HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 211,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=60&ordering=maturity",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=20&ordering=maturity",
"results": [
{
"id": 120,
"name": "Cocoa Genome Hub",
"description": "The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.",
"homepage": "https://cocoa-genome-hub.southgreen.fr/",
"biotoolsID": "Cocoa_Genome_Hub",
"biotoolsCURIE": "biotools:Cocoa_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub",
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_3810",
"http://edamontology.org/topic_0203"
],
"primary_publication": [
"10.1186/s12864-017-4120-9"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Maintainer"
],
"name": "CIRAD",
"email": null,
"url": "https://www.cirad.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "ANR",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Argout",
"email": "xavier.argout@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-0100-5511",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Droc",
"email": "gaetan.droc@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Lanaud",
"email": "claire.lanaud@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-6411-7310",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "http://api.tripal.info/api/tripal/3.x",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:43.154205Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"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": [
"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
},
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "http://aria.pasteur.fr/contact-info",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"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": 84,
"name": "IMGT, the international ImMunoGeneTics information system",
"description": "IMGT®, the international ImMunoGeneTics information system® is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT® consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.",
"homepage": "http://www.imgt.org/",
"biotoolsID": "imgt",
"biotoolsCURIE": "biotools:imgt",
"tool_type": [
"Database portal",
"Bioinformatics portal",
"Web application",
"Ontology"
],
"collection": [
"elixir-fr-sdp-2019",
"DRCAT"
],
"scientific_topics": [
"http://edamontology.org/topic_3948",
"http://edamontology.org/topic_3930"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Documentor"
],
"name": "DRCAT",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "http://www.imgt.org/IMGTinformation/Contact.php",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.imgt.org/FAQ/",
"maturity": "Mature",
"cost": "Free of charge (with restrictions)",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:34:08.902650Z",
"teams": [],
"source_repository": null
},
{
"id": 97,
"name": "Ocean Gene Atlas",
"description": "The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs).\nUser queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.",
"homepage": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/",
"biotoolsID": "Ocean_Gene_Atlas",
"biotoolsCURIE": "biotools:Ocean_Gene_Atlas",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3387",
"http://edamontology.org/topic_3174",
"http://edamontology.org/topic_3941"
],
"primary_publication": [
"10.1093/nar/gky376"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "oceangeneatlas@mio.osupytheas.fr",
"url": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/credits",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "MIO",
"email": null,
"url": "https://www.mio.osupytheas.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "OCEANOMICS",
"email": null,
"url": "http://www.oceanomics.eu/",
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": "ANR-11-BTBR-0008"
}
],
"tool_licence": "Not licensed",
"documentation": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/build/pdf/Ocean-Gene-Atlas_User_Manual.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:34.208631Z",
"teams": [],
"source_repository": null
},
{
"id": 135,
"name": "Askomics",
"description": "AskOmics is a visual SPARQL query interface supporting both intuitive data integration and querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL",
"homepage": "https://github.com/askomics",
"biotoolsID": "askomics",
"biotoolsCURIE": "biotools:askomics",
"tool_type": [
"Desktop application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3366"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Anthony Bretaudeau",
"email": "anthony.bretaudeau@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Olivier Dameron",
"email": "olivier.dameron@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Olivier Filangi",
"email": "olivier.filangi@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "AGPL-3.0",
"documentation": "https://github.com/askomics/askomics",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2025-06-09T11:52:30.706337Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 160,
"name": "Frog",
"description": "Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2",
"biotoolsID": "frog2",
"biotoolsCURIE": "biotools:frog2",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0154",
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gkq325"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Frederic Guyon",
"email": "frederic.guyon@univ-paris-diderot.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Maria A. Miteva",
"email": "maria.mitev@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Pierre Tufféry",
"email": "pierre.tuffery@univ-paris-diderot.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1033-9895",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/Frog2/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 960,
"citations": null,
"annual_visits": 6400,
"last_update": "2024-11-25T14:00:39.981509Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 117,
"name": "AuReMe",
"description": "A unified workspace built around a Python package PADMet (Python library for hAndling metaData of METabolism), to house the reconstruction of genome-scale metabolic models.",
"homepage": "http://aureme.genouest.org",
"biotoolsID": "aureme",
"biotoolsCURIE": "biotools:aureme",
"tool_type": [
"Command-line tool",
"Workbench",
"Workflow"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_2259"
],
"primary_publication": [
"10.1371/journal.pcbi.1006146"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "anne.siegel@inria.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://aureme.genouest.org/aureme.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:31.744031Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"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": [
"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
},
{
"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
}
],
"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"
],
"source_repository": "https://github.com/IFB-ElixirFr/edam-browser"
},
{
"id": 107,
"name": "GENOMICUS",
"description": "Genomicus is a genome browser that enables users to navigate in 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/",
"biotoolsID": "GENOMICUS",
"biotoolsCURIE": "biotools:GENOMICUS",
"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/bioinformatics/btq079",
"10.1093/nar/gkab1091"
],
"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
},
{
"type_role": [],
"name": "IBENS - DYOGEN Team",
"email": null,
"url": "http://www.ibens.ens.fr/?rubrique43&lang=en",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "PB-IBENS",
"email": null,
"url": "https://www.ibens.ens.fr/?rubrique55",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": "https://www.youtube.com/watch?v=CokUh3fUbGQ",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2023-03-06T14:10:23.175189Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 101,
"name": "Genomicus-plants",
"description": "Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "https://www.genomicus.biologie.ens.fr/genomicus-plants",
"biotoolsID": "Genomicus-Plants",
"biotoolsCURIE": "biotools:Genomicus-Plants",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"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",
"http://edamontology.org/topic_0780"
],
"primary_publication": [
"10.1093/nar/gks1156",
"10.1093/pcp/pcu177"
],
"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": 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": 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_0797",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_3673",
"http://edamontology.org/topic_0196",
"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": [
"ABiMS",
"South Green"
],
"source_repository": "https://github.com/galaxyproject/galaxy"
},
{
"id": 150,
"name": "BioMAJ",
"description": "BioMAJ is a workflow engine dedicated to data synchronization and processing. The Software automates the update cycle and the supervision of the locally mirrored databank repository.",
"homepage": "http://biomaj.genouest.org/",
"biotoolsID": "biomaj",
"biotoolsCURIE": "biotools:biomaj",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3071"
],
"primary_publication": [
"10.1093/bioinformatics/btn325"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "GenOuest platform",
"email": "support@genouest.org",
"url": "http://www.genouest.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Olivier Sallou",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "AGPL-3.0",
"documentation": "http://biomaj.readthedocs.io/en/latest/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T16:17:07.096336Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 241,
"name": "iPPI-DB",
"description": "IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large variety of data is stored within IPPI-DB: structural, pharmacological, binding and activity profile, pharmacokinetic and cytotoxicity when available, as well as some data about the PPI targets themselves.",
"homepage": "https://ippidb.pasteur.fr",
"biotoolsID": "ippi-db",
"biotoolsCURIE": "biotools:ippi-db",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3343"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "Olivier Sperandio",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-6610-2729",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-01-14T17:37:37Z",
"teams": [],
"source_repository": "https://gitlab.pasteur.fr/ippidb/ippidb-web/"
},
{
"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": [
"Primary contact",
"Developer"
],
"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": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "https://research.pasteur.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact",
"Support"
],
"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": [],
"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
},
{
"type_role": [
"Primary contact",
"Developer"
],
"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": [
"Contributor"
],
"name": "France Génomique",
"email": null,
"url": "https://www.france-genomique.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"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": 190,
"name": "CRISPRFinder",
"description": "Detects this family of direct repeats found in the DNA of many bacteria and archaea.",
"homepage": "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index",
"biotoolsID": "crisprfinder",
"biotoolsCURIE": "biotools:crisprfinder",
"tool_type": [
"Web application",
"Database portal"
],
"collection": [
"CRISPR"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_2885",
"http://edamontology.org/topic_0203"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Marie Touchon",
"email": "mtouchon@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Unlicense",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 480,
"citations": null,
"annual_visits": 2273,
"last_update": "2024-11-24T21:05:00.924973Z",
"teams": [
"EBIO"
],
"source_repository": null
},
{
"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": 164,
"name": "InterEvDock",
"description": "Ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock2",
"biotoolsID": "interevdock2",
"biotoolsCURIE": "biotools:interevdock2",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275",
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_0080"
],
"primary_publication": [
"10.1093/nar/gky377",
"10.1093/nar/gkw340"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Raphael Guerois",
"email": "raphael.guerois@cea.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-5294-2858",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Jessica Andreani",
"email": "jessica.andreani@cea.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 310,
"citations": null,
"annual_visits": 1120,
"last_update": "2024-11-24T21:00:12.284563Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 4,
"name": "Coffee Genome Hub",
"description": "The Coffee Genome Hub is an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee.",
"homepage": "https://coffee-genome-hub.southgreen.fr/",
"biotoolsID": "Coffee_Genome_Hub",
"biotoolsCURIE": "biotools:Coffee_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/nar/gku1108"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Alexis Dereeper",
"email": "alexis.dereeper@ird.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Gaetan Droc",
"email": "droc@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "http://coffee-genome.org/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:58:58.975865Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 104,
"name": "ANISEED",
"description": "ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). It integrates for each species: \ni) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; \nii) A multispecies genomic browser; \niii) a Genomicus gene synteny browser.",
"homepage": "https://www.aniseed.fr",
"biotoolsID": "ANISEED",
"biotoolsCURIE": "biotools:ANISEED",
"tool_type": [
"Database portal",
"Web API",
"Web application",
"Ontology"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3065",
"http://edamontology.org/topic_3383",
"http://edamontology.org/topic_3679",
"http://edamontology.org/topic_3064",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_2229",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_0219",
"http://edamontology.org/topic_0084",
"http://edamontology.org/topic_3308"
],
"primary_publication": [
"10.1101/gr.108175.110",
"10.1093/nar/gkv966",
"10.1093/nar/gkx1108",
"10.1016/j.cub.2005.12.044",
"10.1093/nar/gkz955"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "contact@aniseed.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Christelle Dantec",
"email": "christelle.dantec@crbm.cnrs.fr",
"url": "http://www.crbm.cnrs.fr/en/team/lemaire/",
"orcidid": "https://orcid.org/0000-0001-7247-6460",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Support"
],
"name": null,
"email": "contact@aniseed.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Patrick Lemaire",
"email": "patrick.lemaire@crbm.cnrs.fr",
"url": "http://www.crbm.cnrs.fr/en/team/lemaire/",
"orcidid": "https://orcid.org/0000-0003-4925-2009",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "https://www.aniseed.fr/api",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2023-09-25T14:25:18.910230Z",
"teams": [],
"source_repository": null
}
]
}