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=160&ordering=-collection",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=120&ordering=-collection",
"results": [
{
"id": 20,
"name": "PRIAM",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": null,
"teams": [],
"source_repository": null
},
{
"id": 25,
"name": "secreton",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": null,
"teams": [],
"source_repository": null
},
{
"id": 26,
"name": "ppRNome Browser",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": null,
"teams": [],
"source_repository": null
},
{
"id": 137,
"name": "SHAMAN",
"description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].",
"homepage": "http://shaman.c3bi.pasteur.fr/",
"biotoolsID": "shaman",
"biotoolsCURIE": "biotools:shaman",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3174"
],
"primary_publication": [
"10.1073/pnas.1523899113"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Pierre Lechat",
"email": null,
"url": "https://research.pasteur.fr/en/member/pierre-lechat/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Amine Ghozlane",
"email": null,
"url": "https://research.pasteur.fr/en/member/amine-ghozlane/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "https://research.pasteur.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "C3BI",
"email": null,
"url": "https://research.pasteur.fr/en/center/c3bi/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Bioinformatics and Biostatistics Hub",
"email": null,
"url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "SHAMAN team",
"email": "shaman@pasteur.fr",
"url": "https://research.pasteur.fr/en/software/shaman-shiny-application-for-metagenomic-analysis/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Stevenn Volant",
"email": null,
"url": "https://research.pasteur.fr/en/member/stevenn-volant/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Hugo Varet",
"email": null,
"url": "https://research.pasteur.fr/en/member/hugo-varet/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://shaman.c3bi.pasteur.fr/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 742,
"citations": null,
"annual_visits": 1855,
"last_update": "2025-10-23T10:46:59.953305Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://github.com/aghozlane/shaman"
},
{
"id": 265,
"name": "MetamORF",
"description": "A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta-analysis.\n\nMetamORF: A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta analysis.",
"homepage": "http://metamorf.hb.univ-amu.fr/",
"biotoolsID": "metamorf",
"biotoolsCURIE": "biotools:metamorf",
"tool_type": [
"Command-line tool",
"Database portal",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0659"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "Christine Brun",
"email": "christine-g.brun@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-02-22T07:55:26Z",
"teams": [
"TAGC-BU"
],
"source_repository": "https://github.com/TAGC-NetworkBiology/MetamORF"
},
{
"id": 136,
"name": "AutoGRAPH",
"description": "Integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.",
"homepage": "http://autograph.genouest.org/",
"biotoolsID": "autograph",
"biotoolsCURIE": "biotools:autograph",
"tool_type": [
"Web service"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0102",
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_0797"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Derrien T",
"email": "toma.derrien@gmail.com",
"url": "http://www-recomgen.univ-rennes1.fr/doggy.html",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://autograph.genouest.org/Tutorial.php",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:04:29.788401Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 196,
"name": "Viral Host Range database",
"description": "The Viral Host Range database represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the years, countless host range experiments have been performed in many laboratories. However, these data are not readily available to the community and are therefore underexploited.\n\nThe VHRdb is an online resource that centralizes experimental data related to the host range of viruses. While it originates from bacteriophages and bacteria interaction studies, its design is compatible with viruses infecting all living forms. Users can browse publicly available data to find which host is infected by a virus, and vice versa. Users can also upload their own data while keeping it private or making it public, analyze results across independent sets of data, generate and visualize outputs. Data implemented in the VHRdb are linked to users and, if available, to publications and sequence identifiers.",
"homepage": "https://viralhostrangedb.pasteur.cloud/",
"biotoolsID": "VHRdb",
"biotoolsCURIE": "biotools:VHRdb",
"tool_type": [
"Database portal",
"Web API",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3489",
"http://edamontology.org/topic_0781"
],
"primary_publication": [
"10.1093/bioinformatics/btab070"
],
"operating_system": [
"Mac",
"Windows",
"Linux"
],
"tool_credit": [
{
"type_role": [
"Contributor",
"Developer"
],
"name": "LAMY-BESNIER Quentin",
"email": null,
"url": "https://research.pasteur.fr/fr/member/fr-quentin-lamy-besnier/",
"orcidid": "https://orcid.org/0000-0002-7141-6340",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Documentor"
],
"name": "MÉNAGER Hervé",
"email": null,
"url": "https://research.pasteur.fr/fr/member/herve-menager/",
"orcidid": "https://orcid.org/0000-0002-7552-1009",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Institut Pasteur",
"email": null,
"url": null,
"orcidid": null,
"gridid": "grid.428999.7",
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer",
"Developer"
],
"name": "Bryan Brancotte",
"email": null,
"url": "https://research.pasteur.fr/en/member/bryan-brancotte",
"orcidid": "https://orcid.org/0000-0001-8669-5525",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "DEBARBIEUX Laurent",
"email": null,
"url": "https://research.pasteur.fr/fr/member/laurent-debarbieux/",
"orcidid": "https://orcid.org/0000-0001-6875-5758",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://hub.pages.pasteur.fr/viralhostrangedb/",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-06-24T08:58:13.476714Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://gitlab.pasteur.fr/hub/viralhostrangedb/"
},
{
"id": 238,
"name": "TOXsIgN",
"description": "The TOXicogenomic sIgNature (TOXsIgN) is a cross-species resource that supports online submission, storage, and retrieval of TOXicogenomic sIgNatures. TOXsIgN aims at complementing existing resources by acting as a distribution hub for the community. One of its unique features is its ability to archive heterogeneous data. TOXsIgN thus allows users to upload lists of genes positively (overexpressed for transcriptomic assays) affected and negatively (underexpressed) affected from distinct –omics experiments (e.g., transcriptomics, proteomics, or epigenomics). It also provides users with a working environment containing a powerful search engine as well as bioinformatics/biostatistics modules that enable cross-species and cross-technology signature comparisons or enrichment analyses. TOXsIgN is thus intended to serve as a warehouse for toxicogenomics and predictive toxicology tools simultaneously based on and able to analyze the overall set of signatures deposited by the community.",
"homepage": "http://toxsign.genouest.org",
"biotoolsID": "toxsign",
"biotoolsCURIE": "biotools:toxsign",
"tool_type": [
"Web application",
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2840"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Chalmel Frédéric",
"email": "frederic.chalmel@univ-rennes1.fr",
"url": null,
"orcidid": null,
"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": "2020-09-28T08:55:30Z",
"teams": [],
"source_repository": null
},
{
"id": 27,
"name": "eDystrophin",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": null,
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"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": 266,
"name": "LedPred",
"description": "This package creates a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, NGS peaks and signals and other numerical scores of the sequences using supervised classification. It contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences.",
"homepage": "http://bioconductor.org/packages/release/bioc/html/LedPred.html",
"biotoolsID": "ledpred",
"biotoolsCURIE": "biotools:ledpred",
"tool_type": [
"Command-line tool",
"Library"
],
"collection": [
"BioConductor"
],
"scientific_topics": [
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_3474"
],
"primary_publication": [
"10.1093/bioinformatics/btv705"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Aitor Gonzalez",
"email": "aitor.gonzalez@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://bioconductor.org/packages/release/bioc/html/LedPred.html",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T15:20:13.683529Z",
"teams": [
"TAGC-BU"
],
"source_repository": null
},
{
"id": 105,
"name": "REPET",
"description": "The REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)\n TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.",
"homepage": "https://urgi.versailles.inrae.fr/Tools/REPET",
"biotoolsID": "repet",
"biotoolsCURIE": "biotools:repet",
"tool_type": [
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI",
"REPET",
"PlantBioinfoPF"
],
"scientific_topics": [
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_0097"
],
"primary_publication": [
"10.1371/journal.pone.0091929",
"10.1371/journal.pone.0016526",
"10.1371/journal.pcbi.0010022",
"10.1007/s00239-003-0007-2"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer",
"Contributor",
"Maintainer",
"Provider",
"Support",
"Documentor"
],
"name": "URGI",
"email": "urgi-repet@versailles.inra.fr",
"url": "http://urgi.versailles.inra.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235"
},
{
"type_role": [
"Developer",
"Contributor",
"Maintainer",
"Provider",
"Support",
"Documentor"
],
"name": "URGI",
"email": "urgi-repet@versailles.inrae.fr",
"url": "http://urgi.versailles.inrae.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235"
}
],
"tool_licence": "CECILL-2.0",
"documentation": "https://urgi.versailles.inrae.fr/Tools/REPET",
"maturity": "Legacy",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-09-09T08:10:41.737859Z",
"teams": [
"URGI"
],
"source_repository": "https://urgi.versailles.inrae.fr/download/repet/"
},
{
"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": 249,
"name": "FROGS",
"description": "The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.",
"homepage": "http://frogs.toulouse.inra.fr/",
"biotoolsID": "frogs",
"biotoolsCURIE": "biotools:frogs",
"tool_type": [
"Command-line tool"
],
"collection": [
"FROGS"
],
"scientific_topics": [
"http://edamontology.org/topic_3697",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_3174",
"http://edamontology.org/topic_0637",
"http://edamontology.org/topic_3168"
],
"primary_publication": [
"10.1093/bioinformatics/btx791",
"10.1093/bib/bbab318"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Géraldine Pascal",
"email": "geraldine.pascal@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Géraldine Pascal",
"email": "geraldine.pascal@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/geraldinepascal/FROGS",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:07:18.846597Z",
"teams": [
"MIGALE"
],
"source_repository": "https://github.com/geraldinepascal/FROGS"
},
{
"id": 190,
"name": "CRISPRFinder",
"description": "Detects this family of direct repeats found in the DNA of many bacteria and archaea.",
"homepage": "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index",
"biotoolsID": "crisprfinder",
"biotoolsCURIE": "biotools:crisprfinder",
"tool_type": [
"Web application",
"Database portal"
],
"collection": [
"CRISPR"
],
"scientific_topics": [
"http://edamontology.org/topic_2885",
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_0749"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Marie Touchon",
"email": "mtouchon@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Unlicense",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 480,
"citations": null,
"annual_visits": 2273,
"last_update": "2024-11-24T21:05:00.924973Z",
"teams": [
"EBIO"
],
"source_repository": null
},
{
"id": 187,
"name": "Nebula",
"description": "Web service powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data.",
"homepage": "https://nebula.curie.fr/",
"biotoolsID": "nebula",
"biotoolsCURIE": "biotools:nebula",
"tool_type": [
"Web application"
],
"collection": [
"Nebula"
],
"scientific_topics": [
"http://edamontology.org/topic_3365",
"http://edamontology.org/topic_3169",
"http://edamontology.org/topic_3125"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "galaxy.contact@curie.fr",
"url": "http://bioinfo-out.curie.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://nebula.curie.fr/static/nebula_tutorial.pdf",
"maturity": null,
"cost": null,
"unique_visits": 7384,
"citations": null,
"annual_visits": 2815653,
"last_update": "2024-11-25T14:22:06.393280Z",
"teams": [
"Institut Curie - Bioinformatique"
],
"source_repository": null
},
{
"id": 182,
"name": "S-MART",
"description": "This tool manages your RNA-Seq and ChIP-seq data.",
"homepage": "http://urgi.versailles.inra.fr/Tools/S-MART",
"biotoolsID": "s-mart",
"biotoolsCURIE": "biotools:s-mart",
"tool_type": [
"Suite"
],
"collection": [
"S-MART"
],
"scientific_topics": [
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_3169",
"http://edamontology.org/topic_0092"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Matthias Zytnicki",
"email": "matthias.zytnicki@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://urgi.versailles.inra.fr/download/s-mart/doc.pdf",
"maturity": "Mature",
"cost": null,
"unique_visits": 267,
"citations": null,
"annual_visits": 474,
"last_update": "2024-11-25T14:22:04.089851Z",
"teams": [],
"source_repository": null
},
{
"id": 176,
"name": "Galaxy",
"description": "Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.",
"homepage": "https://galaxyproject.org/",
"biotoolsID": "galaxy",
"biotoolsCURIE": "biotools:galaxy",
"tool_type": [
"Workflow",
"Bioinformatics portal",
"Web application",
"Web API"
],
"collection": [
"Galaxy",
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_3673",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0196",
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1093/nar/gkw343",
"10.1093/nar/gkac247"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Galaxy support",
"email": null,
"url": "https://biostar.usegalaxy.org/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Galaxy Community",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
}
],
"tool_licence": "AFL-3.0",
"documentation": "https://usegalaxy.org/api/docs",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 400,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:46:57.861339Z",
"teams": [
"South Green"
],
"source_repository": "https://github.com/galaxyproject/galaxy"
},
{
"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": 165,
"name": "T-Coffee",
"description": "A multiple sequence alignment package that can be used for DNA, RNA and protein sequences. It can be used to align sequences or to combine the output of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment.",
"homepage": "http://www.tcoffee.org/Projects/tcoffee/",
"biotoolsID": "tcoffee",
"biotoolsCURIE": "biotools:tcoffee",
"tool_type": [
"Command-line tool"
],
"collection": [
"T-Coffee"
],
"scientific_topics": [
"http://edamontology.org/topic_0080"
],
"primary_publication": [
"10.1006/jmbi.2000.4042"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Cedric Notredame",
"email": "cedric.notredame@gmail.com",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://www.tcoffee.org/Projects/tcoffee/documentation/README",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 11271,
"last_update": "2019-03-14T11:57:50Z",
"teams": [],
"source_repository": null
}
]
}