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=-source_repository",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=180&ordering=-source_repository",
"results": [
{
"id": 196,
"name": "Viral Host Range database",
"description": "The Viral Host Range database represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the years, countless host range experiments have been performed in many laboratories. However, these data are not readily available to the community and are therefore underexploited.\n\nThe VHRdb is an online resource that centralizes experimental data related to the host range of viruses. While it originates from bacteriophages and bacteria interaction studies, its design is compatible with viruses infecting all living forms. Users can browse publicly available data to find which host is infected by a virus, and vice versa. Users can also upload their own data while keeping it private or making it public, analyze results across independent sets of data, generate and visualize outputs. Data implemented in the VHRdb are linked to users and, if available, to publications and sequence identifiers.",
"homepage": "https://viralhostrangedb.pasteur.cloud/",
"biotoolsID": "VHRdb",
"biotoolsCURIE": "biotools:VHRdb",
"tool_type": [
"Database portal",
"Web API",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3489",
"http://edamontology.org/topic_0781"
],
"primary_publication": [
"10.1093/bioinformatics/btab070"
],
"operating_system": [
"Mac",
"Windows",
"Linux"
],
"tool_credit": [
{
"type_role": [
"Contributor",
"Developer"
],
"name": "LAMY-BESNIER Quentin",
"email": null,
"url": "https://research.pasteur.fr/fr/member/fr-quentin-lamy-besnier/",
"orcidid": "https://orcid.org/0000-0002-7141-6340",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Documentor"
],
"name": "MÉNAGER Hervé",
"email": null,
"url": "https://research.pasteur.fr/fr/member/herve-menager/",
"orcidid": "https://orcid.org/0000-0002-7552-1009",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Institut Pasteur",
"email": null,
"url": null,
"orcidid": null,
"gridid": "grid.428999.7",
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer",
"Developer"
],
"name": "Bryan Brancotte",
"email": null,
"url": "https://research.pasteur.fr/en/member/bryan-brancotte",
"orcidid": "https://orcid.org/0000-0001-8669-5525",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "DEBARBIEUX Laurent",
"email": null,
"url": "https://research.pasteur.fr/fr/member/laurent-debarbieux/",
"orcidid": "https://orcid.org/0000-0001-6875-5758",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://hub.pages.pasteur.fr/viralhostrangedb/",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-06-24T08:58:13.476714Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://gitlab.pasteur.fr/hub/viralhostrangedb/"
},
{
"id": 269,
"name": "Galaxy France",
"description": "Galaxy is an open-source platform for FAIR data analysis that enables users to: i) use tools from various domains (that can be plugged into workflows) through its graphical web interface, ii) run code in interactive environments (RStudio, Jupyter, ...) along with other tools or workflows, iii) manage data by sharing and publishing results, workflows, and visualizations, iv) ensure reproducibility by capturing the necessary information to repeat and understand data analyses.\n\nUseGalaxy.fr is the national Galaxy instance for ELIXIR-FR.",
"homepage": "https://usegalaxy.fr/",
"biotoolsID": "galaxy_france",
"biotoolsCURIE": "biotools:galaxy_france",
"tool_type": [],
"collection": [
"COVID-19"
],
"scientific_topics": [
"http://edamontology.org/topic_3172",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_0121",
"http://edamontology.org/topic_3474",
"http://edamontology.org/topic_3955"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Maintainer"
],
"name": "IFB - Institut Français de Bioinformatique",
"email": null,
"url": "https://www.france-bioinformatique.fr/en/home/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "ANR RENABI",
"email": null,
"url": "https://anr.fr/ProjetIA-11-INBS-0013",
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "IFB Core Cluster",
"email": null,
"url": "https://www.france-bioinformatique.fr/en/ifb-core-cluster/",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
}
],
"tool_licence": null,
"documentation": "https://galaxyproject.org/develop/api/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-04-24T09:37:17.765772Z",
"teams": [
"ABiMS",
"IFB Core"
],
"source_repository": "https://gitlab.com/ifb-elixirfr/usegalaxy-fr/infrastructure/"
},
{
"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": 265,
"name": "MetamORF",
"description": "A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta-analysis.\n\nMetamORF: A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta analysis.",
"homepage": "http://metamorf.hb.univ-amu.fr/",
"biotoolsID": "metamorf",
"biotoolsCURIE": "biotools:metamorf",
"tool_type": [
"Command-line tool",
"Database portal",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0659"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "Christine Brun",
"email": "christine-g.brun@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-02-22T07:55:26Z",
"teams": [
"TAGC-BU"
],
"source_repository": "https://github.com/TAGC-NetworkBiology/MetamORF"
},
{
"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_0621",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3334",
"http://edamontology.org/topic_3305",
"http://edamontology.org/topic_3421"
],
"primary_publication": [],
"operating_system": [
"Mac",
"Linux",
"Windows"
],
"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": 264,
"name": "PanExplorer",
"description": "A web-based tool for exploratory analysis and visualization of bacterial pan-genomes.",
"homepage": "http://panexplorer.southgreen.fr",
"biotoolsID": "panexplorer",
"biotoolsCURIE": "biotools:panexplorer",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3382",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_3175"
],
"primary_publication": [],
"operating_system": [
"Mac",
"Linux",
"Windows"
],
"tool_credit": [
{
"type_role": [],
"name": "Alexis Dereeper",
"email": "alexis.dereeper@ird.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-8120-8409",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Damien F Meyer",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Marilyne Summo",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T15:26:52.796766Z",
"teams": [
"South Green"
],
"source_repository": "https://github.com/SouthGreenPlatform/PanExplorer"
},
{
"id": 125,
"name": "Gigwa",
"description": "The Gigwa application, which stands for “Genotype Investigator for Genome-Wide Analyses”, provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time. Gigwa provides the means to export filtered data into several popular formats and features connectivity not only with online genomic tools, but also with standalone software such as FlapJack or IGV. Additionnally, Gigwa-hosted datasets are interoperable via two standard REST APIs: GA4GH and BrAPI.",
"homepage": "http://www.southgreen.fr/content/gigwa",
"biotoolsID": "Gigwa",
"biotoolsCURIE": "biotools:Gigwa",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_2885",
"http://edamontology.org/topic_3071"
],
"primary_publication": [
"10.1093/GIGASCIENCE/GIZ051",
"10.1186/s13742-016-0131-8"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Guilhem Sempéré",
"email": "guilhem.sempere@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-7429-2091",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "gigwa@cirad.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "AGPL-3.0",
"documentation": "http://gigwa.southgreen.fr/gigwa/docs/gigwa_docs.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2020-09-14T08:25:17Z",
"teams": [
"South Green"
],
"source_repository": "https://github.com/SouthGreenPlatform/Gigwa2"
},
{
"id": 262,
"name": "GeMo",
"description": "A web-based platform for the visualization and curation of genome ancestry mosaics.",
"homepage": "https://gemo.southgreen.fr/",
"biotoolsID": "gemo",
"biotoolsCURIE": "biotools:gemo",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_3810",
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_3500"
],
"primary_publication": [],
"operating_system": [
"Mac",
"Linux",
"Windows"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Mathieu Rouard",
"email": "m.rouard@cgiar.org",
"url": null,
"orcidid": "https://orcid.org/0000-0003-0284-1885",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Marilyne Summo",
"email": "marilyne.summo@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-9308-974X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Gaëtan Droc",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Guillaume Martin",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-1801-7500",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": "https://gemo.readthedocs.io",
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T15:31:16.942311Z",
"teams": [
"South Green"
],
"source_repository": "https://github.com/SouthGreenPlatform/GeMo"
},
{
"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": 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": 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": 286,
"name": "pyBRAvo",
"description": "From a list of genes, pyBRAvo produces upstream regulation or signaling networks. pyBRAvo internally leverages the BioPAX ontolgy, the PathwayCommons knowledge graph, and the SPARQL semantic web query language. pyBRAvo can be used through either a Jupyter notebook, or a command line interface.",
"homepage": "https://github.com/pyBRAvo/pyBRAvo",
"biotoolsID": "pybravo",
"biotoolsCURIE": "biotools:pybravo",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_2259"
],
"primary_publication": [
"10.1093/database/baaa113"
],
"operating_system": [],
"tool_credit": [
{
"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"
],
"name": "Alban Gaignard",
"email": "alban.gaignard@univ-nantes.fr",
"url": "http://albangaignard.github.io/",
"orcidid": "https://orcid.org/0000-0002-3597-8557",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Marie Lefebvre",
"email": "marie.lefebvre@inrae.fr",
"url": "https://mariebvr.github.io/marieBvr/",
"orcidid": "https://orcid.org/0000-0002-3093-5873",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Maxime Folschette",
"email": "maxime.folschette@centralelille.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Jeremy Bourdon",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-6674-8626",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Carito Guziolowski",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-5192-0745",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "SyMeTRIC",
"email": null,
"url": "http://symetric.univ-nantes.fr/doku.php",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/pyBRAvo/pyBRAvo",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-05-31T14:22:33.309326Z",
"teams": [
"BiRD"
],
"source_repository": "https://github.com/pyBRAvo/pyBRAvo"
},
{
"id": 138,
"name": "SARTools",
"description": "R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.",
"homepage": "https://github.com/PF2-pasteur-fr/SARTools",
"biotoolsID": "sartools",
"biotoolsCURIE": "biotools:sartools",
"tool_type": [
"Command-line tool"
],
"collection": [
"SARTools"
],
"scientific_topics": [
"http://edamontology.org/topic_2269",
"http://edamontology.org/topic_3308"
],
"primary_publication": [
"10.1371/journal.pone.0157022"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "https://research.pasteur.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "France Génomique",
"email": null,
"url": "https://www.france-genomique.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Developer",
"Primary contact"
],
"name": "Marie-Agnès Dillies",
"email": "marie-agnes.dillies@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/marie-agnes-dillies/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Support",
"Primary contact"
],
"name": "Jean-Yves Coppée",
"email": "jean-yves.coppee@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/jean-yves-coppee/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer",
"Primary contact"
],
"name": "Hugo Varet",
"email": "hugo.varet@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/hugo-varet/",
"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": [
"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-2.0",
"documentation": "https://github.com/PF2-pasteur-fr/SARTools",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2021-04-17T15:12:05Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://github.com/PF2-pasteur-fr/SARTools"
},
{
"id": 274,
"name": "orsum",
"description": "A Python package for filtering and comparing enrichment analyses using a simple principle.",
"homepage": "https://anaconda.org/bioconda/orsum",
"biotoolsID": "orsum",
"biotoolsCURIE": "biotools:orsum",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3407"
],
"primary_publication": [],
"operating_system": [
"Mac",
"Linux",
"Windows"
],
"tool_credit": [
{
"type_role": [],
"name": "Ozan Ozisik",
"email": "ozan.ozisik@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-5980-8002",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Anaïs Baudot",
"email": "anais.baudot@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Morgane Térézol",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-10-29T06:24:51.903827Z",
"teams": [],
"source_repository": "https://github.com/ozanozisik/orsum/"
},
{
"id": 276,
"name": "ODAMNet",
"description": "A Python package to study molecular relationship between environmental factors and rare diseases.",
"homepage": "https://pypi.org/project/ODAMNet/",
"biotoolsID": "odamnet",
"biotoolsCURIE": "biotools:odamnet",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_0602"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [],
"name": "Morgane Térézol",
"email": "morgane.terezol@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-4090-2573",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Anaïs Baudot",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-0885-7933",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Ozan Ozisik",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-5980-8002",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": "https://odamnet.readthedocs.io/en/latest/",
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:02:02.850639Z",
"teams": [],
"source_repository": "https://github.com/MOohTus/ODAMNet"
},
{
"id": 192,
"name": "EDAM-Browser",
"description": "The EDAM Browser is a client-side web-based visualization javascript widget of the EDAM ontology. \nThe EDAM Browser provides users a simple and performant interface to explore EDAM when annotating or searching for bioinformatics resources.\nIts goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.",
"homepage": "https://github.com/IFB-ElixirFr/edam-browser",
"biotoolsID": "edam-browser",
"biotoolsCURIE": "biotools:edam-browser",
"tool_type": [
"Plug-in",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0605",
"http://edamontology.org/topic_0092"
],
"primary_publication": [
"10.21105/joss.00698"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Contributor"
],
"name": "Christophe Blanchet",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Hager Eldakroury",
"email": null,
"url": "https://github.com/HagerDakroury",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Bryan Brancotte",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-8669-5525",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Hervé Ménager",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-7552-1009",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "MIT",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-01-03T15:45:09.883379Z",
"teams": [
"Pasteur HUB",
"IFB Core"
],
"source_repository": "https://github.com/IFB-ElixirFr/edam-browser"
},
{
"id": 249,
"name": "FROGS",
"description": "The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.",
"homepage": "http://frogs.toulouse.inra.fr/",
"biotoolsID": "frogs",
"biotoolsCURIE": "biotools:frogs",
"tool_type": [
"Command-line tool"
],
"collection": [
"FROGS"
],
"scientific_topics": [
"http://edamontology.org/topic_3697",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_3174",
"http://edamontology.org/topic_0637",
"http://edamontology.org/topic_3168"
],
"primary_publication": [
"10.1093/bioinformatics/btx791",
"10.1093/bib/bbab318"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Géraldine Pascal",
"email": "geraldine.pascal@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Géraldine Pascal",
"email": "geraldine.pascal@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/geraldinepascal/FROGS",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:07:18.846597Z",
"teams": [
"MIGALE"
],
"source_repository": "https://github.com/geraldinepascal/FROGS"
},
{
"id": 237,
"name": "D-GENIES",
"description": "D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.",
"homepage": "https://dgenies.toulouse.inrae.fr/",
"biotoolsID": "d-genies",
"biotoolsCURIE": "biotools:d-genies",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0092",
"http://edamontology.org/topic_0080"
],
"primary_publication": [
"10.7717/peerj.4958"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Floréal Cabanettes",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Christophe Klopp",
"email": "christophe.klopp@inrae.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-7126-5477",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact",
"Developer"
],
"name": "Philippe Bordron",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-1975-0920",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Vincent Dominguez",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Christophe Klopp",
"email": "christophe.klopp@toulouse.inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "GenoToul bioinformatics facility",
"email": null,
"url": "http://bioinfo.genotoul.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
}
],
"tool_licence": null,
"documentation": "https://dgenies.readthedocs.io/en/latest/index.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-12-18T10:02:18.098079Z",
"teams": [],
"source_repository": "https://github.com/genotoul-bioinfo/dgenies"
},
{
"id": 145,
"name": "MacSyFinder",
"description": "Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.",
"homepage": "https://github.com/gem-pasteur/macsyfinder",
"biotoolsID": "macsyfinder",
"biotoolsCURIE": "biotools:macsyfinder",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [
"GEM Pasteur"
],
"scientific_topics": [
"http://edamontology.org/topic_0085"
],
"primary_publication": [
"10.1371/journal.pone.0110726",
"10.24072/pcjournal.250"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Bertrand Néron",
"email": "bneron@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Eduardo Rocha",
"email": "eduardo.rocha@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"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
},
{
"type_role": [
"Provider"
],
"name": "Microbial Evolutionary Genomics Unit",
"email": null,
"url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": "CNRS - UMR 352"
},
{
"type_role": [
"Developer"
],
"name": "Bertrand Néron",
"email": "bneron@pasteur.fr",
"url": "https://research.pasteur.fr/en/member/bertrand-neron/",
"orcidid": "https://orcid.org/0000-0002-0220-0482",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Eduardo Rocha",
"email": "eduardo.rocha@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
"orcidid": "https://orcid.org/0000-0001-7704-822X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Bertrand Néron",
"email": "bneron@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Sophie Abby",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-5231-3346",
"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": [],
"name": "C3BI",
"email": null,
"url": "https://research.pasteur.fr/en/center/c3bi/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "https://macsyfinder.readthedocs.io/en/latest/",
"maturity": "Mature",
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T13:49:36.708539Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://github.com/gem-pasteur/macsyfinder"
},
{
"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"
}
]
}