HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 216,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=180&ordering=-homepage",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=140&ordering=-homepage",
"results": [
{
"id": 110,
"name": "RSAT retrieve-ensembl-seq",
"description": "Returns upstream, downstream, intronic, exonic, UTR, transcript, mRNA, CDS or gene sequences for a list of genes from the EnsEMBL database.\nMulti-genome queries are supported: automatic retrieval of sequences for all the orthologs of the query genes, at a given taxonomical level.",
"homepage": "http://rsat.sb-roscoff.fr/retrieve-ensembl-seq_form.cgi",
"biotoolsID": "rsat-retrieve-ensembl-seq",
"biotoolsCURIE": "biotools:rsat-retrieve-ensembl-seq",
"tool_type": [
"Web service",
"Web application",
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"FR",
"Regulatory Sequence Analysis Tools (RSAT)"
],
"scientific_topics": [
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0749"
],
"primary_publication": [
"10.1093/bioinformatics/btp519"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "Université Libre de Bruxelles",
"email": null,
"url": "https://www.ulb.be/",
"orcidid": null,
"gridid": "grid.4989.c",
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Morgane Thomas-Chollier",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-2608-476X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Support",
"Maintainer",
"Primary contact",
"Documentor",
"Developer"
],
"name": "Olivier Sand",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-1465-1640",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "AFL-3.0",
"documentation": "https://rsat-doc.github.io/using-RSAT/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [],
"source_repository": "https://github.com/rsat-doc"
},
{
"id": 119,
"name": "RSAT suite",
"description": "Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows.",
"homepage": "http://rsat.eu",
"biotoolsID": "rsat",
"biotoolsCURIE": "biotools:rsat",
"tool_type": [
"Web application",
"Suite"
],
"collection": [
"elixir-fr-sdp-2019",
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_3125"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Jacques van Helden",
"email": "Jacques.van-Helden@univ-amu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Other",
"documentation": "http://rsat.eu",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:33.330732Z",
"teams": [
"TAGC-BU"
],
"source_repository": null
},
{
"id": 189,
"name": "Erpin",
"description": "Easy RNA Profile IdentificatioN takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.",
"homepage": "http://rna.igmors.u-psud.fr/Software/erpin.php",
"biotoolsID": "erpin",
"biotoolsCURIE": "biotools:erpin",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0099",
"http://edamontology.org/topic_0097",
"http://edamontology.org/topic_3307"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Daniel Gautheret",
"email": "daniel.gautheret@u-psud.fr",
"url": "http://rna.igmors.u-psud.fr/gautheret/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://rna.igmors.u-psud.fr/Software/erpin.php",
"maturity": null,
"cost": null,
"unique_visits": 350,
"citations": null,
"annual_visits": 415,
"last_update": "2024-11-25T15:02:47.019198Z",
"teams": [
"EBIO"
],
"source_repository": null
},
{
"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": 22,
"name": "ProDom protein domain database",
"description": "A comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.",
"homepage": "http://prodom.prabi.fr/prodom/current/html/home.php",
"biotoolsID": "prodom",
"biotoolsCURIE": "biotools:prodom",
"tool_type": [
"Database portal"
],
"collection": [
"DRCAT"
],
"scientific_topics": [
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0736"
],
"primary_publication": [
"10.1093/nar/28.1.267"
],
"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": "http://prodom.prabi.fr/prodom/current/html/prodom_team.php",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://prodom.prabi.fr/prodom/current/documentation/help.php",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:21:05.113834Z",
"teams": [],
"source_repository": null
},
{
"id": 149,
"name": "PepPSy",
"description": "A gene expression-based prioritization system to help investigators to determine in which human tissues they should look for an unseen protein.",
"homepage": "http://peppsy.genouest.org",
"biotoolsID": "peppsy",
"biotoolsCURIE": "biotools:peppsy",
"tool_type": [
"Web application"
],
"collection": [
"Proteomics"
],
"scientific_topics": [
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_0121"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Contributor"
],
"name": "Olivier Collin",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Lydie Lane",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Thomas Darde",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Paula P. Duek",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "frederic.chalmel@univ-rennes1.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Olivier Sallou",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Frédéric Chalmel",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://peppsy.genouest.org/help",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T14:12:40.921423Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 21,
"name": "HOGENOM",
"description": "It allows selection of sets of homologous genes among species, and visualisation of multiple alignments and phylogenetic trees. It is useful for comparative sequence analysis, phylogeny, molecular evolution studies and to get a view of what is known about a peculiar gene family.",
"homepage": "http://pbil.univ-lyon1.fr/databases/hogenom3.html",
"biotoolsID": "hogenom",
"biotoolsCURIE": "biotools:hogenom",
"tool_type": [
"Database portal",
"Web service"
],
"collection": [
"DRCAT"
],
"scientific_topics": [
"http://edamontology.org/topic_0080",
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0194"
],
"primary_publication": [
"10.1186/1471-2105-10-S6-S3"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Documentor"
],
"name": "DRCAT",
"email": null,
"url": "http://drcat.sourceforge.net/",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
},
{
"type_role": [
"Documentor"
],
"name": "BioCatalogue",
"email": null,
"url": "https://www.biocatalogue.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "simon.penel@univ-lyon1.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "http://prodom.prabi.fr/prodom/current/html/home.php",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://doua.prabi.fr/databases/hogenom/home.php?contents=methods",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:20:45.218653Z",
"teams": [],
"source_repository": null
},
{
"id": 126,
"name": "PanGeneHome",
"description": "PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. Several standalone tools (e.g. PGAP, PANNOTATOR, PanGP, Roary and BPGA) and web servers (e.g. Panseq, PGAT and PanWeb) dedicated to pangenome analysis have been developed recently and offer the possibility to compute pangenome analysis for genomes provided by a user. For all these tools and servers, users have to collect genomes and manage to run the tools, which implies a significant effort on the user side. To tackle this problem, we developped PanGeneHome, the only web site offering pre-computed pangenome analysis with up-to-date and large scale data. PanGeneHome provides an easy way to get a glimpse on the pangenome of a microbial group of interest, the analysis being precomputed and available for 615 taxa, covering 182 species and 49 orders. Considering the fast growing number of microbial genomes, the PanGeneHome tool will need to be updated regularly.",
"homepage": "http://pangenehome.lmge.uca.fr/",
"biotoolsID": "PanGeneHome",
"biotoolsCURIE": "biotools:PanGeneHome",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_3407",
"http://edamontology.org/topic_0154"
],
"primary_publication": [],
"operating_system": [
"Mac",
"Linux",
"Windows"
],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:48:31.897688Z",
"teams": [
"AuBi"
],
"source_repository": null
},
{
"id": 264,
"name": "PanExplorer",
"description": "A web-based tool for exploratory analysis and visualization of bacterial pan-genomes.",
"homepage": "http://panexplorer.southgreen.fr",
"biotoolsID": "panexplorer",
"biotoolsCURIE": "biotools:panexplorer",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3382",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_3175"
],
"primary_publication": [],
"operating_system": [
"Mac",
"Linux",
"Windows"
],
"tool_credit": [
{
"type_role": [],
"name": "Alexis Dereeper",
"email": "alexis.dereeper@ird.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-8120-8409",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Damien F Meyer",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Marilyne Summo",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T15:26:52.796766Z",
"teams": [
"South Green"
],
"source_repository": "https://github.com/SouthGreenPlatform/PanExplorer"
},
{
"id": 68,
"name": "NORINE",
"description": "NORINE is a platform that includes a database of nonribosomal peptides together with tools for their analysis.",
"homepage": "http://norine.univ-lille.fr/norine/",
"biotoolsID": "NORINE",
"biotoolsCURIE": "biotools:NORINE",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3332",
"http://edamontology.org/topic_3301",
"http://edamontology.org/topic_3307",
"http://edamontology.org/topic_0078",
"http://edamontology.org/topic_3071"
],
"primary_publication": [
"10.1093/nar/gkz1000"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "Norine team",
"email": "norine@univ-lille.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "CC-BY-NC-SA-4.0",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-07-21T13:25:21.706482Z",
"teams": [
"Bilille"
],
"source_repository": null
},
{
"id": 75,
"name": "NAPP",
"description": "Nucleic Acid Phylogenetic Profile Database: classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes.",
"homepage": "http://napp.u-psud.fr/",
"biotoolsID": "napp",
"biotoolsCURIE": "biotools:napp",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0659",
"http://edamontology.org/topic_0082",
"http://edamontology.org/topic_3511",
"http://edamontology.org/topic_0077",
"http://edamontology.org/topic_0097"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "NAPP Support",
"email": "napp.biologie@u-psud.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://rna.igmors.u-psud.fr/NAPP/Help.php",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T15:05:27.630660Z",
"teams": [],
"source_repository": null
},
{
"id": 38,
"name": "MoonDB",
"description": "MoonDB is a database containing predicted Extreme Multifunctional (EMF) proteins (i.e. proteins with several unrelated functions), as well as a set of manually curated moonlighting proteins. Moonlighting proteins are a subclass of multifunctional proteins.",
"homepage": "http://moondb.hb.univ-amu.fr/",
"biotoolsID": "MoonDB",
"biotoolsCURIE": "biotools:MoonDB",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0623"
],
"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": "2019-11-06T11:40:39Z",
"teams": [
"TAGC-BU"
],
"source_repository": null
},
{
"id": 162,
"name": "HCA (hydrophobic cluster analysis)",
"description": "The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures.",
"homepage": "http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA#forms::HCA",
"biotoolsID": "hca",
"biotoolsCURIE": "biotools:hca",
"tool_type": [
"Web application"
],
"collection": [
"Proteomics"
],
"scientific_topics": [
"http://edamontology.org/topic_0121",
"http://edamontology.org/topic_3542"
],
"primary_publication": [
"10.1007/s000180050082"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Isabelle Callebaut",
"email": "Isabelle.Callebaut@lmcp.jussieu.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://bioserv.rpbs.univ-paris-diderot.fr/services/HCA/",
"maturity": null,
"cost": null,
"unique_visits": 3200,
"citations": null,
"annual_visits": 10000,
"last_update": "2024-11-24T15:47:21.770746Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 132,
"name": "Minia",
"description": "Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.",
"homepage": "http://minia.genouest.org/",
"biotoolsID": "minia",
"biotoolsCURIE": "biotools:minia",
"tool_type": [
"Command-line tool"
],
"collection": [
"GATB"
],
"scientific_topics": [
"http://edamontology.org/topic_0196"
],
"primary_publication": [
"10.1186/1748-7188-9-2"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Guillaume Rizk",
"email": "guillaume.rizk@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Rayan Chikhi",
"email": "chikhi@psu.edu",
"url": "http://rayan.chikhi.name",
"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
}
],
"tool_licence": "CECILL-2.0",
"documentation": "http://minia.genouest.org/files/minia.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:36:01.515486Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"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": 130,
"name": "MEMHDX",
"description": "This tool allows users to perform an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure.",
"homepage": "http://memhdx.c3bi.pasteur.fr/",
"biotoolsID": "memhdx",
"biotoolsCURIE": "biotools:memhdx",
"tool_type": [
"Web application"
],
"collection": [
"Proteomics"
],
"scientific_topics": [
"http://edamontology.org/topic_3520"
],
"primary_publication": [
"10.1093/bioinformatics/btw420"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Developer"
],
"name": "Véronique Hourdel",
"email": "vhourdel@pasteur.fr",
"url": "https://research.pasteur.fr/en/member/veronique-hourdel/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Support",
"Primary contact"
],
"name": "Marie-Agnès Dillies",
"email": "marie-agnes.dillies@pasteur.fr",
"url": "https://research.pasteur.fr/en/member/marie-agnes-dillies/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Support",
"Primary contact"
],
"name": "Sébastien Brier",
"email": "sbrier@pasteur.fr",
"url": "https://research.pasteur.fr/en/member/sebastien-brier/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer",
"Primary contact"
],
"name": "Stevenn Volant",
"email": "svolant@pasteur.fr",
"url": "https://research.pasteur.fr/en/member/stevenn-volant/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Structural Mass Spectrometry and Proteomics",
"email": null,
"url": "https://research.pasteur.fr/en/team/structural-mass-spectrometry-and-proteomics/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"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
}
],
"tool_licence": null,
"documentation": "https://www.youtube.com/watch?v=WeCt1sVyHio&feature=youtu.be",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 833,
"citations": null,
"annual_visits": 1524,
"last_update": "2024-11-25T14:14:10.281449Z",
"teams": [
"Pasteur HUB"
],
"source_repository": null
},
{
"id": 81,
"name": "MatrixDB",
"description": "It is a database focused on interactions established by extracellular proteins and polysaccharides. It takes into account the multimeric nature of several extracellular protein families for the curation of interactions, and reports interactions with individual polypeptide chains or with multimers, considered as permanent complexes.",
"homepage": "http://matrixdb.univ-lyon1.fr/",
"biotoolsID": "matrixdb",
"biotoolsCURIE": "biotools:matrixdb",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0078"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "MatrixDB Support",
"email": "sylvie.ricard-blum@univ-lyon1.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-9263-1851",
"gridid": null,
"typeEntity": "Person",
"note": "Professor at University Lyon 1, head of a team working on structure-interaction-function relationships of the extracellular matrix and extracellular matrix interaction networks."
}
],
"tool_licence": null,
"documentation": "http://matrixdb.univ-lyon1.fr/",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:29:32.794189Z",
"teams": [],
"source_repository": null
},
{
"id": 175,
"name": "Logol",
"description": "Pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).",
"homepage": "http://logol.genouest.org",
"biotoolsID": "logol",
"biotoolsCURIE": "biotools:logol",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0160"
],
"primary_publication": [
"10.1007/978-3-319-09192-1_4"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "GenOuest",
"email": "support@genouest.org",
"url": "http://www.genouest.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "CECILL-2.0",
"documentation": "http://training.genouest.org/claroline/claroline/learnPath/learningPathList.php?cidReset=true&cidReq=LOGOL",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:34Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 106,
"name": "Lifemap",
"description": "Explorer of the entire tree of life. Lifemap allows visualizing the entire NCBI taxonomy on a single page with a deep zoom interface and performing easy search, mrca detection, subtree download, etc.",
"homepage": "http://lifemap.univ-lyon1.fr",
"biotoolsID": "Lifemap",
"biotoolsCURIE": "biotools:Lifemap",
"tool_type": [
"Web service",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_3050"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [],
"tool_licence": "CC-BY-NC-4.0",
"documentation": "http://lifemap.univ-lyon1.fr/help/",
"maturity": "Legacy",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [],
"source_repository": "https://github.com/damiendevienne/Lifemap"
},
{
"id": 65,
"name": "OrthoInspector",
"description": "Software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species.",
"homepage": "http://lbgi.igbmc.fr/orthoinspector/",
"biotoolsID": "orthoinspector",
"biotoolsCURIE": "biotools:orthoinspector",
"tool_type": [
"Database portal",
"Desktop application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_3299"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Odile Lecompte",
"email": "odile.lecompte@unistra.fr",
"url": "http://alnitak.u-strasbg.fr/lbgi/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://lbgi.igbmc.fr/orthoinspector/index.php?option=com_content&view=article&id=50:tutorial-prepare-data-to-create-your-own-database&catid=3:tutorials&Itemid=6",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T13:55:18.202290Z",
"teams": [
"BiGEst"
],
"source_repository": null
}
]
}