HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 233,
"next": null,
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=200&ordering=-collection",
"results": [
{
"id": 13,
"name": "Human Splicing Finder",
"description": "The Human Splicing Finder (HSF) system combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS).",
"homepage": "http://www.umd.be/HSF3/",
"biotoolsID": "human_splicing_finder",
"biotoolsCURIE": "biotools:human_splicing_finder",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_3571",
"http://edamontology.org/topic_3320",
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_0199",
"http://edamontology.org/topic_3063"
],
"primary_publication": [
"10.1093/nar/gkp215"
],
"operating_system": [
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "http://www.umd.be/HSF3/contactus.html",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Christophe Béroud",
"email": "christophe.beroud@inserm.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": null,
"documentation": "http://www.umd.be/HSF3/technicaltips.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T13:49:29.814329Z",
"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_3053",
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_3325"
],
"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": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"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
}
],
"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": 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_3512",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_0199",
"http://edamontology.org/topic_3574",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_0634"
],
"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": 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_3512",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_0199",
"http://edamontology.org/topic_3574",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_0634"
],
"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_3053",
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_3325"
],
"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": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"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
}
],
"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": 13,
"name": "Human Splicing Finder",
"description": "The Human Splicing Finder (HSF) system combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS).",
"homepage": "http://www.umd.be/HSF3/",
"biotoolsID": "human_splicing_finder",
"biotoolsCURIE": "biotools:human_splicing_finder",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_3571",
"http://edamontology.org/topic_3320",
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_0199",
"http://edamontology.org/topic_3063"
],
"primary_publication": [
"10.1093/nar/gkp215"
],
"operating_system": [
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "http://www.umd.be/HSF3/contactus.html",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Christophe Béroud",
"email": "christophe.beroud@inserm.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": null,
"documentation": "http://www.umd.be/HSF3/technicaltips.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T13:49:29.814329Z",
"teams": [],
"source_repository": null
},
{
"id": 9,
"name": "remap",
"description": "Display restriction enzyme binding sites in a nucleotide sequence.",
"homepage": "http://emboss.open-bio.org/rel/rel6/apps/remap.html",
"biotoolsID": "remap",
"biotoolsCURIE": "biotools:remap",
"tool_type": [
"Database portal",
"Command-line tool"
],
"collection": [
"EMBOSS"
],
"scientific_topics": [
"http://edamontology.org/topic_3125"
],
"primary_publication": [
"10.1016/S0168-9525(00)02024-2"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "EMBOSS",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "EMBOSS Contributors",
"email": null,
"url": "http://emboss.open-bio.org/html/use/pr01s01.html",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Support"
],
"name": "EMBOSS",
"email": "emboss@emboss.open-bio.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "EMBL-EBI",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "emboss@emboss.open-bio.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "emboss-bug@emboss.open-bio.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "UK MRC",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Wellcome Trust",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "UK BBSRC",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://emboss.open-bio.org/rel/rel6/apps/remap.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2018-12-10T12:58:55Z",
"teams": [],
"source_repository": "http://emboss.open-bio.org/html/adm/ch01s01.html"
},
{
"id": 105,
"name": "REPET",
"description": "The REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)\n TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.",
"homepage": "https://urgi.versailles.inrae.fr/Tools/REPET",
"biotoolsID": "repet",
"biotoolsCURIE": "biotools:repet",
"tool_type": [
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI",
"REPET",
"PlantBioinfoPF"
],
"scientific_topics": [
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_0097"
],
"primary_publication": [
"10.1371/journal.pone.0091929",
"10.1371/journal.pone.0016526",
"10.1371/journal.pcbi.0010022",
"10.1007/s00239-003-0007-2"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer",
"Contributor",
"Maintainer",
"Provider",
"Support",
"Documentor"
],
"name": "URGI",
"email": "urgi-repet@versailles.inra.fr",
"url": "http://urgi.versailles.inra.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235"
},
{
"type_role": [
"Developer",
"Contributor",
"Maintainer",
"Provider",
"Support",
"Documentor"
],
"name": "URGI",
"email": "urgi-repet@versailles.inrae.fr",
"url": "http://urgi.versailles.inrae.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235"
}
],
"tool_licence": "CECILL-2.0",
"documentation": "https://urgi.versailles.inrae.fr/Tools/REPET",
"maturity": "Legacy",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-09-09T08:10:41.737859Z",
"teams": [
"URGI"
],
"source_repository": "https://urgi.versailles.inrae.fr/download/repet/"
},
{
"id": 8,
"name": "Plant DataDiscovery",
"description": "The purpose of this web portal is to facilitate the discoverability of public data on plant biology managed by different laboratories across the world.\n\nThe web portal indexes and makes findable any kind of plant data. Plant DataDiscovery is an implementation of DataDiscovery.",
"homepage": "https://urgi.versailles.inrae.fr/data-discovery/",
"biotoolsID": "Plant_DataDiscovery",
"biotoolsCURIE": "biotools:Plant_DataDiscovery",
"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_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"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.inrae.fr/data-discovery/about",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-12-12T16:19:23.574076Z",
"teams": [],
"source_repository": null
},
{
"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_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"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"
},
{
"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_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"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": 92,
"name": "RARe",
"description": "RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultivated plants, wild species related to domestic animals, forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms and environmental organisms.\nThe purpose of this web portal is to facilitate the discoverability of these data. \nRARe search is an implementation of DataDiscovery.",
"homepage": "https://urgi.versailles.inrae.fr/rare/",
"biotoolsID": "RARe",
"biotoolsCURIE": "biotools:RARe",
"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_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_3810"
],
"primary_publication": [],
"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.inrae.fr/rare/about",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-07-29T13:42:40.608985Z",
"teams": [
"URGI"
],
"source_repository": null
},
{
"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_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"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": 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_2259",
"http://edamontology.org/topic_3172",
"http://edamontology.org/topic_3307"
],
"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": 88,
"name": "MetExplore",
"description": "Metabolic network curation, visualisation and omics data analysis. It is possible to curate and annotate metabolic networks in a collaborative environment. Several tools are available for metabolomics data mapping in networks and visualisation.",
"homepage": "http://www.metexplore.fr/",
"biotoolsID": "metexplore",
"biotoolsCURIE": "biotools:metexplore",
"tool_type": [
"Web service",
"Web application",
"Workbench"
],
"collection": [
"elixir-fr-sdp-2019",
"EBI Training Tools"
],
"scientific_topics": [
"http://edamontology.org/topic_0602"
],
"primary_publication": [
"10.1093/nar/gky301",
"10.1093/nar/gkq312"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "MetaboHub",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Fabien JOURDAN",
"email": "fabien.jourdan@inra.fr",
"url": "https://sites.google.com/site/fabienjourdan/",
"orcidid": "https://orcid.org/0000-0001-9401-2894",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "ludovic.cottret@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Support"
],
"name": null,
"email": "metexplore@oulouse.inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://metexplore.toulouse.inra.fr/metexploreViz/doc/documentation.php",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-04-28T07:17:11.601858Z",
"teams": [],
"source_repository": null
},
{
"id": 111,
"name": "Galaxy Pasteur",
"description": "A wide variety of tools from the Galaxy instance of Institut Pasteur, France.",
"homepage": "https://galaxy.pasteur.fr/",
"biotoolsID": "Galaxy_Pasteur",
"biotoolsCURIE": "biotools:Galaxy_Pasteur",
"tool_type": [
"Workbench"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0080"
],
"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": "2020-03-16T18:06:05Z",
"teams": [],
"source_repository": null
},
{
"id": 112,
"name": "CRISPRCas",
"description": "Suite of web applications for analysing Clustered Regularly Interspaced Short Palindromic Repeats.",
"homepage": "https://crisprcas.i2bc.paris-saclay.fr/",
"biotoolsID": "CRISPRCas",
"biotoolsCURIE": "biotools:CRISPRCas",
"tool_type": [
"Suite"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0080"
],
"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": "2020-02-07T06:24:26Z",
"teams": [],
"source_repository": null
},
{
"id": 113,
"name": "ParameciumDB",
"description": "Online community database for Paramecium species. Contains annotation of genome sequences and features, genome-wide data sets, advanced capabilities to query, retrieve, visualize and compare data.",
"homepage": "https://paramecium.i2bc.paris-saclay.fr",
"biotoolsID": "parameciumdb",
"biotoolsCURIE": "biotools:parameciumdb",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_3321",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_0080"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "https://paramecium.i2bc.paris-saclay.fr/cgi/user/contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Terms of Use",
"email": null,
"url": "https://paramecium.i2bc.paris-saclay.fr/parawiki/Terms_of_Use",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "CC-BY-4.0",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:30.463079Z",
"teams": [],
"source_repository": null
},
{
"id": 114,
"name": "GalaxEast",
"description": "GalaxEast aims at providing a large range of bioinformatics tools for the analysis of various types of Omics data. It supports reproducible computational research by providing an environment for performing and recording bioinformatics analyses.",
"homepage": "http://www.galaxeast.fr/",
"biotoolsID": "GalaxEast",
"biotoolsCURIE": "biotools:GalaxEast",
"tool_type": [
"Workbench"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3391"
],
"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": "2020-01-24T09:54:41Z",
"teams": [],
"source_repository": null
},
{
"id": 115,
"name": "GalaxyCat",
"description": "An online catalog that lists all the tools available on various Galaxy instances and thus allows through a simple web interface to quickly find on which instances a tool is usable.",
"homepage": "http://galaxycat.france-bioinformatique.fr/",
"biotoolsID": "GalaxyCat",
"biotoolsCURIE": "biotools:GalaxyCat",
"tool_type": [],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0091"
],
"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": "2020-01-24T09:54:19Z",
"teams": [],
"source_repository": null
}
]
}