HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 233,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=200&ordering=-unique_visits",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=160&ordering=-unique_visits",
"results": [
{
"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": 164,
"name": "InterEvDock",
"description": "Ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock2",
"biotoolsID": "interevdock2",
"biotoolsCURIE": "biotools:interevdock2",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275",
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_0080"
],
"primary_publication": [
"10.1093/nar/gky377",
"10.1093/nar/gkw340"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Raphael Guerois",
"email": "raphael.guerois@cea.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-5294-2858",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Jessica Andreani",
"email": "jessica.andreani@cea.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 310,
"citations": null,
"annual_visits": 1120,
"last_update": "2024-11-24T21:00:12.284563Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 168,
"name": "FastME",
"description": "Distance algorithms to infer phylogenies. It's based on balanced minimum evolution, which is the very principle of NJ. It includes Nearest Neighbor Interchange (NNI) and also Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations.",
"homepage": "http://www.atgc-montpellier.fr/fastme/",
"biotoolsID": "fastme",
"biotoolsCURIE": "biotools:fastme",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [
"galaxyPasteur",
"FastME"
],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/molbev/msv150"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "LIRMM",
"email": null,
"url": "http://www.lirmm.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact",
"Contributor"
],
"name": "Vincent Lefort",
"email": "vincent.lefort@lirmm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://www.atgc-montpellier.fr/fastme/usersguide.php",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 300,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T20:59:19.988087Z",
"teams": [
"ATGC"
],
"source_repository": null
},
{
"id": 182,
"name": "S-MART",
"description": "This tool manages your RNA-Seq and ChIP-seq data.",
"homepage": "http://urgi.versailles.inra.fr/Tools/S-MART",
"biotoolsID": "s-mart",
"biotoolsCURIE": "biotools:s-mart",
"tool_type": [
"Suite"
],
"collection": [
"S-MART"
],
"scientific_topics": [
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_3169",
"http://edamontology.org/topic_0092"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Matthias Zytnicki",
"email": "matthias.zytnicki@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://urgi.versailles.inra.fr/download/s-mart/doc.pdf",
"maturity": "Mature",
"cost": null,
"unique_visits": 267,
"citations": null,
"annual_visits": 474,
"last_update": "2024-11-25T14:22:04.089851Z",
"teams": [],
"source_repository": null
},
{
"id": 159,
"name": "SABBAC",
"description": "Tool for the reconstruction of complete protein structures from their alpha-carbon descriptions.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC",
"biotoolsID": "sabbac",
"biotoolsCURIE": "biotools:sabbac",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275"
],
"primary_publication": [],
"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/SABBAC/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 130,
"citations": null,
"annual_visits": 640,
"last_update": "2024-11-24T21:00:10.511557Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 167,
"name": "MPscan",
"description": "MPscan (multi-pattern scan) is a program for mapping short reads (<30bp) exactly on a set of reference sequences (eg, a genome) without indexing the reference. MPscan performs only exact mapping (no substitution, nor indels), is fast (optimal complexity), and easy to use.",
"homepage": "http://www.atgc-montpellier.fr/mpscan/",
"biotoolsID": "mpscan",
"biotoolsCURIE": "biotools:mpscan",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_0622"
],
"primary_publication": [
"10.1007/978-3-642-04241-6_21"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Vincent Lefort",
"email": "Vincent.Lefort@lirmm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/download/papers/mpscan_manual_2008.pdf",
"maturity": null,
"cost": null,
"unique_visits": 100,
"citations": null,
"annual_visits": 0,
"last_update": "2021-04-22T06:40:43Z",
"teams": [
"ATGC"
],
"source_repository": null
},
{
"id": 155,
"name": "HHalign-Kbest",
"description": "Useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.",
"homepage": "http://bioserv.rpbs.univ-paris-diderot.fr/services/HHalign-Kbest/",
"biotoolsID": "hhalign-kbest",
"biotoolsCURIE": "biotools:hhalign-kbest",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0081",
"http://edamontology.org/topic_2814",
"http://edamontology.org/topic_0736"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Raphael Guerois",
"email": null,
"url": "https://scholar.google.com/citations?user=M7Ln2zQAAAAJ&hl=es",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://bioserv.rpbs.univ-paris-diderot.fr/services/HHalign-Kbest/#faq",
"maturity": null,
"cost": null,
"unique_visits": 70,
"citations": null,
"annual_visits": 260,
"last_update": "2024-11-25T14:00:57.608636Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 169,
"name": "BIONJ",
"description": "This software is well suited for distances estimated from DNA or protein sequences. It has better topological accuracy than NJ in all evolutionary conditions; its superiority becomes important when the substitution rates are high and varying among lineages.",
"homepage": "http://www.atgc-montpellier.fr/bionj/",
"biotoolsID": "bionj",
"biotoolsCURIE": "biotools:bionj",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0084",
"http://edamontology.org/topic_0654"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Eric RIVALS",
"email": "Eric.Rivals@lirmm.fr",
"url": "http://www.lirmm.fr/~gascuel/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/bionj/paper.php",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:15:50.001899Z",
"teams": [
"ATGC"
],
"source_repository": null
},
{
"id": 172,
"name": "Mix",
"description": "Tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.",
"homepage": "https://github.com/cbib/MIX",
"biotoolsID": "mix",
"biotoolsCURIE": "biotools:mix",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0196"
],
"primary_publication": [
"10.1186/1471-2105-14-S15-S16"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Developer",
"Contributor"
],
"name": "Alexis Groppi",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "CNRS / LaBRI, Universite Bordeaux 1, 351 cours de la Liberation, 33405 Talence Cedex, France",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "CBiB - Universite Victor Segalen Bordeaux, 146, rue Leo Saignat, 33076 Bordeaux, France",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "CBiB - Universite Victor Segalen Bordeaux, 146, rue Leo Saignat, 33076 Bordeaux, France",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
},
{
"type_role": [],
"name": "CNRS / LaBRI, Universite Bordeaux 1, 351 cours de la Liberation, 33405 Talence Cedex, France",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
},
{
"type_role": [
"Support"
],
"name": "Alexis Groppi",
"email": "alexis.groppi@u-bordeaux.fr",
"url": "http://www.cbib.u-bordeaux2.fr/fr/content/services",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexis Groppi",
"email": "alexis.groppi@u-bordeaux.fr",
"url": "http://www.cbib.u-bordeaux2.fr/fr/content/services",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Heissam Soueidan",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Florence Maurier",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "NKI-AVL, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer",
"Contributor"
],
"name": "Macha Nikolski",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "NKI-AVL, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "u-bordeaux.fr",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "MIT",
"documentation": "https://github.com/cbib/MIX",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T14:18:36.339969Z",
"teams": [
"CBiB"
],
"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": 173,
"name": "Tango",
"description": "A computer algorithm for prediction of aggregating regions in unfolded polypeptide chains. The model used here, is designed to predict cross-beta aggregation in peptides and denatured proteins and consists of a phase-space encompassing the random coil and 4 possible structural states: beta-turn, alpha-helix, beta-sheet aggregation and alpha-helical aggregation.",
"homepage": "http://tango.crg.es/",
"biotoolsID": "tango",
"biotoolsCURIE": "biotools:tango",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0078",
"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_0081"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "http://tango.crg.es/support.jsp",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://tango.crg.es/Tango_Handbook.pdf",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:45Z",
"teams": [
"CBiB"
],
"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_3320",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_0080",
"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": 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": 179,
"name": "MACSIMS",
"description": "Multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods.",
"homepage": "http://www.lbgi.fr/~julie/MACSIMS/",
"biotoolsID": "macsims",
"biotoolsCURIE": "biotools:macsims",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0092"
],
"primary_publication": [
"10.1186/1471-2105-7-318"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "IFB ELIXIR-FR",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Julie Thompson",
"email": "julie@igbmc.u-strasbg.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.lbgi.fr/~julie/MACSIMS/Documentation/",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:53:38.069848Z",
"teams": [
"BiGEst"
],
"source_repository": null
},
{
"id": 145,
"name": "MacSyFinder",
"description": "Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.",
"homepage": "https://github.com/gem-pasteur/macsyfinder",
"biotoolsID": "macsyfinder",
"biotoolsCURIE": "biotools:macsyfinder",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [
"GEM Pasteur"
],
"scientific_topics": [
"http://edamontology.org/topic_0085"
],
"primary_publication": [
"10.1371/journal.pone.0110726",
"10.24072/pcjournal.250"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Bertrand Néron",
"email": "bneron@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Eduardo Rocha",
"email": "eduardo.rocha@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"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": [
"Provider"
],
"name": "Microbial Evolutionary Genomics Unit",
"email": null,
"url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": "CNRS - UMR 352"
},
{
"type_role": [
"Developer"
],
"name": "Bertrand Néron",
"email": "bneron@pasteur.fr",
"url": "https://research.pasteur.fr/en/member/bertrand-neron/",
"orcidid": "https://orcid.org/0000-0002-0220-0482",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Eduardo Rocha",
"email": "eduardo.rocha@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
"orcidid": "https://orcid.org/0000-0001-7704-822X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Bertrand Néron",
"email": "bneron@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Sophie Abby",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-5231-3346",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "https://research.pasteur.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "C3BI",
"email": null,
"url": "https://research.pasteur.fr/en/center/c3bi/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "https://macsyfinder.readthedocs.io/en/latest/",
"maturity": "Mature",
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T13:49:36.708539Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://github.com/gem-pasteur/macsyfinder"
},
{
"id": 123,
"name": "DEPIB",
"description": "Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes.",
"homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipeline",
"biotoolsID": "DEPIB",
"biotoolsCURIE": "biotools:DEPIB",
"tool_type": [
"Workflow"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3308"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Provider",
"Support"
],
"name": "BiRD bioinformatics facility",
"email": "pf-bird@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Solenne Dumont",
"email": "solenne.dumont@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
"orcidid": "https://orcid.org/0000-0003-3237-7382",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "BiRD",
"email": "pf-bird@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Primary contact",
"Developer",
"Support"
],
"name": "Eric Charpentier",
"email": "eric.charpentier@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Audrey Bihouée",
"email": "audrey.bihouee@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
"orcidid": "https://orcid.org/0000-0002-8689-2083",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Erwan Delage",
"email": "erwan.delage@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer",
"Contributor"
],
"name": "Damien Vintache",
"email": "Damien.Vintache@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:40:03.286943Z",
"teams": [
"BiRD"
],
"source_repository": null
},
{
"id": 146,
"name": "fqtools",
"description": "A package that provides tools for efficient FASTQ files manipulation.",
"homepage": "https://bioweb.pasteur.fr/packages/pack@fqtools@1.1",
"biotoolsID": "fqtools",
"biotoolsCURIE": "biotools:fqtools",
"tool_type": [
"Suite"
],
"collection": [
"fqtools"
],
"scientific_topics": [
"http://edamontology.org/topic_0080"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Maintainer"
],
"name": "Nicolas Joly",
"email": "njoly@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": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2020-06-16T10:55:24Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README"
},
{
"id": 152,
"name": "PipeAlign2",
"description": "Takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.",
"homepage": "http://www.lbgi.fr/pipealign",
"biotoolsID": "pipealign",
"biotoolsCURIE": "biotools:pipealign",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_0080",
"http://edamontology.org/topic_0078",
"http://edamontology.org/topic_3168"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "akress@unistra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Unlicense",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T21:03:24.978595Z",
"teams": [
"BiGEst"
],
"source_repository": null
},
{
"id": 147,
"name": "SortMeRNA",
"description": "Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.",
"homepage": "https://bioinfo.cristal.univ-lille.fr/RNA/sortmerna/",
"biotoolsID": "sortmerna",
"biotoolsCURIE": "biotools:sortmerna",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [
"ELIXIR Trainer Tools"
],
"scientific_topics": [
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_3941",
"http://edamontology.org/topic_3174"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://github.com/biocore/sortmerna/issues",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://github.com/sortmerna/sortmerna/issues",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/sortmerna/sortmerna/wiki/User-manual-v4.3.2",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:49:42.747317Z",
"teams": [
"Bilille"
],
"source_repository": null
},
{
"id": 127,
"name": "DiNAMO",
"description": "The DiNAMO software implements an exhaustive algorithm to detect over-represented IUPAC motifs in a set of DNA sequences.",
"homepage": "https://github.com/bonsai-team/DiNAMO",
"biotoolsID": "dinamo",
"biotoolsCURIE": "biotools:dinamo",
"tool_type": [
"Command-line tool",
"Library"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_3169"
],
"primary_publication": [
"10.1186/s12859-018-2215-1"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Chadi Saad",
"email": "chadi.saad@univ-lille1.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "https://github.com/bonsai-team/DiNAMO/blob/master/README.md",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T14:31:44.889611Z",
"teams": [
"Bilille"
],
"source_repository": null
}
]
}