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=140&ordering=primary_publication",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=100&ordering=primary_publication",
"results": [
{
"id": 283,
"name": "3SRP",
"description": "A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis. This 3’ Digital gene expression sequencing technique allows a precise and low-cost transcriptome profiling.\n\nThe main steps of the pipeline are:\n- Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample.\n- Alignment on refseq reference transcriptome is performed using bwa.\n- Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix.\nIf secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2.\n- If DEG are found, annotation is performed using the database GO and KEGG.\n- A report is provided listing the main quality controls performed and the results found.\n\nCite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1",
"homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline",
"biotoolsID": "3SRP",
"biotoolsCURIE": "biotools:3SRP",
"tool_type": [
"Workflow"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3308"
],
"primary_publication": [
"10.1038/s41598-017-14892-x"
],
"operating_system": [
"Linux"
],
"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": [
"Primary contact",
"Developer",
"Support"
],
"name": "Eric Charpentier",
"email": "eric.charpentier@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/about-us/members/",
"orcidid": "https://orcid.org/0000-0002-8571-7603",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Dimitri MEISTERMANN",
"email": "dimitri.meistermann@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Broad Institute",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": "Some scripts of the pipeline regarding sample demultiplexing and UMI counting have been adapated and modified from this paper:\nXiong, Y., Soumillon, M., Wu, J. et al. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries. Sci Rep 7, 14626 (2017)."
},
{
"type_role": [
"Developer"
],
"name": "Philippe Bordron",
"email": "philippe.bordron@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"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": [
"Primary contact",
"Contributor"
],
"name": "Audrey Bihouée",
"email": "audrey.bihouee@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0002-8689-2083",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/wikis/home",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T14:40:06.421826Z",
"teams": [
"BiRD"
],
"source_repository": null
},
{
"id": 286,
"name": "pyBRAvo",
"description": "From a list of genes, pyBRAvo produces upstream regulation or signaling networks. pyBRAvo internally leverages the BioPAX ontolgy, the PathwayCommons knowledge graph, and the SPARQL semantic web query language. pyBRAvo can be used through either a Jupyter notebook, or a command line interface.",
"homepage": "https://github.com/pyBRAvo/pyBRAvo",
"biotoolsID": "pybravo",
"biotoolsCURIE": "biotools:pybravo",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_2259"
],
"primary_publication": [
"10.1093/database/baaa113"
],
"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": [
"Primary contact",
"Developer"
],
"name": "Alban Gaignard",
"email": "alban.gaignard@univ-nantes.fr",
"url": "http://albangaignard.github.io/",
"orcidid": "https://orcid.org/0000-0002-3597-8557",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Marie Lefebvre",
"email": "marie.lefebvre@inrae.fr",
"url": "https://mariebvr.github.io/marieBvr/",
"orcidid": "https://orcid.org/0000-0002-3093-5873",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Maxime Folschette",
"email": "maxime.folschette@centralelille.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Jeremy Bourdon",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-6674-8626",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Carito Guziolowski",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-5192-0745",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "SyMeTRIC",
"email": null,
"url": "http://symetric.univ-nantes.fr/doku.php",
"orcidid": null,
"gridid": null,
"typeEntity": "Project",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/pyBRAvo/pyBRAvo",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2022-05-31T14:22:33.309326Z",
"teams": [
"BiRD"
],
"source_repository": "https://github.com/pyBRAvo/pyBRAvo"
},
{
"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"
},
{
"id": 3,
"name": "Rice Genome Hub",
"description": "An open source database(s) for genetics, genomics and functional research in rice species",
"homepage": "https://rice-genome-hub.southgreen.fr/",
"biotoolsID": "Rice_Genome_Hub",
"biotoolsCURIE": "biotools:Rice_Genome_Hub",
"tool_type": [
"Database portal"
],
"collection": [
"Genome Hub",
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3321",
"http://edamontology.org/topic_3366",
"http://edamontology.org/topic_0780"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"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": null,
"email": "manuel.ruiz@cirad.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-8153-276X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "christine.tranchant@ird.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-6934-1215",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "CRP Rice",
"email": null,
"url": "http://ricecrp.org/",
"orcidid": null,
"gridid": null,
"typeEntity": "Funding agency",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:27Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 61,
"name": "MousePat",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"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": null,
"teams": [],
"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": 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": 121,
"name": "LoRDEC",
"description": "Program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.",
"homepage": "http://www.atgc-montpellier.fr/lordec/",
"biotoolsID": "lordec",
"biotoolsCURIE": "biotools:lordec",
"tool_type": [
"Command-line tool"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0654",
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_3071",
"http://edamontology.org/topic_0091"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Eric Rivals",
"email": "rivals@lirmm.fr",
"url": "http://www.lirmm.fr/~rivals/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Leena Salmela",
"email": "leena.salmela@cs.Helsinki.FI",
"url": "https://www.cs.helsinki.fi/u/lmsalmel/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "LIRMM",
"email": null,
"url": "http://www.lirmm.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/lordec/",
"maturity": "Mature",
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:01:03.046535Z",
"teams": [
"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": 154,
"name": "CompPhy",
"description": "Web-based collaborative platform for comparing phylogenies.",
"homepage": "http://www.atgc-montpellier.fr/compphy/",
"biotoolsID": "compphy",
"biotoolsCURIE": "biotools:compphy",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_3056"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact form",
"email": null,
"url": "http://www.atgc-montpellier.fr/compphy/?p=contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/compphy/?p=userguide",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:57Z",
"teams": [
"ATGC"
],
"source_repository": null
},
{
"id": 35,
"name": "OryGenesDB",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"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": null,
"teams": [],
"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": 188,
"name": "SyntTax",
"description": "A web server linking synteny to prokaryotic taxonomy.",
"homepage": "http://archaea.u-psud.fr/SyntTax/",
"biotoolsID": "synttax",
"biotoolsCURIE": "biotools:synttax",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0637",
"http://edamontology.org/topic_0204",
"http://edamontology.org/topic_3053"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Jacques Oberto",
"email": "jacques.oberto@igmors.u-psud.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://archaea.u-psud.fr/SyntTax/SyntTax_Help.html",
"maturity": null,
"cost": null,
"unique_visits": 1707,
"citations": null,
"annual_visits": 3829,
"last_update": "2018-12-10T12:58:58Z",
"teams": [
"EBIO"
],
"source_repository": null
},
{
"id": 63,
"name": "BAliBASE",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"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": null,
"teams": [],
"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": 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": 118,
"name": "SouthGreen_Galaxy Not found.",
"description": "A Galaxy instance focused on agriculture, food, biodiversity and environment, from the Agropolis campus in France.",
"homepage": "http://galaxy.southgreen.fr/galaxy",
"biotoolsID": "SouthGreen_Galaxy",
"biotoolsCURIE": "biotools:SouthGreen_Galaxy",
"tool_type": [
"Workbench"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_3810"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": "https://southgreen.fr/content/galaxy-tool",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-01-24T09:53:10Z",
"teams": [],
"source_repository": null
},
{
"id": 272,
"name": "IMGT-ONTOLOGY",
"description": "IMGT-ONTOLOGY is the first ontology for immunogenetics and immunoinformatics. It provides a semantic specification of the terms to be used in immunogenetics and immunoinformatics and manages the related knowledge, thus allowing the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. IMGT-ONTOLOGY manages the knowledge through diverse facets relying on seven axioms, \"IDENTIFICATION\", \"CLASSIFICATION\", \"DESCRIPTION\", \"NUMEROTATION\", \"LOCALIZATION\", \"ORIENTATION\" and \"OBTENTION\". These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized.",
"homepage": "http://www.imgt.org/IMGTindex/ontology.php",
"biotoolsID": "IMGT-ONTOLOGY",
"biotoolsCURIE": "biotools:IMGT-ONTOLOGY",
"tool_type": [
"Ontology"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3930",
"http://edamontology.org/topic_3948"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "Patrice Duroux",
"email": "patrice.duroux@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Sofia Kossida",
"email": "sofia.kossida@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Véronique Giudicelli",
"email": "veronique.giudicelli@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Marie-Paule Lefranc",
"email": "marie-paule.lefranc@igh.cnrs.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://www.imgt.org/IMGTindex/ontology.php",
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:20.932052Z",
"teams": [
"IMGT"
],
"source_repository": "http://bioportal.bioontology.org/ontologies/IMGT-ONTOLOGY"
},
{
"id": 240,
"name": "SMS",
"description": "Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection.",
"homepage": "http://www.atgc-montpellier.fr/sms/",
"biotoolsID": "PhyMLSMS",
"biotoolsCURIE": "biotools:PhyMLSMS",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [
"PhyML"
],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091",
"http://edamontology.org/topic_2269"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [],
"tool_licence": null,
"documentation": "http://www.atgc-montpellier.fr/download/papers/sms-HowItWorks.pdf",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:18.380055Z",
"teams": [],
"source_repository": null
},
{
"id": 7,
"name": "PhROGs",
"description": "",
"homepage": null,
"biotoolsID": "",
"biotoolsCURIE": "",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [],
"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": null,
"teams": [],
"source_repository": null
}
]
}