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=120&ordering=-scientific_topics",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=80&ordering=-scientific_topics",
"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": 254,
"name": "MOGAMUN",
"description": "A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks.\n\nMOGAMUN is a Multi Objective Genetic Algorithm to find active modules (i.e., highly connected subnetworks with an overall deregulation) in MUltiplex biological Networks. For a detailed description of MOGAMUN check out the preprint https://www.biorxiv.org/content/10.1101/2020.05.25.114215v1. All the expression datasets and networks that we used to obtain the results reported in our preprint are available in the GitHub repository https://github.com/elvanov/MOGAMUN-data.",
"homepage": "https://github.com/elvanov/MOGAMUN",
"biotoolsID": "mogamun",
"biotoolsCURIE": "biotools:mogamun",
"tool_type": [
"Library"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_0121"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": null,
"email": "anais.baudot@univ-amu.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": "2021-02-26T09:22:38Z",
"teams": [
"NSBD"
],
"source_repository": null
},
{
"id": 14,
"name": "UMD-Predictor",
"description": "A tool that provides a combinatorial approach to identify potential pathogenic variations, that associates the following data: localization within the protein, conservation, biochemical properties of the mutant and wild-type residues, and the potential impact of the variation on mRNA.",
"homepage": "http://umd-predictor.eu",
"biotoolsID": "umd-predictor",
"biotoolsCURIE": "biotools:umd-predictor",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_0199",
"http://edamontology.org/topic_3574",
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_3063"
],
"primary_publication": [
"10.1002/humu.22965"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Christophe Beroud",
"email": "christophe.beroud@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2019-07-24T20:06:47Z",
"teams": [],
"source_repository": null
},
{
"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": 208,
"name": "MindTheGap",
"description": "Performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.",
"homepage": "https://gatb.inria.fr/software/mind-the-gap/",
"biotoolsID": "mindthegap",
"biotoolsCURIE": "biotools:mindthegap",
"tool_type": [
"Command-line tool"
],
"collection": [
"GATB"
],
"scientific_topics": [
"http://edamontology.org/topic_0199"
],
"primary_publication": [
"10.1093/bioinformatics/btu545"
],
"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": "Claire Lemaitre",
"email": "claire.lemaitre@inria.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://gatb.inria.fr/software/mind-the-gap/",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:58:48.627968Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 14,
"name": "UMD-Predictor",
"description": "A tool that provides a combinatorial approach to identify potential pathogenic variations, that associates the following data: localization within the protein, conservation, biochemical properties of the mutant and wild-type residues, and the potential impact of the variation on mRNA.",
"homepage": "http://umd-predictor.eu",
"biotoolsID": "umd-predictor",
"biotoolsCURIE": "biotools:umd-predictor",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"Developed_RD-Connect",
"RD-Connect",
"Rare Disease",
"ELIXIR-FR"
],
"scientific_topics": [
"http://edamontology.org/topic_0199",
"http://edamontology.org/topic_3574",
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3325",
"http://edamontology.org/topic_3063"
],
"primary_publication": [
"10.1002/humu.22965"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Christophe Beroud",
"email": "christophe.beroud@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "David Salgado",
"email": "david.salgado@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2019-07-24T20:06:47Z",
"teams": [],
"source_repository": null
},
{
"id": 39,
"name": "SPROUTS",
"description": "SPROUTS has two general functions.\nThe first is to provide existing mutation data given a protein specified by a PDB ID. This is Query mode.\nThe second is to generate new mutation data based on a new PDB ID or a user input. This is Submit mode.",
"homepage": "http://sprouts.rpbs.univ-paris-diderot.fr/",
"biotoolsID": "SPROUTS",
"biotoolsCURIE": "biotools:SPROUTS",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0199"
],
"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": "2022-11-30T13:37:17.543436Z",
"teams": [],
"source_repository": null
},
{
"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": 205,
"name": "DiscoSNP",
"description": "This software is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).",
"homepage": "https://colibread.inria.fr/software/discosnp/",
"biotoolsID": "discosnp",
"biotoolsCURIE": "biotools:discosnp",
"tool_type": [
"Command-line tool"
],
"collection": [
"GATB"
],
"scientific_topics": [
"http://edamontology.org/topic_2885",
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_0199"
],
"primary_publication": [
"10.1093/nar/gku1187"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Pierre Peterlongo",
"email": "pierre.peterlongo@inria.fr",
"url": "https://colibread.inria.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://colibread.inria.fr/software/discosnp/",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:25:58.458039Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 166,
"name": "CRAC",
"description": "CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.",
"homepage": "http://crac.gforge.inria.fr",
"biotoolsID": "crac",
"biotoolsCURIE": "biotools:crac",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3320",
"http://edamontology.org/topic_0114",
"http://edamontology.org/topic_3170"
],
"primary_publication": [
"10.1186/gb-2013-14-3-r30"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "For question regarding the software",
"email": "crac-bugs@lists.gforge.inria.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "For questions, comments, remarks on the algorithm or the article",
"email": "crac-article@lists.gforge.inria.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "CECILL-2.0",
"documentation": "http://crac.gforge.inria.fr/documentation/",
"maturity": "Mature",
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:59Z",
"teams": [
"Bilille",
"ATGC"
],
"source_repository": null
},
{
"id": 183,
"name": "SHOW",
"description": "Enables self-learning of HMM on a set of sequences, sequence segmentation based on the Baum-Welch or the Viterbi algorithms,and sequence simulation under a given HMM. Allows the user to specify any highly structured model and also to process large sets of sequences. Successfully used in diverse tasks such as DNA segmentation in homogeneous segments, bacterial gene prediction and human splice sites detection.",
"homepage": "http://genome.jouy.inra.fr/ssb/SHOW/",
"biotoolsID": "show",
"biotoolsCURIE": "biotools:show",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0080",
"http://edamontology.org/topic_3320",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_3372"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://www.ssbgroup.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://genome.jouy.inra.fr/ssb/SHOW/show_doc.pdf",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:58Z",
"teams": [
"MIGALE"
],
"source_repository": null
},
{
"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": 1,
"name": "VirHostnet",
"description": "Virus-Host Network is a knowledge-base system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains). VirHostNet contains high quality and up-to-date information gathered and curated from public databases.",
"homepage": "http://virhostnet.prabi.fr/",
"biotoolsID": "virhostnet",
"biotoolsCURIE": "biotools:virhostnet",
"tool_type": [
"Database portal",
"Bioinformatics portal",
"Web service"
],
"collection": [
"COVID-19",
"PRABI"
],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_3957",
"http://edamontology.org/topic_0781",
"http://edamontology.org/topic_3324"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "VirHostNet Support",
"email": "vincent.navratil@univ-lyon1.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-9974-1877",
"gridid": null,
"typeEntity": "Person",
"note": "Head of the prabi-amsb bioinformatics core facility (http://amsb.prabi.fr)"
}
],
"tool_licence": "Not licensed",
"documentation": "https://pbil.univ-lyon1.fr/redmine/projects/virhostscape/wiki",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-12-08T10:41:55Z",
"teams": [],
"source_repository": null
},
{
"id": 48,
"name": "European Hepatitis C virus database (euHCVdb)",
"description": "European Hepatitis C virus database.",
"homepage": "http://euhcvdb.ibcp.fr/euHCVdb/",
"biotoolsID": "euhcvdb",
"biotoolsCURIE": "biotools:euhcvdb",
"tool_type": [
"Database portal"
],
"collection": [
"DRCAT"
],
"scientific_topics": [
"http://edamontology.org/topic_0781"
],
"primary_publication": [
"10.1093/nar/gkl970"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Documentor"
],
"name": "DRCAT",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://euhcvdb.ibcp.fr/euHCVdb/jsp/sendMail.jsp",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://euhcvdb.ibcp.fr/euHCVdb/jsp/help.jsp",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T16:04:26.299102Z",
"teams": [],
"source_repository": null
},
{
"id": 181,
"name": "CARNAC",
"description": "Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.",
"homepage": "http://bioinfo.lifl.fr/carnac",
"biotoolsID": "carnac",
"biotoolsCURIE": "biotools:carnac",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0099",
"http://edamontology.org/topic_0082",
"http://edamontology.org/topic_0097",
"http://edamontology.org/topic_0659",
"http://edamontology.org/topic_0781"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Carnac team",
"email": "carnac@univ-lille1.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://bioinfo.lifl.fr/carnac/help.php",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T14:52:06.002489Z",
"teams": [
"Bilille"
],
"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": 1,
"name": "VirHostnet",
"description": "Virus-Host Network is a knowledge-base system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains). VirHostNet contains high quality and up-to-date information gathered and curated from public databases.",
"homepage": "http://virhostnet.prabi.fr/",
"biotoolsID": "virhostnet",
"biotoolsCURIE": "biotools:virhostnet",
"tool_type": [
"Database portal",
"Bioinformatics portal",
"Web service"
],
"collection": [
"COVID-19",
"PRABI"
],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_3957",
"http://edamontology.org/topic_0781",
"http://edamontology.org/topic_3324"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "VirHostNet Support",
"email": "vincent.navratil@univ-lyon1.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-9974-1877",
"gridid": null,
"typeEntity": "Person",
"note": "Head of the prabi-amsb bioinformatics core facility (http://amsb.prabi.fr)"
}
],
"tool_licence": "Not licensed",
"documentation": "https://pbil.univ-lyon1.fr/redmine/projects/virhostscape/wiki",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-12-08T10:41:55Z",
"teams": [],
"source_repository": null
},
{
"id": 1,
"name": "VirHostnet",
"description": "Virus-Host Network is a knowledge-base system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains). VirHostNet contains high quality and up-to-date information gathered and curated from public databases.",
"homepage": "http://virhostnet.prabi.fr/",
"biotoolsID": "virhostnet",
"biotoolsCURIE": "biotools:virhostnet",
"tool_type": [
"Database portal",
"Bioinformatics portal",
"Web service"
],
"collection": [
"COVID-19",
"PRABI"
],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_3957",
"http://edamontology.org/topic_0781",
"http://edamontology.org/topic_3324"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "VirHostNet Support",
"email": "vincent.navratil@univ-lyon1.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-9974-1877",
"gridid": null,
"typeEntity": "Person",
"note": "Head of the prabi-amsb bioinformatics core facility (http://amsb.prabi.fr)"
}
],
"tool_licence": "Not licensed",
"documentation": "https://pbil.univ-lyon1.fr/redmine/projects/virhostscape/wiki",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-12-08T10:41:55Z",
"teams": [],
"source_repository": null
},
{
"id": 141,
"name": "DroPNet",
"description": "DroPNet is a webserver for generating and analyzing Drosophila protein-protein interaction networks. Input data is a list of genes from an experiment such as RNAi screen.",
"homepage": "http://dropnet.isima.fr",
"biotoolsID": "dropnet",
"biotoolsCURIE": "biotools:dropnet",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_3957",
"http://edamontology.org/topic_3523",
"http://edamontology.org/topic_3678"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "RENAUD Yoan",
"email": "renaud@isima.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://dropnet.gred-clermont.fr/DroPNet_project/UserManual.pdf",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 72000,
"last_update": "2018-12-10T12:58:56Z",
"teams": [
"AuBi"
],
"source_repository": null
},
{
"id": 86,
"name": "BIII (BioImage Informatics Index, biii.eu)",
"description": "BIII (BioImage Informatics Index, biii.eu) is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis. Software tools are organized as either a full protocol of analysis (workflow), a specific component to construct a workflow, or a software platform or library (collection). They are described using EDAM-bioimaging. All entries are exposed following FAIR principles and accessible for other usage with ODC-By v1.0 license.",
"homepage": "https://biii.eu",
"biotoolsID": "BISE",
"biotoolsCURIE": "biotools:BISE",
"tool_type": [
"Database portal",
"Bioinformatics portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"NEUBIAS"
],
"scientific_topics": [
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_0769",
"http://edamontology.org/topic_3298",
"http://edamontology.org/topic_3382"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Contributor"
],
"name": "Matúš Kalaš",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-1509-4981",
"gridid": null,
"typeEntity": "Person",
"note": "Coordinator of the EDAM-bioimaging ontology development"
},
{
"type_role": [
"Contributor"
],
"name": "Kota Miura",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-6926-191X",
"gridid": null,
"typeEntity": "Person",
"note": "Main technical support and one of the founders of the project"
},
{
"type_role": [
"Documentor"
],
"name": "Taggers",
"email": null,
"url": "http://biii.eu/show-taggers",
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": "People curating tools"
},
{
"type_role": [
"Contributor"
],
"name": "Chong Zhang",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": "Co-leader of the developement"
},
{
"type_role": [
"Provider"
],
"name": "NEUBIAS Network of Bioimage Analysts",
"email": null,
"url": "https://neubias.eu",
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": "COST action having supported the creation and curation of this database"
},
{
"type_role": [
"Contributor"
],
"name": "Leandro Scholz",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-2411-0429",
"gridid": null,
"typeEntity": "Person",
"note": "Worked on the curation instructions"
},
{
"type_role": [
"Primary contact"
],
"name": "Perrine Paul-Gilloteaux",
"email": "perrine.paul-gilloteaux@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-4822-165X",
"gridid": null,
"typeEntity": "Person",
"note": "Leader of the project"
},
{
"type_role": [
"Contributor"
],
"name": "Alban Gaignard",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-3597-8557",
"gridid": null,
"typeEntity": "Person",
"note": "Developed the core ontology (data model) and enabled reuse of the content through W3C standards"
},
{
"type_role": [
"Contributor"
],
"name": "Florian Levet",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-4009-6225",
"gridid": null,
"typeEntity": "Person",
"note": "Development of Python scripts"
}
],
"tool_licence": "Other",
"documentation": "https://github.com/NeuBIAS/bise/wiki",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-03-26T15:45:10Z",
"teams": [],
"source_repository": null
}
]
}