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=160&ordering=-maturity",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=120&ordering=-maturity",
"results": [
{
"id": 240,
"name": "SMS",
"description": "Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection.",
"homepage": "http://www.atgc-montpellier.fr/sms/",
"biotoolsID": "PhyMLSMS",
"biotoolsCURIE": "biotools:PhyMLSMS",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [
"PhyML"
],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_2269"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/download/papers/sms-HowItWorks.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:18.380055Z",
"teams": [],
"source_repository": null
},
{
"id": 101,
"name": "Genomicus-plants",
"description": "Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "https://www.genomicus.biologie.ens.fr/genomicus-plants",
"biotoolsID": "Genomicus-Plants",
"biotoolsCURIE": "biotools:Genomicus-Plants",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0780"
],
"primary_publication": [
"10.1093/nar/gks1156",
"10.1093/pcp/pcu177"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 176,
"name": "Galaxy",
"description": "Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.",
"homepage": "https://galaxyproject.org/",
"biotoolsID": "galaxy",
"biotoolsCURIE": "biotools:galaxy",
"tool_type": [
"Workflow",
"Bioinformatics portal",
"Web application",
"Web API"
],
"collection": [
"Galaxy",
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_3673",
"http://edamontology.org/topic_0196",
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1093/nar/gkw343",
"10.1093/nar/gkac247"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Galaxy support",
"email": null,
"url": "https://biostar.usegalaxy.org/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Galaxy Community",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
}
],
"tool_licence": "AFL-3.0",
"documentation": "https://usegalaxy.org/api/docs",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 400,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:46:57.861339Z",
"teams": [
"ABiMS"
],
"source_repository": "https://github.com/galaxyproject/galaxy"
},
{
"id": 9,
"name": "remap",
"description": "Display restriction enzyme binding sites in a nucleotide sequence.",
"homepage": "http://emboss.open-bio.org/rel/rel6/apps/remap.html",
"biotoolsID": "remap",
"biotoolsCURIE": "biotools:remap",
"tool_type": [
"Database portal",
"Command-line tool"
],
"collection": [
"EMBOSS"
],
"scientific_topics": [
"http://edamontology.org/topic_3125"
],
"primary_publication": [
"10.1016/S0168-9525(00)02024-2"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Contributor"
],
"name": "EMBOSS Contributors",
"email": null,
"url": "http://emboss.open-bio.org/html/use/pr01s01.html",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "EMBL-EBI",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "UK MRC",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Wellcome Trust",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "UK BBSRC",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "EMBOSS",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Support"
],
"name": "EMBOSS",
"email": "emboss@emboss.open-bio.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "emboss@emboss.open-bio.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "emboss-bug@emboss.open-bio.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://emboss.open-bio.org/rel/rel6/apps/remap.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2018-12-10T12:58:55Z",
"teams": [
"TAGC-BU"
],
"source_repository": "http://emboss.open-bio.org/html/adm/ch01s01.html"
},
{
"id": 151,
"name": "ReproGenomics Viewer",
"description": "The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community.",
"homepage": "http://rgv.genouest.org",
"biotoolsID": "reprogenomics_viewer",
"biotoolsCURIE": "biotools:reprogenomics_viewer",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3420"
],
"primary_publication": [
"10.1093/nar/gkv345"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Thomas Darde",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "irisa.fr",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Olivier Sallou",
"email": "olivier.sallou@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer",
"Primary contact"
],
"name": "Frédéric Chalmel",
"email": "frederic.chalmel@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://rgv.genouest.org/tuto.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:22:51.040462Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 100,
"name": "Genomicus-fungi",
"description": "Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus-fungi/",
"biotoolsID": "Genomicus-fungi",
"biotoolsCURIE": "biotools:Genomicus-fungi",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1093/nar/gks1156"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 99,
"name": "Genomicus-protists",
"description": "Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus-protists/",
"biotoolsID": "Genomicus-protists",
"biotoolsCURIE": "biotools:Genomicus-protists",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1093/nar/gks1156"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 98,
"name": "Genomicus-metazoa",
"description": "Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "http://www.genomicus.biologie.ens.fr/genomicus-metazoa/",
"biotoolsID": "Genomicus-metazoa",
"biotoolsCURIE": "biotools:Genomicus-metazoa",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1093/nar/gks1156"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:56:24.333237Z",
"teams": [
"PB-IBENS"
],
"source_repository": null
},
{
"id": 96,
"name": "GINsim",
"description": "Computer tool for the modeling and simulation of genetic regulatory networks.",
"homepage": "http://ginsim.org/",
"biotoolsID": "ginsim",
"biotoolsCURIE": "biotools:ginsim",
"tool_type": [
"Desktop application"
],
"collection": [
"elixir-fr-sdp-2019",
"FR",
"EBI Training Tools",
"PerMedCoE"
],
"scientific_topics": [
"http://edamontology.org/topic_2259",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0204"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support",
"Developer"
],
"name": null,
"email": null,
"url": "http://ginsim.org/contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://ginsim.org/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:09:51.625867Z",
"teams": [],
"source_repository": "http://ginsim.org/models_repository"
},
{
"id": 113,
"name": "ParameciumDB",
"description": "Online community database for Paramecium species. Contains annotation of genome sequences and features, genome-wide data sets, advanced capabilities to query, retrieve, visualize and compare data.",
"homepage": "https://paramecium.i2bc.paris-saclay.fr",
"biotoolsID": "parameciumdb",
"biotoolsCURIE": "biotools:parameciumdb",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_0080",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_3321"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "https://paramecium.i2bc.paris-saclay.fr/cgi/user/contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Terms of Use",
"email": null,
"url": "https://paramecium.i2bc.paris-saclay.fr/parawiki/Terms_of_Use",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "CC-BY-4.0",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:30.463079Z",
"teams": [],
"source_repository": null
},
{
"id": 163,
"name": "PEP-FOLD",
"description": "PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3",
"biotoolsID": "pep-fold",
"biotoolsCURIE": "biotools:pep-fold",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gkp323",
"10.1093/nar/gks419",
"10.1093/nar/gkw329"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Pierre Tufféry",
"email": "pierre.tuffery@univ-paris-diderot.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1033-9895",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 3900,
"citations": null,
"annual_visits": 30000,
"last_update": "2024-11-24T20:59:57.942237Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 241,
"name": "iPPI-DB",
"description": "IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large variety of data is stored within IPPI-DB: structural, pharmacological, binding and activity profile, pharmacokinetic and cytotoxicity when available, as well as some data about the PPI targets themselves.",
"homepage": "https://ippidb.pasteur.fr",
"biotoolsID": "ippi-db",
"biotoolsCURIE": "biotools:ippi-db",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3343"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "Olivier Sperandio",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-6610-2729",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-01-14T17:37:37Z",
"teams": [],
"source_repository": "https://gitlab.pasteur.fr/ippidb/ippidb-web/"
},
{
"id": 161,
"name": "PEP-SiteFinder",
"description": "PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder",
"biotoolsID": "pep-sitefinder",
"biotoolsCURIE": "biotools:pep-sitefinder",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3534",
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gku404"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Pierre Tufféry",
"email": "pierre.tuffery@univ-paris-diderot.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1033-9895",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-SiteFinder",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 347,
"citations": null,
"annual_visits": 1482,
"last_update": "2024-11-24T20:59:55.640056Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 144,
"name": "SynTView",
"description": "Comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic genome browser with sub-maps holding information about genomic objects. The software is characterized by the presentation of syntenic organisations of microbial genomes and the visualization of polymorphism data along these genomes; these features are accessible to the user in an integrated way.",
"homepage": "http://genopole.pasteur.fr/SynTView/",
"biotoolsID": "syntview",
"biotoolsCURIE": "biotools:syntview",
"tool_type": [
"Web application",
"Desktop application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_0797"
],
"primary_publication": [
"10.1186/1471-2105-14-277"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "plechat@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "LGPL-3.0",
"documentation": "http://hub18.hosting.pasteur.fr/SynTView/documentation/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2021-05-19T14:52:04Z",
"teams": [
"Pasteur HUB"
],
"source_repository": null
},
{
"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": 197,
"name": "JASS",
"description": "software package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface.",
"homepage": "http://statistical-genetics.pages.pasteur.fr/jass/",
"biotoolsID": "jass",
"biotoolsCURIE": "biotools:jass",
"tool_type": [
"Command-line tool",
"Web application",
"Web service"
],
"collection": [
"Institut Pasteur"
],
"scientific_topics": [
"http://edamontology.org/topic_3517",
"http://edamontology.org/topic_2269",
"http://edamontology.org/topic_3053"
],
"primary_publication": [
"10.1093/nargab/lqaa003",
"10.1101/714832v1"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Pierre Lechat",
"email": "pierre.lechat@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/pierre-lechat/",
"orcidid": "https://orcid.org/0000-0003-1050-5582",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Carla Lasry",
"email": null,
"url": "https://research.pasteur.fr/fr/member/carla-lasry/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Chunzi Yao",
"email": "chunzi.yao@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/chunzi-yao/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Vincent Laville",
"email": "vincent.laville@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Bjarni Vilhjalmsson",
"email": null,
"url": "https://pure.au.dk/portal/en/persons/bjarni-johann-vilhjlmsson(35c047ab-0899-4434-91bb-121e4878ec76).html",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Hervé Ménager",
"email": "herve.menager@pasteur.fr",
"url": "https://research.pasteur.fr/fr/search/herve%20menager",
"orcidid": "https://orcid.org/0000-0002-7552-1009",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Aschard",
"email": "hugues.aschard@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/hugues-aschard/",
"orcidid": "http://orcid.org/0000-0002-7554-6783",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Hanna Julienne",
"email": "hanna.julienne@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/hanna-julienne/",
"orcidid": "https://orcid.org/0000-0001-8214-9412",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Vincent Guillemot",
"email": "vincent.guillemot@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/vincent-guillemot/",
"orcidid": "https://orcid.org/0000-0002-7421-0655",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://statistical-genetics.pages.pasteur.fr/jass/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:46:08.475046Z",
"teams": [],
"source_repository": "https://gitlab.pasteur.fr/statistical-genetics/jass"
},
{
"id": 190,
"name": "CRISPRFinder",
"description": "Detects this family of direct repeats found in the DNA of many bacteria and archaea.",
"homepage": "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index",
"biotoolsID": "crisprfinder",
"biotoolsCURIE": "biotools:crisprfinder",
"tool_type": [
"Web application",
"Database portal"
],
"collection": [
"CRISPR"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_2885",
"http://edamontology.org/topic_0203"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Marie Touchon",
"email": "mtouchon@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Unlicense",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 480,
"citations": null,
"annual_visits": 2273,
"last_update": "2024-11-24T21:05:00.924973Z",
"teams": [
"EBIO"
],
"source_repository": null
},
{
"id": 138,
"name": "SARTools",
"description": "R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.",
"homepage": "https://github.com/PF2-pasteur-fr/SARTools",
"biotoolsID": "sartools",
"biotoolsCURIE": "biotools:sartools",
"tool_type": [
"Command-line tool"
],
"collection": [
"SARTools"
],
"scientific_topics": [
"http://edamontology.org/topic_2269",
"http://edamontology.org/topic_3308"
],
"primary_publication": [
"10.1371/journal.pone.0157022"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer",
"Primary contact"
],
"name": "Marie-Agnès Dillies",
"email": "marie-agnes.dillies@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/marie-agnes-dillies/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "https://research.pasteur.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Support",
"Primary contact"
],
"name": "Jean-Yves Coppée",
"email": "jean-yves.coppee@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/jean-yves-coppee/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "C3BI",
"email": null,
"url": "https://research.pasteur.fr/en/center/c3bi/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Bioinformatics and Biostatistics Hub",
"email": null,
"url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Developer",
"Primary contact"
],
"name": "Hugo Varet",
"email": "hugo.varet@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/hugo-varet/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "France Génomique",
"email": null,
"url": "https://www.france-genomique.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "https://github.com/PF2-pasteur-fr/SARTools",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2021-04-17T15:12:05Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://github.com/PF2-pasteur-fr/SARTools"
},
{
"id": 13,
"name": "Human Splicing Finder",
"description": "The Human Splicing Finder (HSF) system combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS).",
"homepage": "http://www.umd.be/HSF3/",
"biotoolsID": "human_splicing_finder",
"biotoolsCURIE": "biotools:human_splicing_finder",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_3320",
"http://edamontology.org/topic_0199",
"http://edamontology.org/topic_3571",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_3063"
],
"primary_publication": [
"10.1093/nar/gkp215"
],
"operating_system": [
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "http://www.umd.be/HSF3/contactus.html",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Christophe Béroud",
"email": "christophe.beroud@inserm.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": null,
"documentation": "http://www.umd.be/HSF3/technicaltips.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T13:49:29.814329Z",
"teams": [],
"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"
}
]
}