled reuse of the content through W3C standards"
},
{
"type_role": [
"Contributor"
],
"name": "Matúš Kalaš",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-1509-4981",
"gridid": null,
"typeEntity": "Person",
"note": "Coordinator of the EDAM-bioimaging ontology development"
},
{
"type_role": [
"Contributor"
],
"name": "Leandro Scholz",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-2411-0429",
"gridid": null,
"typeEntity": "Person",
"note": "Worked on the curation instructions"
},
{
"type_role": [
"Contributor"
],
"name": "Florian Levet",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-4009-6225",
"gridid": null,
"typeEntity": "Person",
"note": "Development of Python scripts"
},
{
"type_role": [
"Documentor"
],
"name": "Taggers",
"email": null,
"url": "http://biii.eu/show-taggers",
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": "People curating tools"
}
],
"tool_licence": "Other",
"documentation": "https://github.com/NeuBIAS/bise/wiki",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-03-26T15:45:10Z",
"teams": [],
"source_repository": null
},
{
"id": 268,
"name": "ChagasDB",
"description": "Manual-curated database regrouping published results referenced in Pubmed.",
"homepage": "https://chagasdb.tagc.univ-amu.fr",
"biotoolsID": "chagasdb",
"biotoolsCURIE": "biotools:chagasdb",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3334",
"http://edamontology.org/topic_3305",
"http://edamontology.org/topic_3421",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0634"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "Edecio Cunha-Neto",
"email": "edecunha@gmail.com",
"url": null,
"orcidid": "https://orcid.org/0000-0002-3699-3345",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Lionel Spinelli",
"email": "lionel.spinelli@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-9228-8141",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Christophe Chevillard",
"email": "christophe.chevillard@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-5269-8813",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:25:34.821693Z",
"teams": [],
"source_repository": "https://github.com/TAGC-ComplexDisease/ChagasDB"
},
{
"id": 91,
"name": "DataDiscovery",
"description": "DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters.\n\nThis tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.",
"homepage": "https://urgi.versailles.inrae.fr/data-discovery/",
"biotoolsID": "DataDiscovery",
"biotoolsCURIE": "biotools:DataDiscovery",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI",
"FR"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3810"
],
"primary_publication": [
"10.3835/plantgenome2015.06.0038"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"name": "urgi-support",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-07-29T13:42:39.375595Z",
"teams": [
"URGI"
],
"source_repository": "https://forgemia.inra.fr/urgi-is/data-discovery"
},
{
"id": 90,
"name": "FAIDARE",
"description": "FAIDARE: FAIR Data-finder for Agronomic Research. \nThe purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.\n\nIt is based on the Breeding API (BrAPI) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface. It also provides a standard interface that can be accessed programatically through web services.\n\nIt is an extension of the generic DataDiscovery portal, a web portal that allows finding any type of data across several databases through a lightweight keyword based search. FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.",
"homepage": "https://urgi.versailles.inrae.fr/faidare/",
"biotoolsID": "faidare",
"biotoolsCURIE": "biotools:faidare",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI"
],
"scientific_topics": [
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3810"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"name": "URGI support",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://urgi.versailles.inrae.fr/faidare/help",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-09-02T05:04:34.812991Z",
"teams": [
"URGI"
],
"source_repository": "https://forgemia.inra.fr/urgi-is/faidare"
}
]
}