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=200&ordering=-collection",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=160&ordering=-collection",
"results": [
{
"id": 100,
"name": "Genomicus-fungi",
"description": "Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus-fungi/",
"biotoolsID": "Genomicus-fungi",
"biotoolsCURIE": "biotools:Genomicus-fungi",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0623"
],
"primary_publication": [
"10.1093/nar/gks1156"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"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_0749",
"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_3511"
],
"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": 109,
"name": "RSAT dyad-analysis",
"description": "Detect over- or under-represented dyads (spaced pairs of k-mers) in sequences.",
"homepage": "http://teaching.rsat.eu/dyad-analysis_form.cgi",
"biotoolsID": "RSAT_dyad-analysis",
"biotoolsCURIE": "biotools:RSAT_dyad-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_0204",
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0749"
],
"primary_publication": [
"10.1093/nar/28.8.1808"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "UNAM",
"email": null,
"url": null,
"orcidid": null,
"gridid": "grid.9486.3",
"typeEntity": "Institute",
"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
},
{
"type_role": [
"Primary contact",
"Developer",
"Documentor",
"Maintainer",
"Support",
"Provider"
],
"name": "Jacques van Helden",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"gridid": null,
"typeEntity": "Person",
"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": 108,
"name": "RSAT position-analysis",
"description": "Detect oligomers (k-mers) whose positional distribution significantly discard from a homogeneous distribution.",
"homepage": "http://teaching.rsat.eu/position-analysis_form.cgi",
"biotoolsID": "RSAT-position-analysis",
"biotoolsCURIE": "biotools:RSAT-position-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_0204",
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0749"
],
"primary_publication": [
"10.1093/nar/28.4.1000"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Developer",
"Documentor",
"Maintainer",
"Support",
"Provider"
],
"name": "Jacques van Helden",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"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": 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_0204",
"http://edamontology.org/topic_3511",
"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": [],
"name": "Université Libre de Bruxelles",
"email": null,
"url": "https://www.ulb.be/",
"orcidid": null,
"gridid": "grid.4989.c",
"typeEntity": "Institute",
"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
}
],
"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": 93,
"name": "MicroScope platform",
"description": "MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.",
"homepage": "https://mage.genoscope.cns.fr/microscope/",
"biotoolsID": "MicroScope_platform",
"biotoolsCURIE": "biotools:MicroScope_platform",
"tool_type": [
"Bioinformatics portal",
"Web application",
"Workbench"
],
"collection": [
"elixir-fr-sdp-2019",
"fr"
],
"scientific_topics": [
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_3301",
"http://edamontology.org/topic_0219",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_2259"
],
"primary_publication": [
"10.1093/nar/gks1194",
"10.1093/database/bap021",
"10.1093/nar/gkj406",
"10.1093/nar/gkw1101",
"10.1093/bib/bbx113",
"10.1093/nar/gkz926"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Provider",
"Developer",
"Support",
"Primary contact"
],
"name": "LABGeM - CEA/Genosocope - UMR8030",
"email": "labgem@genoscope.cns.fr",
"url": "https://labgem.genoscope.cns.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": null,
"documentation": "https://microscope.readthedocs.io/en/stable/",
"maturity": "Mature",
"cost": "Free of charge (with restrictions)",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:28Z",
"teams": [
"MicroScope"
],
"source_repository": null
},
{
"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": 96,
"name": "GINsim",
"description": "Computer tool for the modeling and simulation of genetic regulatory networks.",
"homepage": "http://ginsim.org/",
"biotoolsID": "ginsim",
"biotoolsCURIE": "biotools:ginsim",
"tool_type": [
"Desktop application"
],
"collection": [
"elixir-fr-sdp-2019",
"FR",
"EBI Training Tools",
"PerMedCoE"
],
"scientific_topics": [
"http://edamontology.org/topic_2259",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0204"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support",
"Developer"
],
"name": null,
"email": null,
"url": "http://ginsim.org/contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://ginsim.org/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:09:51.625867Z",
"teams": [],
"source_repository": "http://ginsim.org/models_repository"
},
{
"id": 119,
"name": "RSAT suite",
"description": "Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows.",
"homepage": "http://rsat.eu",
"biotoolsID": "rsat",
"biotoolsCURIE": "biotools:rsat",
"tool_type": [
"Web application",
"Suite"
],
"collection": [
"elixir-fr-sdp-2019",
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_3125",
"http://edamontology.org/topic_3512"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Jacques van Helden",
"email": "Jacques.van-Helden@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Other",
"documentation": "http://rsat.eu",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:33.330732Z",
"teams": [
"TAGC-BU"
],
"source_repository": null
},
{
"id": 178,
"name": "NGS-QC Generator",
"description": "Comparative analysis between ChIP-seq and other enrichment-related NGS datasets requires prior characterization of their degree of technical similarity. The Galaxy tool NGS-QC Generator is a computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies to improve the quality of sample-derived datasets.",
"homepage": "http://www.ngs-qc.org/",
"biotoolsID": "ngs-qc_generator",
"biotoolsCURIE": "biotools:ngs-qc_generator",
"tool_type": [
"Web application"
],
"collection": [
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_3572",
"http://edamontology.org/topic_3169"
],
"primary_publication": [
"10.1007/978-1-4939-3578-9_13"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "contact@ngs-qc.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "http://www.ngs-qc.org/tutorial.php",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T14:05:15.865852Z",
"teams": [
"BiGEst"
],
"source_repository": null
},
{
"id": 176,
"name": "Galaxy",
"description": "Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.",
"homepage": "https://galaxyproject.org/",
"biotoolsID": "galaxy",
"biotoolsCURIE": "biotools:galaxy",
"tool_type": [
"Workflow",
"Bioinformatics portal",
"Web application",
"Web API"
],
"collection": [
"Galaxy",
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_3673",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_0196",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1093/nar/gkw343",
"10.1093/nar/gkac247"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Galaxy support",
"email": null,
"url": "https://biostar.usegalaxy.org/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Galaxy Community",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
}
],
"tool_licence": "AFL-3.0",
"documentation": "https://usegalaxy.org/api/docs",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 400,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:46:57.861339Z",
"teams": [
"South Green"
],
"source_repository": "https://github.com/galaxyproject/galaxy"
},
{
"id": 87,
"name": "Genetic and Genomic Information System (GnpIS)",
"description": "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.\nAccessible via a public web portal, GnpIS enables different types of data to be managed, browsed and retrieved via specialized search tools and web services.\nGnpIS is used by the French National Research Institute for Agriculture, Food and Environment (INRAE) and its partners in major national and international projects.",
"homepage": "https://urgi.versailles.inrae.fr/gnpis",
"biotoolsID": "gnpis",
"biotoolsCURIE": "biotools:gnpis",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_0625"
],
"primary_publication": [
"10.1093/database/bat058",
"10.1007/978-1-4939-6658-5_5",
"10.3835/plantgenome2015.06.0038"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "urgi-contact@versailles.inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "URGI helpdesk",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
}
],
"tool_licence": "CC-BY-4.0",
"documentation": "https://urgi.versailles.inrae.fr/Data-Services/Data-Access/GnpIS",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-12-19T17:15:16.754031Z",
"teams": [
"URGI"
],
"source_repository": "https://forge.inrae.fr/urgi/is/gnpis"
},
{
"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": "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"
},
{
"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"
}
],
"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": 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_0204",
"http://edamontology.org/topic_3511",
"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": [],
"name": "Université Libre de Bruxelles",
"email": null,
"url": "https://www.ulb.be/",
"orcidid": null,
"gridid": "grid.4989.c",
"typeEntity": "Institute",
"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
}
],
"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": 85,
"name": "ARIA",
"description": "A software for automated NOE assignment and NMR structure calculation.",
"homepage": "http://aria.pasteur.fr/",
"biotoolsID": "aria",
"biotoolsCURIE": "biotools:aria",
"tool_type": [
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"Institut Pasteur",
"FR"
],
"scientific_topics": [
"http://edamontology.org/topic_1317",
"http://edamontology.org/topic_0593",
"http://edamontology.org/topic_0176",
"http://edamontology.org/topic_3306",
"http://edamontology.org/topic_3332",
"http://edamontology.org/topic_2275",
"http://edamontology.org/topic_0081",
"http://edamontology.org/topic_0078"
],
"primary_publication": [
"10.1093/bioinformatics/btl589"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "http://aria.pasteur.fr/contact-info",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Michael Nilges",
"email": "michael.nilges@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Benjamin Bardiaux",
"email": "benjamin.bardiaux@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "MIT",
"documentation": "http://aria.pasteur.fr/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:37:34.670261Z",
"teams": [],
"source_repository": null
},
{
"id": 109,
"name": "RSAT dyad-analysis",
"description": "Detect over- or under-represented dyads (spaced pairs of k-mers) in sequences.",
"homepage": "http://teaching.rsat.eu/dyad-analysis_form.cgi",
"biotoolsID": "RSAT_dyad-analysis",
"biotoolsCURIE": "biotools:RSAT_dyad-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_0204",
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0749"
],
"primary_publication": [
"10.1093/nar/28.8.1808"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "UNAM",
"email": null,
"url": null,
"orcidid": null,
"gridid": "grid.9486.3",
"typeEntity": "Institute",
"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
},
{
"type_role": [
"Primary contact",
"Developer",
"Documentor",
"Maintainer",
"Support",
"Provider"
],
"name": "Jacques van Helden",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"gridid": null,
"typeEntity": "Person",
"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": 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_0749",
"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_3511"
],
"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": 108,
"name": "RSAT position-analysis",
"description": "Detect oligomers (k-mers) whose positional distribution significantly discard from a homogeneous distribution.",
"homepage": "http://teaching.rsat.eu/position-analysis_form.cgi",
"biotoolsID": "RSAT-position-analysis",
"biotoolsCURIE": "biotools:RSAT-position-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_0204",
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0749"
],
"primary_publication": [
"10.1093/nar/28.4.1000"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Developer",
"Documentor",
"Maintainer",
"Support",
"Provider"
],
"name": "Jacques van Helden",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"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": 96,
"name": "GINsim",
"description": "Computer tool for the modeling and simulation of genetic regulatory networks.",
"homepage": "http://ginsim.org/",
"biotoolsID": "ginsim",
"biotoolsCURIE": "biotools:ginsim",
"tool_type": [
"Desktop application"
],
"collection": [
"elixir-fr-sdp-2019",
"FR",
"EBI Training Tools",
"PerMedCoE"
],
"scientific_topics": [
"http://edamontology.org/topic_2259",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0204"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support",
"Developer"
],
"name": null,
"email": null,
"url": "http://ginsim.org/contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://ginsim.org/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:09:51.625867Z",
"teams": [],
"source_repository": "http://ginsim.org/models_repository"
},
{
"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"
}
]
}