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=100&ordering=description",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=60&ordering=description",
"results": [
{
"id": 111,
"name": "Galaxy Pasteur",
"description": "A wide variety of tools from the Galaxy instance of Institut Pasteur, France.",
"homepage": "https://galaxy.pasteur.fr/",
"biotoolsID": "Galaxy_Pasteur",
"biotoolsCURIE": "biotools:Galaxy_Pasteur",
"tool_type": [
"Workbench"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0080"
],
"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": "2020-03-16T18:06:05Z",
"teams": [],
"source_repository": null
},
{
"id": 47,
"name": "BYKdb",
"description": "Bacterial protein tYrosine Kinase database (BYKdb). Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences.",
"homepage": "http://bykdb.ibcp.fr/BYKdb/",
"biotoolsID": "bykdb",
"biotoolsCURIE": "biotools:bykdb",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0078",
"http://edamontology.org/topic_0080"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact form",
"email": null,
"url": "https://bykdb.ibcp.fr/BYKdb/BYKdbContact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://bykdb.ibcp.fr/BYKdb/BYKdbHelp",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T15:08:37.507577Z",
"teams": [],
"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_3298",
"http://edamontology.org/topic_0769",
"http://edamontology.org/topic_3382",
"http://edamontology.org/topic_3063",
"http://edamontology.org/topic_0091"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"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": [
"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": "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": [
"Contributor"
],
"name": "Chong Zhang",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": "Co-leader of the developement"
},
{
"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"
},
{
"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": "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": "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": "Leandro Scholz",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-2411-0429",
"gridid": null,
"typeEntity": "Person",
"note": "Worked on the curation instructions"
}
],
"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
},
{
"id": 150,
"name": "BioMAJ",
"description": "BioMAJ is a workflow engine dedicated to data synchronization and processing. The Software automates the update cycle and the supervision of the locally mirrored databank repository.",
"homepage": "http://biomaj.genouest.org/",
"biotoolsID": "biomaj",
"biotoolsCURIE": "biotools:biomaj",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3071"
],
"primary_publication": [
"10.1093/bioinformatics/btn325"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "GenOuest platform",
"email": "support@genouest.org",
"url": "http://www.genouest.org",
"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": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "AGPL-3.0",
"documentation": "http://biomaj.readthedocs.io/en/latest/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T16:17:07.096336Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 72,
"name": "Insyght",
"description": "Browser that helps navigate among abundant homologies, syntenies and genes annotations.",
"homepage": "http://genome.jouy.inra.fr/Insyght",
"biotoolsID": "insyght",
"biotoolsCURIE": "biotools:insyght",
"tool_type": [
"Database portal",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0080",
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_3301",
"http://edamontology.org/topic_3071"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "insyght@inra.fr",
"url": "http://genome.jouy.inra.fr/Insyght",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://genome.jouy.inra.fr/Insyght_doc_online/",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:51:03.945288Z",
"teams": [],
"source_repository": null
},
{
"id": 129,
"name": "GATB",
"description": "C++ library of high level functions designed to benefit from recent advances in NGS data structures for handling huge datasets of sequencing data.",
"homepage": "http://gatb.inria.fr/",
"biotoolsID": "gatb",
"biotoolsCURIE": "biotools:gatb",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_3071"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://gatb.inria.fr/about/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://gatb.inria.fr/gatb-global-architecture/",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T16:00:25.170196Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 178,
"name": "NGS-QC Generator",
"description": "Comparative analysis between ChIP-seq and other enrichment-related NGS datasets requires prior characterization of their degree of technical similarity. The Galaxy tool NGS-QC Generator is a computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies to improve the quality of sample-derived datasets.",
"homepage": "http://www.ngs-qc.org/",
"biotoolsID": "ngs-qc_generator",
"biotoolsCURIE": "biotools:ngs-qc_generator",
"tool_type": [
"Web application"
],
"collection": [
"Animal and Crop Genomics"
],
"scientific_topics": [
"http://edamontology.org/topic_3572",
"http://edamontology.org/topic_3169"
],
"primary_publication": [
"10.1007/978-1-4939-3578-9_13"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "contact@ngs-qc.org",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "http://www.ngs-qc.org/tutorial.php",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T14:05:15.865852Z",
"teams": [
"BiGEst"
],
"source_repository": null
},
{
"id": 144,
"name": "SynTView",
"description": "Comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic genome browser with sub-maps holding information about genomic objects. The software is characterized by the presentation of syntenic organisations of microbial genomes and the visualization of polymorphism data along these genomes; these features are accessible to the user in an integrated way.",
"homepage": "http://genopole.pasteur.fr/SynTView/",
"biotoolsID": "syntview",
"biotoolsCURIE": "biotools:syntview",
"tool_type": [
"Web application",
"Desktop application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_0797"
],
"primary_publication": [
"10.1186/1471-2105-14-277"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "plechat@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "LGPL-3.0",
"documentation": "http://hub18.hosting.pasteur.fr/SynTView/documentation/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2021-05-19T14:52:04Z",
"teams": [
"Pasteur HUB"
],
"source_repository": null
},
{
"id": 95,
"name": "RSAT oligo-analysis",
"description": "Compute k-mer frequencies (oligonucleotides or oligopeptides) and various statistics to discover exceptional motifs (over-represented or under-represented). Typical applications include discovery of transcription factor binding motifs, restriction sites in bacterial genomes, RNA termination and polyadenylation signals, detection of motifs associated with replication origins, analysis of oligopeptide frequencies in protein sequences.",
"homepage": "http://teaching.rsat.eu/oligo-analysis_form.cgi",
"biotoolsID": "oligo-analysis",
"biotoolsCURIE": "biotools:oligo-analysis",
"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_0749",
"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_3511"
],
"primary_publication": [
"10.1006/jmbi.1998.1947"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "RSAT",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "Jacques van Helden",
"email": "Jacques.van-Helden@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Jacques van Helden",
"email": "Jacques.van-Helden@univ-amu.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "AFL-3.0",
"documentation": "http://rsat.eu/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:23.505699Z",
"teams": [],
"source_repository": null
},
{
"id": 96,
"name": "GINsim",
"description": "Computer tool for the modeling and simulation of genetic regulatory networks.",
"homepage": "http://ginsim.org/",
"biotoolsID": "ginsim",
"biotoolsCURIE": "biotools:ginsim",
"tool_type": [
"Desktop application"
],
"collection": [
"elixir-fr-sdp-2019",
"FR",
"EBI Training Tools",
"PerMedCoE"
],
"scientific_topics": [
"http://edamontology.org/topic_2259",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_0204"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Support",
"Developer"
],
"name": null,
"email": null,
"url": "http://ginsim.org/contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://ginsim.org/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:09:51.625867Z",
"teams": [],
"source_repository": "http://ginsim.org/models_repository"
},
{
"id": 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": 157,
"name": "OCG",
"description": "Creates an overlapping class system from an unweighted simple graph G = (V,E).OCG is essentially a hierarchical ascending algorithm. By default, it will fuse the initial classes until further fusions do not increase the modularity but other options are available.",
"homepage": "http://tagc.univ-mrs.fr/tagc/index.php/software/17",
"biotoolsID": "ocg",
"biotoolsCURIE": "biotools:ocg",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_1775"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Brun C",
"email": "brun@tagc.univ-mrs.fr",
"url": "http://tagc.univ-mrs.fr/tagc/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://tagc.univ-mrs.fr/tagc/index.php/software/17",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T16:02:04.280293Z",
"teams": [
"TAGC-BU"
],
"source_repository": null
},
{
"id": 260,
"name": "CulebrONT",
"description": "CulebrONT is a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes.",
"homepage": "https://github.com/SouthGreenPlatform/CulebrONT_pipeline",
"biotoolsID": "culebront",
"biotoolsCURIE": "biotools:culebront",
"tool_type": [
"Workflow"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0196",
"http://edamontology.org/topic_0769",
"http://edamontology.org/topic_0621"
],
"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": "2022-01-10T14:00:06.343876Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 44,
"name": "Molligen",
"description": "Database dedicated to the comparative genomics of bacteria belonging to the class Mollicutes. It provides annotated sequence data and analysis for 72 genomes belonging to 51 species. The database provides genome and genetic element pages, homology relationship defined by various methods, pre-computed statistics, metabolic pathways, and a huge collection of tools for exploring and comparing genomes.",
"homepage": "https://services.cbib.u-bordeaux.fr/molligen4/",
"biotoolsID": "molligen",
"biotoolsCURIE": "biotools:molligen",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_3301"
],
"primary_publication": [
"10.1093/nar/gkh114"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "Université de Bordeaux",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Aurelien Barré",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Alain Blanchard",
"email": null,
"url": null,
"orcidid": "http://orcid.org/0000-0003-4223-5185",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Centre de Bioinformatique de Bordeaux (CBiB)",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Pascal Sirand-Pugnet",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Support"
],
"name": "Aurelien Barré",
"email": "aurelien.barre@u-bordeaux.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Aurélien Barré",
"email": "aurelien.barre@u-bordeaux.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "INRA",
"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": null,
"documentation": "http://services.cbib.u-bordeaux.fr/molligen/CREDITS/data/MolliGen_Tutorial_2012.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T15:35:08.058762Z",
"teams": [
"CBiB"
],
"source_repository": null
},
{
"id": 91,
"name": "DataDiscovery",
"description": "DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters.\n\nThis tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.",
"homepage": "https://urgi.versailles.inrae.fr/data-discovery/",
"biotoolsID": "DataDiscovery",
"biotoolsCURIE": "biotools:DataDiscovery",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI",
"FR"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_3810"
],
"primary_publication": [
"10.3835/plantgenome2015.06.0038"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support"
],
"name": "urgi-support",
"email": "urgi-support@inrae.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "BSD-3-Clause",
"documentation": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-07-29T13:42:39.375595Z",
"teams": [
"URGI"
],
"source_repository": "https://forgemia.inra.fr/urgi-is/data-discovery"
},
{
"id": 180,
"name": "Assemble2",
"description": "Design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.",
"homepage": "http://bioinformatics.org/assemble/",
"biotoolsID": "assemble2",
"biotoolsCURIE": "biotools:assemble2",
"tool_type": [
"Web API"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0097"
],
"primary_publication": [
"10.1093/bioinformatics/btq321"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"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": null,
"url": "http://www.bioinformatics.org/assemble/contacts.html",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://bioinformatics.org/assemble/",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-25T15:45:38.090886Z",
"teams": [
"BiGEst"
],
"source_repository": null
},
{
"id": 108,
"name": "RSAT position-analysis",
"description": "Detect oligomers (k-mers) whose positional distribution significantly discard from a homogeneous distribution.",
"homepage": "http://teaching.rsat.eu/position-analysis_form.cgi",
"biotoolsID": "RSAT-position-analysis",
"biotoolsCURIE": "biotools:RSAT-position-analysis",
"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/nar/28.4.1000"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Developer",
"Documentor",
"Maintainer",
"Support",
"Provider"
],
"name": "Jacques van Helden",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Université Libre de Bruxelles",
"email": null,
"url": "https://www.ulb.be/",
"orcidid": null,
"gridid": "grid.4989.c",
"typeEntity": "Institute",
"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": 109,
"name": "RSAT dyad-analysis",
"description": "Detect over- or under-represented dyads (spaced pairs of k-mers) in sequences.",
"homepage": "http://teaching.rsat.eu/dyad-analysis_form.cgi",
"biotoolsID": "RSAT_dyad-analysis",
"biotoolsCURIE": "biotools:RSAT_dyad-analysis",
"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/nar/28.8.1808"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [],
"name": "UNAM",
"email": null,
"url": null,
"orcidid": null,
"gridid": "grid.9486.3",
"typeEntity": "Institute",
"note": null
},
{
"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": [
"Primary contact",
"Developer",
"Documentor",
"Maintainer",
"Support",
"Provider"
],
"name": "Jacques van Helden",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0002-8799-8584",
"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": 190,
"name": "CRISPRFinder",
"description": "Detects this family of direct repeats found in the DNA of many bacteria and archaea.",
"homepage": "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index",
"biotoolsID": "crisprfinder",
"biotoolsCURIE": "biotools:crisprfinder",
"tool_type": [
"Web application",
"Database portal"
],
"collection": [
"CRISPR"
],
"scientific_topics": [
"http://edamontology.org/topic_2885",
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0203"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Marie Touchon",
"email": "mtouchon@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Unlicense",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 480,
"citations": null,
"annual_visits": 2273,
"last_update": "2024-11-24T21:05:00.924973Z",
"teams": [
"EBIO"
],
"source_repository": null
},
{
"id": 237,
"name": "D-GENIES",
"description": "D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.",
"homepage": "https://dgenies.toulouse.inrae.fr/",
"biotoolsID": "d-genies",
"biotoolsCURIE": "biotools:d-genies",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0092",
"http://edamontology.org/topic_0080"
],
"primary_publication": [
"10.7717/peerj.4958"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Floréal Cabanettes",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Christophe Klopp",
"email": "christophe.klopp@inrae.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-7126-5477",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact",
"Developer"
],
"name": "Philippe Bordron",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0003-1975-0920",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Vincent Dominguez",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Christophe Klopp",
"email": "christophe.klopp@toulouse.inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "GenoToul bioinformatics facility",
"email": null,
"url": "http://bioinfo.genotoul.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
}
],
"tool_licence": null,
"documentation": "https://dgenies.readthedocs.io/en/latest/index.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-12-18T10:02:18.098079Z",
"teams": [],
"source_repository": "https://github.com/genotoul-bioinfo/dgenies"
}
]
}