HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 207,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=200&ordering=-cost",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=160&ordering=-cost",
"results": [
{
"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": [
"10.1093/nar/gkx1108",
"10.1016/j.cub.2005.12.044",
"10.1093/nar/gkz955",
"10.1101/gr.108175.110",
"10.1093/nar/gkv966"
],
"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
},
{
"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": 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": "2019-11-15T09:29:04Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 153,
"name": "xHeinz",
"description": "Software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions. Active subnetwork modules are sets of genes, one for each species, which: - induce a connected subnetwork in a species-specific interaction network, - show overall differential behavior, and - contain a large number of orthologous genes.",
"homepage": "https://github.com/ls-cwi/xheinz",
"biotoolsID": "xheinz",
"biotoolsCURIE": "biotools:xheinz",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602"
],
"primary_publication": [
"10.1093/bioinformatics/btv316"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Tobias Müller",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://github.com/ls-cwi/xheinz",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "u-bordeaux.fr",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Hayssam Soueidan",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Marcus Dittrich",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Mohammed El-Kebir",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Thomas Hume",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Daniela Beisser",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Macha Nikolski",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Lodewyk F. A. Wessels",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Jaap Heringa",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Gunnar W. Klau",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Guillaume Blin",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Bordeaux University, CBiB, France",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "The Netherlands",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Würzburg University, Germany",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "University Duisburg-Essen",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "The Netherlands Cancer Institute, Amsterdam",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Univ. Bordeaux, CNRS/LaBRI, 33405 Talence, France,",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "MIT",
"documentation": "https://github.com/ls-cwi/xheinz",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2019-03-12T14:52:11Z",
"teams": [
"CBiB"
],
"source_repository": "https://software.cwi.nl/software/xheinz/releases/1.0"
},
{
"id": 36,
"name": "Banana Genome Hub",
"description": "A Next-Generation Information System for Musa genomics",
"homepage": "https://banana-genome-hub.southgreen.fr/",
"biotoolsID": "Banana_Genome_Hub",
"biotoolsCURIE": "biotools:Banana_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub",
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_3810",
"http://edamontology.org/topic_0797"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "ANR",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Gaëtan Droc",
"email": "gaetan.droc@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Mathieu Rouard",
"email": "m.rouard@cgiar.org",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Bioversity International",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "CIRAD",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "https://banana-genome-hub.southgreen.fr/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:38.690746Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 86,
"name": "BIII (BioImage Informatics Index, biii.eu)",
"description": "BIII (BioImage Informatics Index, biii.eu) is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis. Software tools are organized as either a full protocol of analysis (workflow), a specific component to construct a workflow, or a software platform or library (collection). They are described using EDAM-bioimaging. All entries are exposed following FAIR principles and accessible for other usage with ODC-By v1.0 license.",
"homepage": "https://biii.eu",
"biotoolsID": "BISE",
"biotoolsCURIE": "biotools:BISE",
"tool_type": [
"Database portal",
"Bioinformatics portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"NEUBIAS"
],
"scientific_topics": [
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_0769",
"http://edamontology.org/topic_3298",
"http://edamontology.org/topic_3382"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Contributor"
],
"name": "Matúš Kalaš",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-1509-4981",
"gridid": null,
"typeEntity": "Person",
"note": "Coordinator of the EDAM-bioimaging ontology development"
},
{
"type_role": [
"Contributor"
],
"name": "Kota Miura",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-6926-191X",
"gridid": null,
"typeEntity": "Person",
"note": "Main technical support and one of the founders of the project"
},
{
"type_role": [
"Documentor"
],
"name": "Taggers",
"email": null,
"url": "http://biii.eu/show-taggers",
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": "People curating tools"
},
{
"type_role": [
"Contributor"
],
"name": "Chong Zhang",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": "Co-leader of the developement"
},
{
"type_role": [
"Provider"
],
"name": "NEUBIAS Network of Bioimage Analysts",
"email": null,
"url": "https://neubias.eu",
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": "COST action having supported the creation and curation of this database"
},
{
"type_role": [
"Contributor"
],
"name": "Leandro Scholz",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-2411-0429",
"gridid": null,
"typeEntity": "Person",
"note": "Worked on the curation instructions"
},
{
"type_role": [
"Primary contact"
],
"name": "Perrine Paul-Gilloteaux",
"email": "perrine.paul-gilloteaux@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-4822-165X",
"gridid": null,
"typeEntity": "Person",
"note": "Leader of the project"
},
{
"type_role": [
"Contributor"
],
"name": "Alban Gaignard",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-3597-8557",
"gridid": null,
"typeEntity": "Person",
"note": "Developed the core ontology (data model) and enabled reuse of the content through W3C standards"
},
{
"type_role": [
"Contributor"
],
"name": "Florian Levet",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-4009-6225",
"gridid": null,
"typeEntity": "Person",
"note": "Development of Python scripts"
}
],
"tool_licence": "Other",
"documentation": "https://github.com/NeuBIAS/bise/wiki",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-03-26T15:45:10Z",
"teams": [],
"source_repository": null
},
{
"id": 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": 94,
"name": "VarAFT",
"description": "VarAFT (Variant Analysis and Filtration Tool) is a standalone and multiplatform tool for annotation and prioritization of potential disease causing genes. With this tool users can annotate variant (VCF) files, combine multiple samples from various individuals, prioritize list of variants by multi-filtering parameters. Additionally, users can perform a coverage analysis and quality check from any BAM file.",
"homepage": "http://varaft.eu",
"biotoolsID": "varaft",
"biotoolsCURIE": "biotools:varaft",
"tool_type": [
"Desktop application"
],
"collection": [
"elixir-fr-sdp-2019",
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_3325"
],
"primary_publication": [
"10.1093/nar/gky471"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact form",
"email": null,
"url": "http://varaft.eu/#contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Jean-Pierre Desvignes",
"email": "jean-pierre.desvignes@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "Other",
"documentation": "http://varaft.eu/download_files/VarAFT_Documentation_V2.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-04-02T21:35:23.173094Z",
"teams": [
"MMG-GBIT"
],
"source_repository": null
},
{
"id": 1,
"name": "VirHostnet",
"description": "Virus-Host Network is a knowledge-base system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains). VirHostNet contains high quality and up-to-date information gathered and curated from public databases.",
"homepage": "http://virhostnet.prabi.fr/",
"biotoolsID": "virhostnet",
"biotoolsCURIE": "biotools:virhostnet",
"tool_type": [
"Database portal",
"Bioinformatics portal",
"Web service"
],
"collection": [
"COVID-19",
"PRABI"
],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_3957",
"http://edamontology.org/topic_0781",
"http://edamontology.org/topic_3324"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "VirHostNet Support",
"email": "vincent.navratil@univ-lyon1.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-9974-1877",
"gridid": null,
"typeEntity": "Person",
"note": "Head of the prabi-amsb bioinformatics core facility (http://amsb.prabi.fr)"
}
],
"tool_licence": "Not licensed",
"documentation": "https://pbil.univ-lyon1.fr/redmine/projects/virhostscape/wiki",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-12-08T10:41:55Z",
"teams": [],
"source_repository": null
},
{
"id": 110,
"name": "RSAT retrieve-ensembl-seq",
"description": "Returns upstream, downstream, intronic, exonic, UTR, transcript, mRNA, CDS or gene sequences for a list of genes from the EnsEMBL database.\nMulti-genome queries are supported: automatic retrieval of sequences for all the orthologs of the query genes, at a given taxonomical level.",
"homepage": "http://rsat.sb-roscoff.fr/retrieve-ensembl-seq_form.cgi",
"biotoolsID": "rsat-retrieve-ensembl-seq",
"biotoolsCURIE": "biotools:rsat-retrieve-ensembl-seq",
"tool_type": [
"Web service",
"Web application",
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"FR",
"Regulatory Sequence Analysis Tools (RSAT)"
],
"scientific_topics": [
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0749"
],
"primary_publication": [
"10.1093/bioinformatics/btp519"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"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
},
{
"type_role": [
"Documentor",
"Maintainer",
"Support",
"Developer",
"Primary contact"
],
"name": "Olivier Sand",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-1465-1640",
"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": 103,
"name": "Ciona robusta Anatomy and Development Ontology",
"description": "The first ontology describing the anatomy and the development of Ciona robusta, based on the Hotta developmental table.",
"homepage": "https://www.aniseed.fr/aniseed/anatomy/find_devstage",
"biotoolsID": "Ciona_robusta_Anatomy_and_Development_Ontology",
"biotoolsCURIE": "biotools:Ciona_robusta_Anatomy_and_Development_Ontology",
"tool_type": [
"Ontology"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3064"
],
"primary_publication": [
"10.1101/gr.108175.110",
"10.1093/nar/gkv966"
],
"operating_system": [],
"tool_credit": [],
"tool_licence": "Freeware",
"documentation": null,
"maturity": "Legacy",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2023-09-25T13:07:23.980491Z",
"teams": [],
"source_repository": null
},
{
"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": 57,
"name": "AnnotQTL",
"description": "Tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region.",
"homepage": "http://annotqtl.genouest.org/",
"biotoolsID": "annotqtl",
"biotoolsCURIE": "biotools:annotqtl",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0085"
],
"primary_publication": [
"10.1093/nar/gkr361"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "GenOuest",
"email": "support@genouest.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://annotqtl.genouest.org/tutorial",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T16:06:26.428724Z",
"teams": [],
"source_repository": null
},
{
"id": 54,
"name": "AphidBase",
"description": "An aphid genome database.",
"homepage": "http://aphidbase.com/",
"biotoolsID": "aphidbase",
"biotoolsCURIE": "biotools:aphidbase",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1111/j.1365-2583.2009.00930.x"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "BIPAA platform",
"email": "bipaa@rennes.inra.fr",
"url": "http://www.inra.fr/bipaa",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://bipaa.genouest.org/is/aphidbase/",
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2018-12-10T12:58:49Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 244,
"name": "NGphylogeny.fr",
"description": "Free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.",
"homepage": "https://ngphylogeny.fr/",
"biotoolsID": "NGphylogeny.fr",
"biotoolsCURIE": "biotools:NGphylogeny.fr",
"tool_type": [
"Web application",
"Workflow",
"Bioinformatics portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/nar/gkz303"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer",
"Maintainer",
"Primary contact"
],
"name": "Frédéric Lemoine",
"email": "frederic.lemoine@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Damien Correia",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Fabien Mareuil",
"email": "fmareuil@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"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": null,
"documentation": "https://ngphylogeny.fr/documentation",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:31.390401Z",
"teams": [],
"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": 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": 91,
"name": "DataDiscovery",
"description": "DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters.\n\nThis tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.",
"homepage": "https://urgi.versailles.inrae.fr/data-discovery/",
"biotoolsID": "DataDiscovery",
"biotoolsCURIE": "biotools:DataDiscovery",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI",
"FR"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_3810"
],
"primary_publication": [
"10.3835/plantgenome2015.06.0038"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Support",
"Primary contact"
],
"name": "urgi-support",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-09-06T15:57:35.550435Z",
"teams": [
"PlantBioinfoPF"
],
"source_repository": "https://forgemia.inra.fr/urgi-is/data-discovery"
},
{
"id": 68,
"name": "NORINE",
"description": "NORINE is a platform that includes a database of nonribosomal peptides together with tools for their analysis.",
"homepage": "http://norine.univ-lille.fr/norine/",
"biotoolsID": "NORINE",
"biotoolsCURIE": "biotools:NORINE",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3332",
"http://edamontology.org/topic_3301",
"http://edamontology.org/topic_3307",
"http://edamontology.org/topic_0078",
"http://edamontology.org/topic_3071"
],
"primary_publication": [
"10.1093/nar/gkz1000"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "Norine team",
"email": "norine@univ-lille.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "CC-BY-NC-SA-4.0",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-07-21T13:25:21.706482Z",
"teams": [
"Bilille"
],
"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
}
]
}