HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 216,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=160&ordering=-maturity",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=120&ordering=-maturity",
"results": [
{
"id": 151,
"name": "ReproGenomics Viewer",
"description": "The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community.",
"homepage": "http://rgv.genouest.org",
"biotoolsID": "reprogenomics_viewer",
"biotoolsCURIE": "biotools:reprogenomics_viewer",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3420"
],
"primary_publication": [
"10.1093/nar/gkv345"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Thomas Darde",
"email": null,
"url": null,
"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": [
"Provider"
],
"name": "irisa.fr",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Olivier Sallou",
"email": "olivier.sallou@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer",
"Primary contact"
],
"name": "Frédéric Chalmel",
"email": "frederic.chalmel@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://rgv.genouest.org/tuto.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:22:51.040462Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 87,
"name": "Genetic and Genomic Information System (GnpIS)",
"description": "A multispecies integrative information system dedicated to plant and fungi pests.. It allows researchers to access genetic, phenotypic and genomic data. It is used by both large international projects and the French National Research Institute for Agriculture, Food and Environment",
"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
}
],
"tool_licence": "CC-BY-4.0",
"documentation": "https://urgi.versailles.inra.fr/gnpis/",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-07-29T13:42:38.871501Z",
"teams": [
"URGI"
],
"source_repository": null
},
{
"id": 158,
"name": "Fpocket",
"description": "Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::fpocket",
"biotoolsID": "fpocket",
"biotoolsCURIE": "biotools:fpocket",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0166"
],
"primary_publication": [
"10.1186/1471-2105-10-168"
],
"operating_system": [],
"tool_credit": [
{
"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/fpocket/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 960,
"citations": null,
"annual_visits": 2470,
"last_update": "2024-11-24T20:59:53.208420Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 146,
"name": "fqtools",
"description": "A package that provides tools for efficient FASTQ files manipulation.",
"homepage": "https://bioweb.pasteur.fr/packages/pack@fqtools@1.1",
"biotoolsID": "fqtools",
"biotoolsCURIE": "biotools:fqtools",
"tool_type": [
"Suite"
],
"collection": [
"fqtools"
],
"scientific_topics": [
"http://edamontology.org/topic_0080"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Maintainer",
"Primary contact"
],
"name": "Nicolas Joly",
"email": "njoly@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": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2020-06-16T10:55:24Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README"
},
{
"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": 113,
"name": "ParameciumDB",
"description": "Online community database for Paramecium species. Contains annotation of genome sequences and features, genome-wide data sets, advanced capabilities to query, retrieve, visualize and compare data.",
"homepage": "https://paramecium.i2bc.paris-saclay.fr",
"biotoolsID": "parameciumdb",
"biotoolsCURIE": "biotools:parameciumdb",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_0080",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_3321"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "https://paramecium.i2bc.paris-saclay.fr/cgi/user/contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Terms of Use",
"email": null,
"url": "https://paramecium.i2bc.paris-saclay.fr/parawiki/Terms_of_Use",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "CC-BY-4.0",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:30.463079Z",
"teams": [],
"source_repository": null
},
{
"id": 163,
"name": "PEP-FOLD",
"description": "PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3",
"biotoolsID": "pep-fold",
"biotoolsCURIE": "biotools:pep-fold",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gkp323",
"10.1093/nar/gks419",
"10.1093/nar/gkw329"
],
"operating_system": [],
"tool_credit": [
{
"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/PEP-FOLD3",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 3900,
"citations": null,
"annual_visits": 30000,
"last_update": "2024-11-24T20:59:57.942237Z",
"teams": [
"RPBS"
],
"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": 168,
"name": "FastME",
"description": "Distance algorithms to infer phylogenies. It's based on balanced minimum evolution, which is the very principle of NJ. It includes Nearest Neighbor Interchange (NNI) and also Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations.",
"homepage": "http://www.atgc-montpellier.fr/fastme/",
"biotoolsID": "fastme",
"biotoolsCURIE": "biotools:fastme",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [
"galaxyPasteur",
"FastME"
],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/molbev/msv150"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "LIRMM",
"email": null,
"url": "http://www.lirmm.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact",
"Contributor"
],
"name": "Vincent Lefort",
"email": "vincent.lefort@lirmm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://www.atgc-montpellier.fr/fastme/usersguide.php",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 300,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T20:59:19.988087Z",
"teams": [
"ATGC"
],
"source_repository": null
},
{
"id": 149,
"name": "PepPSy",
"description": "A gene expression-based prioritization system to help investigators to determine in which human tissues they should look for an unseen protein.",
"homepage": "http://peppsy.genouest.org",
"biotoolsID": "peppsy",
"biotoolsCURIE": "biotools:peppsy",
"tool_type": [
"Web application"
],
"collection": [
"Proteomics"
],
"scientific_topics": [
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_0121"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Contributor"
],
"name": "Olivier Collin",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Lydie Lane",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Thomas Darde",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Paula P. Duek",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "frederic.chalmel@univ-rennes1.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Olivier Sallou",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Frédéric Chalmel",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://peppsy.genouest.org/help",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T14:12:40.921423Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 161,
"name": "PEP-SiteFinder",
"description": "PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder",
"biotoolsID": "pep-sitefinder",
"biotoolsCURIE": "biotools:pep-sitefinder",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3534",
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gku404"
],
"operating_system": [],
"tool_credit": [
{
"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/PEP-SiteFinder",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 347,
"citations": null,
"annual_visits": 1482,
"last_update": "2024-11-24T20:59:55.640056Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"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": 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": 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": 99,
"name": "Genomicus-protists",
"description": "Genomicus-protists is a genome browser that enables users to navigate in protists 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-protists/",
"biotoolsID": "Genomicus-protists",
"biotoolsCURIE": "biotools:Genomicus-protists",
"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": 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": 82,
"name": "PhyML",
"description": "Phylogenetic estimation software using Maximum Likelihood",
"homepage": "https://www.atgc-montpellier.fr/phyml/",
"biotoolsID": "phyml",
"biotoolsCURIE": "biotools:phyml",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"PhyML",
"galaxyPasteur"
],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/sysbio/syq010"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support",
"Maintainer",
"Primary contact",
"Developer"
],
"name": "Stephane Guindon",
"email": "guindon@lirmm.fr",
"url": "http://stephaneguindon.github.io/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "LIRMM",
"email": null,
"url": "http://www.lirmm.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact",
"Developer",
"Maintainer",
"Support"
],
"name": "Stephane Guindon",
"email": "guindon@lirmm.fr",
"url": "https://stephaneguindon.github.io/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "LIRMM",
"email": null,
"url": "https://www.lirmm.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "https://github.com/stephaneguindon/phyml/blob/master/doc/phyml-manual.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:34:19.190685Z",
"teams": [
"ATGC"
],
"source_repository": null
},
{
"id": 152,
"name": "PipeAlign2",
"description": "Takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.",
"homepage": "http://www.lbgi.fr/pipealign",
"biotoolsID": "pipealign",
"biotoolsCURIE": "biotools:pipealign",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0078",
"http://edamontology.org/topic_0080",
"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_3168"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "akress@unistra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Unlicense",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T21:03:24.978595Z",
"teams": [
"BiGEst"
],
"source_repository": null
},
{
"id": 8,
"name": "Plant DataDiscovery",
"description": "The purpose of this web portal is to facilitate the discoverability of public data on plant biology managed by different laboratories across the world.\n\nThe web portal indexes and makes findable any kind of plant data. Plant DataDiscovery is an implementation of DataDiscovery.",
"homepage": "https://urgi.versailles.inrae.fr/data-discovery/",
"biotoolsID": "Plant_DataDiscovery",
"biotoolsCURIE": "biotools:Plant_DataDiscovery",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_3810"
],
"primary_publication": [
"10.1186/s13059-018-1491-4"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support",
"Primary contact"
],
"name": "Support service",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://urgi.versailles.inrae.fr/data-discovery/about",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-12-12T16:19:23.574076Z",
"teams": [],
"source_repository": null
}
]
}