HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 229,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=140&ordering=-operating_system",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=100&ordering=-operating_system",
"results": [
{
"id": 32,
"name": "Orphanet",
"description": "Information on rare diseases and orphan drugs.",
"homepage": "http://www.orpha.net/consor/cgi-bin/index.php",
"biotoolsID": "orphanet",
"biotoolsCURIE": "biotools:orphanet",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"Rare Disease",
"DRCAT"
],
"scientific_topics": [
"http://edamontology.org/topic_0154",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3325"
],
"primary_publication": [
"10.1002/humu.22078"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "Inserm US14",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "http://www.orpha.net/consor/cgi-bin/Directory_Contact.php?lng=EN",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.orpha.net/consor/cgi-bin/Education_EducationTools.php?stapage=HM_BLOC_HEADER_HELP_SITEMAP&lng=EN",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:58:27.798370Z",
"teams": [],
"source_repository": null
},
{
"id": 122,
"name": "microSysMics",
"description": "This workflow provides an automated microbiome data analysis, starting with sequenced taxonomic markers (such as 16SrRNA) and using the standard QIIME2 toolbox to produce an abundance table and preliminary diversity, phylogeny and taxonomy analysis.",
"homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/microSysMics",
"biotoolsID": "microSysMics",
"biotoolsCURIE": "biotools:microSysMics",
"tool_type": [
"Workflow"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3697"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "BiRD bioinformatics facility",
"email": "pf-bird@univ-nantes.fr",
"url": "http://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "LS2N",
"email": null,
"url": "http://www.ls2n.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Erwan Delage",
"email": "erwan.delage@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Audrey Bihouée",
"email": "audrey.bihouee@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-8689-2083",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "TENS",
"email": null,
"url": "https://www.inserm-tens.com/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer",
"Contributor"
],
"name": "Damien Vintache",
"email": "Damien.Vintache@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Samuel Chaffron",
"email": "samuel.chaffron@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-5903-617X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Michel Neunlist",
"email": "michel.neunlist@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1892-5071",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "BiRD",
"email": "pf-bird@univ-nantes.fr",
"url": "http://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
}
],
"tool_licence": "Other",
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2023-09-19T15:06:56.878425Z",
"teams": [
"BiRD"
],
"source_repository": null
},
{
"id": 162,
"name": "HCA (hydrophobic cluster analysis)",
"description": "The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures.",
"homepage": "http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA#forms::HCA",
"biotoolsID": "hca",
"biotoolsCURIE": "biotools:hca",
"tool_type": [
"Web application"
],
"collection": [
"Proteomics"
],
"scientific_topics": [
"http://edamontology.org/topic_0121",
"http://edamontology.org/topic_3542"
],
"primary_publication": [
"10.1007/s000180050082"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Isabelle Callebaut",
"email": "Isabelle.Callebaut@lmcp.jussieu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://bioserv.rpbs.univ-paris-diderot.fr/services/HCA/",
"maturity": null,
"cost": null,
"unique_visits": 3200,
"citations": null,
"annual_visits": 10000,
"last_update": "2024-11-24T15:47:21.770746Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 55,
"name": "GAG",
"description": "Generates an NCBI .tbl file of annotations on a genome.",
"homepage": "https://github.com/genomeannotation/GAG",
"biotoolsID": "gag",
"biotoolsCURIE": "biotools:gag",
"tool_type": [
"Database portal",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0077",
"http://edamontology.org/topic_3673"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Scott M Geib",
"email": "scott.geib@ars.usda.gov",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "MIT",
"documentation": "https://github.com/genomeannotation/GAG",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:31:52.130383Z",
"teams": [],
"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": 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": 156,
"name": "ORDO",
"description": "The Orphanet Rare Disease Ontology (ORDO) - structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features. It integrates a classification of rare diseases, relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).",
"homepage": "http://www.ebi.ac.uk/ols/ontologies/ordo",
"biotoolsID": "ordo",
"biotoolsCURIE": "biotools:ordo",
"tool_type": [
"Ontology",
"Web application",
"Database portal"
],
"collection": [
"RD-connect",
"Rare Disease"
],
"scientific_topics": [
"http://edamontology.org/topic_3572",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3307"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "https://www.ebi.ac.uk/support/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Inserm US14",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "ols-submission@ebi.ac.uk",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Apache-2.0",
"documentation": "https://www.ebi.ac.uk/ols/docs/index",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2020-09-16T07:06:49Z",
"teams": [
"Orphanet"
],
"source_repository": null
},
{
"id": 169,
"name": "BIONJ",
"description": "This software is well suited for distances estimated from DNA or protein sequences. It has better topological accuracy than NJ in all evolutionary conditions; its superiority becomes important when the substitution rates are high and varying among lineages.",
"homepage": "http://www.atgc-montpellier.fr/bionj/",
"biotoolsID": "bionj",
"biotoolsCURIE": "biotools:bionj",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0084",
"http://edamontology.org/topic_0654"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Eric RIVALS",
"email": "Eric.Rivals@lirmm.fr",
"url": "http://www.lirmm.fr/~gascuel/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/bionj/paper.php",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:15:50.001899Z",
"teams": [
"ATGC"
],
"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": [],
"name": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"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
}
],
"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": 154,
"name": "CompPhy",
"description": "Web-based collaborative platform for comparing phylogenies.",
"homepage": "http://www.atgc-montpellier.fr/compphy/",
"biotoolsID": "compphy",
"biotoolsCURIE": "biotools:compphy",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_3056"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact form",
"email": null,
"url": "http://www.atgc-montpellier.fr/compphy/?p=contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/compphy/?p=userguide",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:57Z",
"teams": [
"ATGC"
],
"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": [
"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": [
"Provider"
],
"name": "u-bordeaux.fr",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"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": 279,
"name": "FINSURF",
"description": "FINSURF (Functional Identification of Non-coding Sequences Using Random Forests) is a tool designed to analyse lists of sequences variants in the human genome.\nIt assigns a score to each variant, reflecting its functional importance and therefore its likelihood to disrupt the physiology of its carrier. FINSURF scores Single Nucleotide Variants (SNV), insertions and deletions. Among SNVs, transitions and transversions are treated separately. Insertions are characterised by a score given to each base flanking the insertion point. Deletions are characterised by a score at every deleted base. FINSURF can (optionally) use a list of known or suspected disease genes, in order to restrict results to variants overlapping cis-regulatory elements linked to these genes.\n\nFor a variant of interest, users can generate a graphical representation of \"feature contributions », showing the relative contributions of genomic, functional or evolutionary information to its score.",
"homepage": "https://www.finsurf.bio.ens.psl.eu/",
"biotoolsID": "finsurf",
"biotoolsCURIE": "biotools:finsurf",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3673",
"http://edamontology.org/topic_3577",
"http://edamontology.org/topic_3300"
],
"primary_publication": [
"10.1371/journal.pgen.1010191"
],
"operating_system": [
"Mac",
"Linux"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "finsurf@bio.ens.psl.eu",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "IBENS - DYOGEN Team",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@bio.ens.psl.eu",
"url": null,
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Lambert Moyon",
"email": "moyon@bio.ens.psl.eu",
"url": null,
"orcidid": "https://orcid.org/0000-0003-2390-3942",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Alexandra Louis",
"email": "alexandra.louis@bio.ens.psl.eu",
"url": null,
"orcidid": "https://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Camille Berthelot",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-5054-2690",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:55:59.341655Z",
"teams": [
"PB-IBENS"
],
"source_repository": "https://github.com/DyogenIBENS/FINSURF/"
},
{
"id": 275,
"name": "IMGT 3Dstructure-DB",
"description": "IMGT/3Dstructure-DB is the IMGT® database for 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins, related proteins of the immune system (RPI) and fusion proteins for immune applications (FPIA).\nAnnotation is based on the IMGT-ONTOLOGY concepts.",
"homepage": "http://www.imgt.org/3Dstructure-DB/",
"biotoolsID": "imgt_3dstructure",
"biotoolsCURIE": "biotools:imgt_3dstructure",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0154",
"http://edamontology.org/topic_3930",
"http://edamontology.org/topic_3948",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0804"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Marie-Paule Lefranc",
"email": "marie-paule.lefranc@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Patrice Duroux",
"email": "patrice.duroux@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Sofia Kossida",
"email": "sofia.kossida@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.imgt.org/3Dstructure-DB/doc/IMGT3DstructureDBHelp.shtml",
"maturity": "Mature",
"cost": "Free of charge (with restrictions)",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:15.256998Z",
"teams": [
"IMGT"
],
"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": 277,
"name": "IMGT mAb-DB",
"description": "IMGT/mAb-DB is the IMGT® database for monoclonal antibodies (mAb) or immunoglobulins (IG), fusion proteins for immune applications (FPIA) and composite proteins for clinical applications (CPCA).\nIMGT/mAb-DB provides links to IMGT/2Dstructure-DB and IMGT/3Dstructure-DB.",
"homepage": "http://www.imgt.org/mAb-DB/",
"biotoolsID": "IMGT_mAb-DB",
"biotoolsCURIE": "biotools:IMGT_mAb-DB",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3930",
"http://edamontology.org/topic_3948",
"http://edamontology.org/topic_0804",
"http://edamontology.org/topic_3400"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "Patrice Duroux",
"email": "patrice.duroux@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Marie-Paule Lefranc",
"email": "marie-paule.Lefranc@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Sofia Kossida",
"email": "sofia.Kossida@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.imgt.org/mAb-DB/doc",
"maturity": "Mature",
"cost": "Free of charge (with restrictions)",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T13:59:20.810745Z",
"teams": [
"IMGT"
],
"source_repository": null
},
{
"id": 89,
"name": "Workflow4Metabolomics",
"description": "First fully open-source and collaborative online platform for computational metabolomics. It includes preprocessing, normalization, quality control, statistical analysis of LC/MS, FIA-MS, GC/MS and NMR data.",
"homepage": "https://workflow4metabolomics.org/",
"biotoolsID": "workflow4metabolomics",
"biotoolsCURIE": "biotools:workflow4metabolomics",
"tool_type": [
"Bioinformatics portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_2259",
"http://edamontology.org/topic_3172",
"http://edamontology.org/topic_3307"
],
"primary_publication": [
"10.1093/bioinformatics/btu813"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "MetaboHUB - National infrastructure in metabolomics & fluxomics",
"email": null,
"url": "https://www.metabohub.fr/home.html",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Christophe Caron",
"email": null,
"url": "http://abims.sb-roscoff.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Christophe Duperier",
"email": null,
"url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Franck Giacomoni",
"email": "franck.giacomoni@inrae.fr",
"url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse",
"orcidid": "https://orcid.org/0000-0001-6063-4214",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Gildas Le Corguillé",
"email": "lecorguille@sb-roscoff.fr",
"url": "http://abims.sb-roscoff.fr",
"orcidid": "https://orcid.org/0000-0003-1742-9711",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Marie Tremblay-Franco",
"email": null,
"url": "https://www6.toulouse.inrae.fr/axiomm",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Jean-François Martin",
"email": null,
"url": "https://www6.toulouse.inrae.fr/axiomm",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Pierrick Roger-Melee",
"email": null,
"url": "http://www-list.cea.fr/index.php/en/",
"orcidid": "https://orcid.org/0000-0001-8177-4873",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Yann Guitton",
"email": null,
"url": "https://www.laberca.org/plateforme-analytique/presentation/",
"orcidid": "https://orcid.org/0000-0002-4479-0636",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Documentor"
],
"name": "Cécile Canlet",
"email": null,
"url": "https://www6.toulouse.inrae.fr/axiomm",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Misharl Monsoor",
"email": null,
"url": "http://abims.sb-roscoff.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Etienne A. Thévenot",
"email": null,
"url": "http://www-list.cea.fr/index.php/en/",
"orcidid": "https://orcid.org/0000-0003-1019-4577",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Mélanie Pétéra",
"email": null,
"url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Workflow4Metabolomics Team",
"email": "contact@workflow4metabolomics.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Marion Landi",
"email": null,
"url": "https://www6.clermont.inrae.fr/unh/Plateaux-Techniques/Metabolisme-et-Spectrometrie-de-Masse",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "IFB - Institut Français de Bioinformatique",
"email": null,
"url": "https://www.france-bioinformatique.fr/en",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Pierre Pericard",
"email": null,
"url": "http://abims.sb-roscoff.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Alexis Delabrière",
"email": null,
"url": "http://www-list.cea.fr/index.php/en/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Sophie Goulitquer",
"email": null,
"url": "http://www.sb-roscoff.fr/en/research-and-training-centre-marine-biology-and-oceanography/services/technological-core-facilities/mass-spectrometry-core-facility",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://workflow4metabolomics.org/howto",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-12-16T14:17:30Z",
"teams": [
"ABiMS"
],
"source_repository": "https://github.com/workflow4metabolomics"
},
{
"id": 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_0157",
"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_0078",
"http://edamontology.org/topic_0080",
"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": 274,
"name": "orsum",
"description": "A Python package for filtering and comparing enrichment analyses using a simple principle.",
"homepage": "https://anaconda.org/bioconda/orsum",
"biotoolsID": "orsum",
"biotoolsCURIE": "biotools:orsum",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3407"
],
"primary_publication": [],
"operating_system": [
"Mac",
"Linux",
"Windows"
],
"tool_credit": [
{
"type_role": [],
"name": "Ozan Ozisik",
"email": "ozan.ozisik@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-5980-8002",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Anaïs Baudot",
"email": "anais.baudot@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Morgane Térézol",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-10-29T06:24:51.903827Z",
"teams": [],
"source_repository": "https://github.com/ozanozisik/orsum/"
},
{
"id": 278,
"name": "metabocloud",
"description": "Web portal to gather tools to improve metabolomic annotations through API microservices based on a cloud infrastructure.",
"homepage": "https://metabocloud.mesocentre.uca.fr/",
"biotoolsID": "metabocloud",
"biotoolsCURIE": "biotools:metabocloud",
"tool_type": [
"Bioinformatics portal"
],
"collection": [
"metabolomic platform"
],
"scientific_topics": [
"http://edamontology.org/topic_3172"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac",
"Windows"
],
"tool_credit": [
{
"type_role": [
"Contributor"
],
"name": "Franck Giacomoni",
"email": "franck.giacomoni@inrae.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-6063-4214",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer",
"Provider"
],
"name": "Nadia Goué",
"email": "nadia.goue@uca.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-2750-1473",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer",
"Contributor"
],
"name": "Nils Paulhe",
"email": "nils.paulhe@inrae.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-4550-1258",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer",
"Provider"
],
"name": "Thomas Bellembois",
"email": "thomas.bellembois@uca.fr",
"url": null,
"orcidid": "https://orcid.org/0009-0001-6661-0691",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Faustine Souc",
"email": "faustine.souc@inrae.fr",
"url": null,
"orcidid": "https://orcid.org/0009-0004-9172-0632",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Antoine Mahul",
"email": "antoine.mahul@uca.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-9729-1603",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-01-22T10:11:29.320362Z",
"teams": [
"AuBi"
],
"source_repository": null
},
{
"id": 31,
"name": "Orphadata",
"description": "A comprehensive, high-quality and freely-accessible dataset related to rare diseases and orphan drugs, in a reusable format.",
"homepage": "http://www.orphadata.org/",
"biotoolsID": "orphadata",
"biotoolsCURIE": "biotools:orphadata",
"tool_type": [
"Database portal",
"Web API",
"SPARQL endpoint"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_3068"
],
"primary_publication": [
"10.1002/humu.22078"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Marc Hanauer",
"email": "marc.hanauer@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Inserm US14",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Céline Rousselot",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Samuel Demarest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Orphanet Inserm",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "CC-BY-4.0",
"documentation": "http://www.orphadata.org/cgi-bin/index.php/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T13:46:06.717312Z",
"teams": [],
"source_repository": null
}
]
}