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=20&ordering=cost",
"previous": null,
"results": [
{
"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
},
{
"id": 36,
"name": "Banana Genome Hub",
"description": "A Next-Generation Information System for Musa genomics",
"homepage": "https://banana-genome-hub.southgreen.fr/",
"biotoolsID": "Banana_Genome_Hub",
"biotoolsCURIE": "biotools:Banana_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub",
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_3308",
"http://edamontology.org/topic_3810",
"http://edamontology.org/topic_0797"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "ANR",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Gaëtan Droc",
"email": "gaetan.droc@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Mathieu Rouard",
"email": "m.rouard@cgiar.org",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Bioversity International",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer"
],
"name": "CIRAD",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "https://banana-genome-hub.southgreen.fr/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:38.690746Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 90,
"name": "FAIDARE",
"description": "FAIDARE: FAIR Data-finder for Agronomic Research. \nThe purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.\n\nIt is based on the Breeding API (BrAPI) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface. It also provides a standard interface that can be accessed programatically through web services.\n\nIt is an extension of the generic DataDiscovery portal, a web portal that allows finding any type of data across several databases through a lightweight keyword based search. FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.",
"homepage": "https://urgi.versailles.inrae.fr/faidare/",
"biotoolsID": "faidare",
"biotoolsCURIE": "biotools:faidare",
"tool_type": [
"Database portal",
"Web service",
"Web API",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"URGI"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_3810",
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Support",
"Primary contact"
],
"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://urgi.versailles.inrae.fr/faidare/help",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-09-02T05:04:34.812991Z",
"teams": [
"PlantBioinfoPF"
],
"source_repository": "https://forgemia.inra.fr/urgi-is/faidare"
},
{
"id": 258,
"name": "FAIR-Checker",
"description": "FAIR-Checker is a tool aimed at assessing FAIR principles and empowering data provider to enhance the quality of their digital resources. Data providers and consumers can check how FAIR are web resources. Developers can explore and inspect metadata exposed in web resources.",
"homepage": "https://fair-checker.france-bioinformatique.fr",
"biotoolsID": "fair-checker",
"biotoolsCURIE": "biotools:fair-checker",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3316",
"http://edamontology.org/topic_0089"
],
"primary_publication": [
"10.1186/s13326-023-00289-5"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:45:19.260708Z",
"teams": [
"IFB Core"
],
"source_repository": null
},
{
"id": 4,
"name": "Coffee Genome Hub",
"description": "The Coffee Genome Hub is an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee.",
"homepage": "https://coffee-genome-hub.southgreen.fr/",
"biotoolsID": "Coffee_Genome_Hub",
"biotoolsCURIE": "biotools:Coffee_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub"
],
"scientific_topics": [
"http://edamontology.org/topic_0780",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/nar/gku1108"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Alexis Dereeper",
"email": "alexis.dereeper@ird.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Gaetan Droc",
"email": "droc@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1849-1269",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "http://coffee-genome.org/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:58:58.975865Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 135,
"name": "Askomics",
"description": "AskOmics is a visual SPARQL query interface supporting both intuitive data integration and querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL",
"homepage": "https://github.com/askomics",
"biotoolsID": "askomics",
"biotoolsCURIE": "biotools:askomics",
"tool_type": [
"Desktop application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3366"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Anthony Bretaudeau",
"email": "anthony.bretaudeau@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Olivier Dameron",
"email": "olivier.dameron@irisa.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Olivier Filangi",
"email": "olivier.filangi@inra.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "AGPL-3.0",
"documentation": "https://github.com/askomics/askomics",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2019-11-15T09:29:04Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 238,
"name": "TOXsIgN",
"description": "The TOXicogenomic sIgNature (TOXsIgN) is a cross-species resource that supports online submission, storage, and retrieval of TOXicogenomic sIgNatures. TOXsIgN aims at complementing existing resources by acting as a distribution hub for the community. One of its unique features is its ability to archive heterogeneous data. TOXsIgN thus allows users to upload lists of genes positively (overexpressed for transcriptomic assays) affected and negatively (underexpressed) affected from distinct –omics experiments (e.g., transcriptomics, proteomics, or epigenomics). It also provides users with a working environment containing a powerful search engine as well as bioinformatics/biostatistics modules that enable cross-species and cross-technology signature comparisons or enrichment analyses. TOXsIgN is thus intended to serve as a warehouse for toxicogenomics and predictive toxicology tools simultaneously based on and able to analyze the overall set of signatures deposited by the community.",
"homepage": "http://toxsign.genouest.org",
"biotoolsID": "toxsign",
"biotoolsCURIE": "biotools:toxsign",
"tool_type": [
"Web application",
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2840"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Chalmel Frédéric",
"email": "frederic.chalmel@univ-rennes1.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-09-28T08:55:30Z",
"teams": [],
"source_repository": null
},
{
"id": 138,
"name": "SARTools",
"description": "R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.",
"homepage": "https://github.com/PF2-pasteur-fr/SARTools",
"biotoolsID": "sartools",
"biotoolsCURIE": "biotools:sartools",
"tool_type": [
"Command-line tool"
],
"collection": [
"SARTools"
],
"scientific_topics": [
"http://edamontology.org/topic_2269",
"http://edamontology.org/topic_3308"
],
"primary_publication": [
"10.1371/journal.pone.0157022"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer",
"Primary contact"
],
"name": "Marie-Agnès Dillies",
"email": "marie-agnes.dillies@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/marie-agnes-dillies/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "https://research.pasteur.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Support",
"Primary contact"
],
"name": "Jean-Yves Coppée",
"email": "jean-yves.coppee@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/jean-yves-coppee/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "C3BI",
"email": null,
"url": "https://research.pasteur.fr/en/center/c3bi/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Bioinformatics and Biostatistics Hub",
"email": null,
"url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Developer",
"Primary contact"
],
"name": "Hugo Varet",
"email": "hugo.varet@pasteur.fr",
"url": "https://research.pasteur.fr/fr/member/hugo-varet/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "France Génomique",
"email": null,
"url": "https://www.france-genomique.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
}
],
"tool_licence": "GPL-2.0",
"documentation": "https://github.com/PF2-pasteur-fr/SARTools",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2021-04-17T15:12:05Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://github.com/PF2-pasteur-fr/SARTools"
},
{
"id": 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": 97,
"name": "Ocean Gene Atlas",
"description": "The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs).\nUser queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.",
"homepage": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/",
"biotoolsID": "Ocean_Gene_Atlas",
"biotoolsCURIE": "biotools:Ocean_Gene_Atlas",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0610",
"http://edamontology.org/topic_3387",
"http://edamontology.org/topic_3174",
"http://edamontology.org/topic_3941"
],
"primary_publication": [
"10.1093/nar/gky376"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "oceangeneatlas@mio.osupytheas.fr",
"url": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/credits",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "MIO",
"email": null,
"url": "https://www.mio.osupytheas.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [],
"name": "OCEANOMICS",
"email": null,
"url": "http://www.oceanomics.eu/",
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": "ANR-11-BTBR-0008"
}
],
"tool_licence": "Not licensed",
"documentation": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/build/pdf/Ocean-Gene-Atlas_User_Manual.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:34.208631Z",
"teams": [],
"source_repository": null
},
{
"id": 207,
"name": "Commet",
"description": "This software provides a global similarity overview between all datasets of a large metagenomic project.",
"homepage": "https://colibread.inria.fr/software/commet/",
"biotoolsID": "commet",
"biotoolsCURIE": "biotools:commet",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0080"
],
"primary_publication": [
"10.1109/BIBM.2014.6999135"
],
"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": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/pierrepeterlongo/commet/blob/master/doc/commet_user_guide.pdf",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2018-12-10T12:58:49Z",
"teams": [
"GenOuest"
],
"source_repository": null
},
{
"id": 58,
"name": "Crispi",
"description": "A CRISPR Interactive database.",
"homepage": "http://crispi.genouest.org/",
"biotoolsID": "crispi",
"biotoolsCURIE": "biotools:crispi",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0160"
],
"primary_publication": [
"10.1093/bioinformatics/btp586"
],
"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 platform",
"email": "support@genouest.org",
"url": "http://www.genouest.org",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/help/crispri.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T16:06:25.068541Z",
"teams": [],
"source_repository": null
},
{
"id": 104,
"name": "ANISEED",
"description": "ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). It integrates for each species: \ni) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; \nii) A multispecies genomic browser; \niii) a Genomicus gene synteny browser.",
"homepage": "https://www.aniseed.fr",
"biotoolsID": "ANISEED",
"biotoolsCURIE": "biotools:ANISEED",
"tool_type": [
"Database portal",
"Web API",
"Web application",
"Ontology"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3065",
"http://edamontology.org/topic_3383",
"http://edamontology.org/topic_3679",
"http://edamontology.org/topic_3064",
"http://edamontology.org/topic_0194",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_2229",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_0219",
"http://edamontology.org/topic_0084",
"http://edamontology.org/topic_3308"
],
"primary_publication": [
"10.1093/nar/gkx1108",
"10.1016/j.cub.2005.12.044",
"10.1093/nar/gkz955",
"10.1101/gr.108175.110",
"10.1093/nar/gkv966"
],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "contact@aniseed.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Christelle Dantec",
"email": "christelle.dantec@crbm.cnrs.fr",
"url": "http://www.crbm.cnrs.fr/en/team/lemaire/",
"orcidid": "https://orcid.org/0000-0001-7247-6460",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Support"
],
"name": null,
"email": "contact@aniseed.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Patrick Lemaire",
"email": "patrick.lemaire@crbm.cnrs.fr",
"url": "http://www.crbm.cnrs.fr/en/team/lemaire/",
"orcidid": "https://orcid.org/0000-0003-4925-2009",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "https://www.aniseed.fr/api",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2023-09-25T14:25:18.910230Z",
"teams": [],
"source_repository": null
},
{
"id": 85,
"name": "ARIA",
"description": "A software for automated NOE assignment and NMR structure calculation.",
"homepage": "http://aria.pasteur.fr/",
"biotoolsID": "aria",
"biotoolsCURIE": "biotools:aria",
"tool_type": [
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019",
"Institut Pasteur",
"FR"
],
"scientific_topics": [
"http://edamontology.org/topic_1317",
"http://edamontology.org/topic_0593",
"http://edamontology.org/topic_0176",
"http://edamontology.org/topic_3306",
"http://edamontology.org/topic_3332",
"http://edamontology.org/topic_2275",
"http://edamontology.org/topic_0081",
"http://edamontology.org/topic_0078"
],
"primary_publication": [
"10.1093/bioinformatics/btl589"
],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Michael Nilges",
"email": "michael.nilges@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Benjamin Bardiaux",
"email": "benjamin.bardiaux@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "Institut Pasteur",
"email": null,
"url": "http://aria.pasteur.fr/contact-info",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": "MIT",
"documentation": "http://aria.pasteur.fr/documentation",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:37:34.670261Z",
"teams": [],
"source_repository": null
},
{
"id": 174,
"name": "Linda",
"description": "The web application Linda offers a complete tool for entering and managing metadata associated with a phenotyping experiment on plants. It thus makes it possible to intuitively describe experimental related information such as, for example, the experimental design, the growth protocols, the environmental variable measurements, etc. Linda is coupled with a database that stores this information in a structured manneer using oriented graphs. This database uses reference ontologies (e.g., Plant Ontology, Crop Ontology, etc.) and standards dedicated to this type of experiment such as the Minimal Information About Plant Phenotyping Experiment (MIAPPE) standard. Data sharing is facilitated on the one hand by respecting the FAIR principles (Findable Accessible Interoperable Reusable) and oon the other hand, by exporting this metadata relating to the experiment in tabulated formats or formatted for submission in the international databases (ISA-tab).",
"homepage": "https://services.cbib.u-bordeaux.fr/linda/",
"biotoolsID": "xeml-lab",
"biotoolsCURIE": "biotools:xeml-lab",
"tool_type": [
"Desktop application",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3053",
"http://edamontology.org/topic_3292",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_0219",
"http://edamontology.org/topic_0089"
],
"primary_publication": [
"10.1111/j.1365-3040.2009.01964.x"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Contributor"
],
"name": "CHen Zhui",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Emmanuel Bouilhol",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Yves Gibon",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Cecile Cabasson",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "Université de Bordeaux (CGFB)",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Consortium",
"note": null
},
{
"type_role": [
"Support"
],
"name": "Benjamin Dartigues",
"email": "benjamin.dartigues@u-bordeaux.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Benjamin Dartigues",
"email": "benjamin.dartigues@u-bordeaux.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer",
"Primary contact"
],
"name": "Benjamin Dartigues",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Yves Gibon",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Cecile Cabasson",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "UMR 1332 - Biologie du Fruit et Pathologie",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer",
"Contributor"
],
"name": "Alexis Groppi",
"email": null,
"url": null,
"orcidid": null,
"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": [
"Developer",
"Contributor"
],
"name": "Macha Nikolski",
"email": null,
"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": "MIT",
"documentation": "https://services.cbib.u-bordeaux.fr/linda",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2022-09-27T14:48:43.394660Z",
"teams": [
"CBiB"
],
"source_repository": "https://services.cbib.u-bordeaux.fr/linda/"
},
{
"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": 56,
"name": "CyanoLyase",
"description": "Manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases.",
"homepage": "http://cyanolyase.genouest.org/",
"biotoolsID": "cyanolyase",
"biotoolsCURIE": "biotools:cyanolyase",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0623"
],
"primary_publication": [
"10.1093/nar/gks1091"
],
"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": null,
"documentation": "http://cyanolyase.genouest.org/help",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T16:06:21.263559Z",
"teams": [],
"source_repository": null
},
{
"id": 190,
"name": "CRISPRFinder",
"description": "Detects this family of direct repeats found in the DNA of many bacteria and archaea.",
"homepage": "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index",
"biotoolsID": "crisprfinder",
"biotoolsCURIE": "biotools:crisprfinder",
"tool_type": [
"Web application",
"Database portal"
],
"collection": [
"CRISPR"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0157",
"http://edamontology.org/topic_2885",
"http://edamontology.org/topic_0203"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Marie Touchon",
"email": "mtouchon@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Unlicense",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 480,
"citations": null,
"annual_visits": 2273,
"last_update": "2024-11-24T21:05:00.924973Z",
"teams": [
"EBIO"
],
"source_repository": null
},
{
"id": 125,
"name": "Gigwa",
"description": "The Gigwa application, which stands for “Genotype Investigator for Genome-Wide Analyses”, provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time. Gigwa provides the means to export filtered data into several popular formats and features connectivity not only with online genomic tools, but also with standalone software such as FlapJack or IGV. Additionnally, Gigwa-hosted datasets are interoperable via two standard REST APIs: GA4GH and BrAPI.",
"homepage": "http://www.southgreen.fr/content/gigwa",
"biotoolsID": "Gigwa",
"biotoolsCURIE": "biotools:Gigwa",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0625",
"http://edamontology.org/topic_2885",
"http://edamontology.org/topic_3071"
],
"primary_publication": [
"10.1093/GIGASCIENCE/GIZ051",
"10.1186/s13742-016-0131-8"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Guilhem Sempéré",
"email": "guilhem.sempere@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-7429-2091",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "gigwa@cirad.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "AGPL-3.0",
"documentation": "http://gigwa.southgreen.fr/gigwa/docs/gigwa_docs.html",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2020-09-14T08:25:17Z",
"teams": [
"South Green"
],
"source_repository": "https://github.com/SouthGreenPlatform/Gigwa2"
},
{
"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": [
"Provider"
],
"name": "GenOuest",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Olivier Sallou",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"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
}
]
}