HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"count": 211,
"next": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=100&ordering=homepage",
"previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&offset=60&ordering=homepage",
"results": [
{
"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": 124,
"name": "TOGGLE",
"description": "Toolbox for generic NGS analyses.",
"homepage": "https://github.com/SouthGreenPlatform/TOGGLE",
"biotoolsID": "toggle",
"biotoolsCURIE": "biotools:toggle",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_0080"
],
"primary_publication": [],
"operating_system": [
"Linux"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Support",
"email": "toggle@ird.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://github.com/SouthGreenPlatform/TOGGLE",
"maturity": null,
"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:58Z",
"teams": [
"South Green"
],
"source_repository": null
},
{
"id": 255,
"name": "Kmerator",
"description": "Kmerator is a prototype tool designed for the prediction of specific k-mers (also called tags) from input sequences, considering a reference genome and an ENSEMBL-like transcriptome. From these specific k-mers, it also outputs their corresponding specific contigs which are sequences of consecutive k-mers (overlapping length between k-mers must be k-1, otherwise, it's a new contig). Kmerator first uses Jellyfish to create 2 requestable indexes from the reference genome and transcriptome, and second, decomposes your input transcript or gene sequences to count the occurences of each k-mer in the genome and transcriptome.",
"homepage": "https://github.com/Transipedia/kmerator",
"biotoolsID": "kmerator",
"biotoolsCURIE": "biotools:kmerator",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_0203",
"http://edamontology.org/topic_3512",
"http://edamontology.org/topic_0659",
"http://edamontology.org/topic_3360"
],
"primary_publication": [
"10.1093/nargab/lqab058"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Thérèse Commes",
"email": "therese.commes@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T16:01:46.602609Z",
"teams": [
"Bio2M"
],
"source_repository": null
},
{
"id": 122,
"name": "microSysMics",
"description": "This workflow provides an automated microbiome data analysis, starting with sequenced taxonomic markers (such as 16SrRNA) and using the standard QIIME2 toolbox to produce an abundance table and preliminary diversity, phylogeny and taxonomy analysis.",
"homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/microSysMics",
"biotoolsID": "microSysMics",
"biotoolsCURIE": "biotools:microSysMics",
"tool_type": [
"Workflow"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3697"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "BiRD bioinformatics facility",
"email": "pf-bird@univ-nantes.fr",
"url": "http://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "LS2N",
"email": null,
"url": "http://www.ls2n.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Erwan Delage",
"email": "erwan.delage@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"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
},
{
"type_role": [
"Provider"
],
"name": "TENS",
"email": null,
"url": "https://www.inserm-tens.com/",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Maintainer",
"Contributor"
],
"name": "Damien Vintache",
"email": "Damien.Vintache@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Samuel Chaffron",
"email": "samuel.chaffron@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-5903-617X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Michel Neunlist",
"email": "michel.neunlist@univ-nantes.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1892-5071",
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Provider"
],
"name": "BiRD",
"email": "pf-bird@univ-nantes.fr",
"url": "http://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
}
],
"tool_licence": "Other",
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2023-09-19T15:06:56.878425Z",
"teams": [
"BiRD"
],
"source_repository": null
},
{
"id": 123,
"name": "DEPIB",
"description": "Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes.",
"homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipeline",
"biotoolsID": "DEPIB",
"biotoolsCURIE": "biotools:DEPIB",
"tool_type": [
"Workflow"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3308"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Provider"
],
"name": "BiRD bioinformatics facility",
"email": "pf-bird@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Audrey Bihouée",
"email": "audrey.bihouee@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
"orcidid": "https://orcid.org/0000-0002-8689-2083",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Provider"
],
"name": "BiRD",
"email": "pf-bird@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Division",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Erwan Delage",
"email": "erwan.delage@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"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",
"Support",
"Developer"
],
"name": "Eric Charpentier",
"email": "eric.charpentier@univ-nantes.fr",
"url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Maintainer",
"Contributor"
],
"name": "Damien Vintache",
"email": "Damien.Vintache@univ-nantes.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2024-11-24T14:40:03.286943Z",
"teams": [
"BiRD"
],
"source_repository": null
},
{
"id": 137,
"name": "SHAMAN",
"description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].",
"homepage": "http://shaman.c3bi.pasteur.fr/",
"biotoolsID": "shaman",
"biotoolsCURIE": "biotools:shaman",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3174"
],
"primary_publication": [
"10.1073/pnas.1523899113"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer"
],
"name": "Pierre Lechat",
"email": null,
"url": "https://research.pasteur.fr/en/member/pierre-lechat/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Amine Ghozlane",
"email": null,
"url": "https://research.pasteur.fr/en/member/amine-ghozlane/",
"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": [],
"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": [
"Primary contact"
],
"name": "SHAMAN team",
"email": "shaman@pasteur.fr",
"url": "https://research.pasteur.fr/en/software/shaman-shiny-application-for-metagenomic-analysis/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Stevenn Volant",
"email": null,
"url": "https://research.pasteur.fr/en/member/stevenn-volant/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Hugo Varet",
"email": null,
"url": "https://research.pasteur.fr/en/member/hugo-varet/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "GPL-3.0",
"documentation": "http://shaman.c3bi.pasteur.fr/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 742,
"citations": null,
"annual_visits": 1855,
"last_update": "2025-10-23T10:46:59.953305Z",
"teams": [
"Pasteur HUB"
],
"source_repository": "https://github.com/aghozlane/shaman"
},
{
"id": 241,
"name": "iPPI-DB",
"description": "IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large variety of data is stored within IPPI-DB: structural, pharmacological, binding and activity profile, pharmacokinetic and cytotoxicity when available, as well as some data about the PPI targets themselves.",
"homepage": "https://ippidb.pasteur.fr",
"biotoolsID": "ippi-db",
"biotoolsCURIE": "biotools:ippi-db",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3343"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [],
"name": "Olivier Sperandio",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-6610-2729",
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": null,
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2021-01-14T17:37:37Z",
"teams": [],
"source_repository": "https://gitlab.pasteur.fr/ippidb/ippidb-web/"
},
{
"id": 93,
"name": "MicroScope platform",
"description": "MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.",
"homepage": "https://mage.genoscope.cns.fr/microscope/",
"biotoolsID": "MicroScope_platform",
"biotoolsCURIE": "biotools:MicroScope_platform",
"tool_type": [
"Bioinformatics portal",
"Web application",
"Workbench"
],
"collection": [
"elixir-fr-sdp-2019",
"fr"
],
"scientific_topics": [
"http://edamontology.org/topic_3301",
"http://edamontology.org/topic_0085",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_2259",
"http://edamontology.org/topic_0219"
],
"primary_publication": [
"10.1093/nar/gks1194",
"10.1093/database/bap021",
"10.1093/nar/gkj406",
"10.1093/nar/gkw1101",
"10.1093/bib/bbx113",
"10.1093/nar/gkz926"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact",
"Support",
"Developer",
"Provider"
],
"name": "LABGeM - CEA/Genosocope - UMR8030",
"email": "labgem@genoscope.cns.fr",
"url": "https://labgem.genoscope.cns.fr",
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
}
],
"tool_licence": null,
"documentation": "https://microscope.readthedocs.io/en/stable/",
"maturity": "Mature",
"cost": "Free of charge (with restrictions)",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2020-06-16T10:55:28Z",
"teams": [
"MicroScope"
],
"source_repository": null
},
{
"id": 158,
"name": "Fpocket",
"description": "Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::fpocket",
"biotoolsID": "fpocket",
"biotoolsCURIE": "biotools:fpocket",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0166"
],
"primary_publication": [
"10.1186/1471-2105-10-168"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Pierre Tufféry",
"email": "pierre.tuffery@univ-paris-diderot.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1033-9895",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/fpocket/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 960,
"citations": null,
"annual_visits": 2470,
"last_update": "2024-11-24T20:59:53.208420Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 160,
"name": "Frog",
"description": "Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2",
"biotoolsID": "frog2",
"biotoolsCURIE": "biotools:frog2",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0154",
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gkq325"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Frederic Guyon",
"email": "frederic.guyon@univ-paris-diderot.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Maria A. Miteva",
"email": "maria.mitev@inserm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Pierre Tufféry",
"email": "pierre.tuffery@univ-paris-diderot.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1033-9895",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/Frog2/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 960,
"citations": null,
"annual_visits": 6400,
"last_update": "2024-11-25T14:00:39.981509Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 164,
"name": "InterEvDock",
"description": "Ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock2",
"biotoolsID": "interevdock2",
"biotoolsCURIE": "biotools:interevdock2",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275",
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_0080"
],
"primary_publication": [
"10.1093/nar/gky377",
"10.1093/nar/gkw340"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Raphael Guerois",
"email": "raphael.guerois@cea.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0001-5294-2858",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Jessica Andreani",
"email": "jessica.andreani@cea.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 310,
"citations": null,
"annual_visits": 1120,
"last_update": "2024-11-24T21:00:12.284563Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 163,
"name": "PEP-FOLD",
"description": "PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3",
"biotoolsID": "pep-fold",
"biotoolsCURIE": "biotools:pep-fold",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gkp323",
"10.1093/nar/gks419",
"10.1093/nar/gkw329"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Pierre Tufféry",
"email": "pierre.tuffery@univ-paris-diderot.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1033-9895",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 3900,
"citations": null,
"annual_visits": 30000,
"last_update": "2024-11-24T20:59:57.942237Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 161,
"name": "PEP-SiteFinder",
"description": "PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder",
"biotoolsID": "pep-sitefinder",
"biotoolsCURIE": "biotools:pep-sitefinder",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3534",
"http://edamontology.org/topic_2275"
],
"primary_publication": [
"10.1093/nar/gku404"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Pierre Tufféry",
"email": "pierre.tuffery@univ-paris-diderot.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1033-9895",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-SiteFinder",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 347,
"citations": null,
"annual_visits": 1482,
"last_update": "2024-11-24T20:59:55.640056Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 159,
"name": "SABBAC",
"description": "Tool for the reconstruction of complete protein structures from their alpha-carbon descriptions.",
"homepage": "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC",
"biotoolsID": "sabbac",
"biotoolsCURIE": "biotools:sabbac",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2275"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Pierre Tufféry",
"email": "pierre.tuffery@univ-paris-diderot.fr",
"url": null,
"orcidid": "https://orcid.org/0000-0003-1033-9895",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": "Freeware",
"documentation": "https://bioserv.rpbs.univ-paris-diderot.fr/services/SABBAC/",
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": 130,
"citations": null,
"annual_visits": 640,
"last_update": "2024-11-24T21:00:10.511557Z",
"teams": [
"RPBS"
],
"source_repository": null
},
{
"id": 171,
"name": "RNAbrowse",
"description": "The tool permits sequencing facilities and, even small, bioinformatic teams to give a user-friendly access to RNA-Seq de novo results, helping biologists to analyse and extract meaningful information from their data.",
"homepage": "https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/ngspipelines/index.php/RNA-seq_denovo",
"biotoolsID": "rnabrowse",
"biotoolsCURIE": "biotools:rnabrowse",
"tool_type": [
"Command-line tool",
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0099",
"http://edamontology.org/topic_3170",
"http://edamontology.org/topic_3168",
"http://edamontology.org/topic_0219"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": null,
"url": "https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/ngspipelines/index.php/RNA-seq_denovo",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/ngspipelines/index.php/RNA-seq_denovo",
"maturity": null,
"cost": null,
"unique_visits": 2250,
"citations": null,
"annual_visits": 4720,
"last_update": "2018-12-10T12:58:51Z",
"teams": [],
"source_repository": null
},
{
"id": 187,
"name": "Nebula",
"description": "Web service powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data.",
"homepage": "https://nebula.curie.fr/",
"biotoolsID": "nebula",
"biotoolsCURIE": "biotools:nebula",
"tool_type": [
"Web application"
],
"collection": [
"Nebula"
],
"scientific_topics": [
"http://edamontology.org/topic_3365",
"http://edamontology.org/topic_3169",
"http://edamontology.org/topic_3125"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": null,
"email": "galaxy.contact@curie.fr",
"url": "http://bioinfo-out.curie.fr/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "http://nebula.curie.fr/static/nebula_tutorial.pdf",
"maturity": null,
"cost": null,
"unique_visits": 7384,
"citations": null,
"annual_visits": 2815653,
"last_update": "2024-11-25T14:22:06.393280Z",
"teams": [
"Curie Bioinfo"
],
"source_repository": null
},
{
"id": 244,
"name": "NGphylogeny.fr",
"description": "Free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.",
"homepage": "https://ngphylogeny.fr/",
"biotoolsID": "NGphylogeny.fr",
"biotoolsCURIE": "biotools:NGphylogeny.fr",
"tool_type": [
"Web application",
"Workflow",
"Bioinformatics portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_3293",
"http://edamontology.org/topic_0091"
],
"primary_publication": [
"10.1093/nar/gkz303"
],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Developer",
"Maintainer",
"Primary contact"
],
"name": "Frédéric Lemoine",
"email": "frederic.lemoine@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Damien Correia",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Contributor"
],
"name": "Fabien Mareuil",
"email": "fmareuil@pasteur.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact",
"Contributor"
],
"name": "Vincent Lefort",
"email": "vincent.lefort@lirmm.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
"documentation": "https://ngphylogeny.fr/documentation",
"maturity": "Emerging",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-24T20:59:31.390401Z",
"teams": [],
"source_repository": null
},
{
"id": 113,
"name": "ParameciumDB",
"description": "Online community database for Paramecium species. Contains annotation of genome sequences and features, genome-wide data sets, advanced capabilities to query, retrieve, visualize and compare data.",
"homepage": "https://paramecium.i2bc.paris-saclay.fr",
"biotoolsID": "parameciumdb",
"biotoolsCURIE": "biotools:parameciumdb",
"tool_type": [
"Database portal"
],
"collection": [
"elixir-fr-sdp-2019"
],
"scientific_topics": [
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0089",
"http://edamontology.org/topic_0080",
"http://edamontology.org/topic_0160",
"http://edamontology.org/topic_3321"
],
"primary_publication": [],
"operating_system": [
"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Contact Form",
"email": null,
"url": "https://paramecium.i2bc.paris-saclay.fr/cgi/user/contact",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [],
"name": "Terms of Use",
"email": null,
"url": "https://paramecium.i2bc.paris-saclay.fr/parawiki/Terms_of_Use",
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
}
],
"tool_licence": "CC-BY-4.0",
"documentation": null,
"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2024-11-25T14:00:30.463079Z",
"teams": [],
"source_repository": null
},
{
"id": 39,
"name": "SPROUTS",
"description": "SPROUTS has two general functions.\nThe first is to provide existing mutation data given a protein specified by a PDB ID. This is Query mode.\nThe second is to generate new mutation data based on a new PDB ID or a user input. This is Submit mode.",
"homepage": "http://sprouts.rpbs.univ-paris-diderot.fr/",
"biotoolsID": "SPROUTS",
"biotoolsCURIE": "biotools:SPROUTS",
"tool_type": [
"Database portal"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0199"
],
"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": "2022-11-30T13:37:17.543436Z",
"teams": [],
"source_repository": null
},
{
"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": "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
},
{
"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
}
],
"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
}
]
}