GET /api/tool/?format=api&offset=20&ordering=teams
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=40&ordering=teams",
    "previous": "https://catalogue.france-bioinformatique.fr/api/tool/?format=api&limit=20&ordering=teams",
    "results": [
        {
            "id": 83,
            "name": "Phylogeny.fr",
            "description": "Free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.",
            "homepage": "http://www.phylogeny.fr/",
            "biotoolsID": "phylogeny.fr",
            "biotoolsCURIE": "biotools:phylogeny.fr",
            "tool_type": [
                "Web application",
                "Workbench"
            ],
            "collection": [
                "elixir-fr-sdp-2019"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3293"
            ],
            "primary_publication": [
                "10.1093/nar/gkn180"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "IGS",
                    "email": null,
                    "url": "http://www.igs.cnrs-mrs.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Alexis Dereeper",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Valentin Guignon",
                    "email": null,
                    "url": null,
                    "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
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": null,
                    "email": null,
                    "url": "http://www.phylogeny.fr/contacts.cgi",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "http://www.phylogeny.fr/documentation.cgi",
            "maturity": "Legacy",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:33:44.667229Z",
            "teams": [
                "ATGC",
                "PACA-Bioinfo"
            ],
            "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": 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": "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": [
                        "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": [
                        "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": 166,
            "name": "CRAC",
            "description": "CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.",
            "homepage": "http://crac.gforge.inria.fr",
            "biotoolsID": "crac",
            "biotoolsCURIE": "biotools:crac",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3320",
                "http://edamontology.org/topic_0114",
                "http://edamontology.org/topic_3170"
            ],
            "primary_publication": [
                "10.1186/gb-2013-14-3-r30"
            ],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "For question regarding the software",
                    "email": "crac-bugs@lists.gforge.inria.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "For questions, comments, remarks on the algorithm or the article",
                    "email": "crac-article@lists.gforge.inria.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "CECILL-2.0",
            "documentation": "http://crac.gforge.inria.fr/documentation/",
            "maturity": "Mature",
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2018-12-10T12:58:59Z",
            "teams": [
                "Bilille",
                "ATGC"
            ],
            "source_repository": null
        },
        {
            "id": 168,
            "name": "FastME",
            "description": "Distance algorithms to infer phylogenies. It's based on balanced minimum evolution, which is the very principle of NJ. It includes Nearest Neighbor Interchange (NNI) and also Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations.",
            "homepage": "http://www.atgc-montpellier.fr/fastme/",
            "biotoolsID": "fastme",
            "biotoolsCURIE": "biotools:fastme",
            "tool_type": [
                "Command-line tool",
                "Web application"
            ],
            "collection": [
                "galaxyPasteur",
                "FastME"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3293",
                "http://edamontology.org/topic_0091"
            ],
            "primary_publication": [
                "10.1093/molbev/msv150"
            ],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "LIRMM",
                    "email": null,
                    "url": "http://www.lirmm.fr/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact",
                        "Contributor"
                    ],
                    "name": "Vincent Lefort",
                    "email": "vincent.lefort@lirmm.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "GPL-3.0",
            "documentation": "http://www.atgc-montpellier.fr/fastme/usersguide.php",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 300,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-24T20:59:19.988087Z",
            "teams": [
                "ATGC"
            ],
            "source_repository": null
        },
        {
            "id": 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": 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_0080",
                "http://edamontology.org/topic_3320",
                "http://edamontology.org/topic_0160",
                "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": 185,
            "name": "GPCRautomodel",
            "description": "Allows the user to upload a GPCR sequence, choose a ligand in a library and obtain the 3D structure of the free receptor and ligand-receptor complex.",
            "homepage": "http://genome.jouy.inra.fr/GPCRautomodel",
            "biotoolsID": "gpcrautomodel",
            "biotoolsCURIE": "biotools:gpcrautomodel",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0078",
                "http://edamontology.org/topic_0082",
                "http://edamontology.org/topic_0128"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Jean-François Gibrat",
                    "email": "jean-francois.gibrat@jouy.inra.fr",
                    "url": "http://genome.jouy.inra.fr/GPCRautomdl/cgi-bin/welcome.pl",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": null,
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-25T16:14:23.225464Z",
            "teams": [
                "MIGALE"
            ],
            "source_repository": null
        },
        {
            "id": 184,
            "name": "VAST",
            "description": "Tool for viewing protein structure neighbours.",
            "homepage": "http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml",
            "biotoolsID": "vast",
            "biotoolsCURIE": "biotools:vast",
            "tool_type": [
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_2814",
                "http://edamontology.org/topic_0078",
                "http://edamontology.org/topic_0082",
                "http://edamontology.org/topic_0736"
            ],
            "primary_publication": [],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Stephen HBryant",
                    "email": "bryant@ncbi.nlm.nih.gov",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://www.ncbi.nlm.nih.gov/Structure/VAST/vasthelp.html",
            "maturity": null,
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2021-04-25T13:21:04Z",
            "teams": [
                "MIGALE"
            ],
            "source_repository": null
        },
        {
            "id": 192,
            "name": "EDAM-Browser",
            "description": "The EDAM Browser is a client-side web-based visualization javascript widget of the EDAM ontology. \nThe EDAM Browser provides users a simple and performant interface to explore EDAM when annotating or searching for bioinformatics resources.\nIts goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.",
            "homepage": "https://github.com/IFB-ElixirFr/edam-browser",
            "biotoolsID": "edam-browser",
            "biotoolsCURIE": "biotools:edam-browser",
            "tool_type": [
                "Plug-in",
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0605",
                "http://edamontology.org/topic_0092"
            ],
            "primary_publication": [
                "10.21105/joss.00698"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Bryan Brancotte",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-8669-5525",
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [
                        "Maintainer"
                    ],
                    "name": "Hervé Ménager",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-7552-1009",
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [
                        "Contributor"
                    ],
                    "name": "Christophe Blanchet",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Hager Eldakroury",
                    "email": null,
                    "url": "https://github.com/HagerDakroury",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                }
            ],
            "tool_licence": "MIT",
            "documentation": null,
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2022-01-03T15:45:09.883379Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": "https://github.com/IFB-ElixirFr/edam-browser"
        },
        {
            "id": 145,
            "name": "MacSyFinder",
            "description": "Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.",
            "homepage": "https://github.com/gem-pasteur/macsyfinder",
            "biotoolsID": "macsyfinder",
            "biotoolsCURIE": "biotools:macsyfinder",
            "tool_type": [
                "Web application",
                "Command-line tool"
            ],
            "collection": [
                "GEM Pasteur"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0085"
            ],
            "primary_publication": [
                "10.1371/journal.pone.0110726",
                "10.24072/pcjournal.250"
            ],
            "operating_system": [
                "Linux",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Eduardo Rocha",
                    "email": "eduardo.rocha@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Bioinformatics and Biostatistics HUB",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Microbial Evolutionary Genomics Unit",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": "CNRS - UMR 352"
                },
                {
                    "type_role": [
                        "Developer"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": "https://research.pasteur.fr/en/member/bertrand-neron/",
                    "orcidid": "https://orcid.org/0000-0002-0220-0482",
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "Eduardo Rocha",
                    "email": "eduardo.rocha@pasteur.fr",
                    "url": "https://research.pasteur.fr/fr/member/eduardo-rocha/",
                    "orcidid": "https://orcid.org/0000-0001-7704-822X",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Bertrand Néron",
                    "email": "bneron@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "Sophie Abby",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-5231-3346",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Institut Pasteur",
                    "email": null,
                    "url": "https://research.pasteur.fr",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [],
                    "name": "C3BI",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/center/c3bi/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "note": null
                }
            ],
            "tool_licence": "GPL-3.0",
            "documentation": "https://macsyfinder.readthedocs.io/en/latest/",
            "maturity": "Mature",
            "cost": null,
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2024-11-24T13:49:36.708539Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": "https://github.com/gem-pasteur/macsyfinder"
        },
        {
            "id": 146,
            "name": "fqtools",
            "description": "A package that provides tools for efficient FASTQ files manipulation.",
            "homepage": "https://bioweb.pasteur.fr/packages/pack@fqtools@1.1",
            "biotoolsID": "fqtools",
            "biotoolsCURIE": "biotools:fqtools",
            "tool_type": [
                "Suite"
            ],
            "collection": [
                "fqtools"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0080"
            ],
            "primary_publication": [],
            "operating_system": [],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact",
                        "Maintainer"
                    ],
                    "name": "Nicolas Joly",
                    "email": "njoly@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": "Unlicense",
            "documentation": null,
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 0,
            "citations": null,
            "annual_visits": 0,
            "last_update": "2020-06-16T10:55:24Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README"
        },
        {
            "id": 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": [
                        "Primary contact",
                        "Developer"
                    ],
                    "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": [
                        "Primary contact",
                        "Support"
                    ],
                    "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": [
                        "Primary contact",
                        "Developer"
                    ],
                    "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": 130,
            "name": "MEMHDX",
            "description": "This tool allows users to perform an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure.",
            "homepage": "http://memhdx.c3bi.pasteur.fr/",
            "biotoolsID": "memhdx",
            "biotoolsCURIE": "biotools:memhdx",
            "tool_type": [
                "Web application"
            ],
            "collection": [
                "Proteomics"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3520"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btw420"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact",
                        "Developer"
                    ],
                    "name": "Véronique Hourdel",
                    "email": "vhourdel@pasteur.fr",
                    "url": "https://research.pasteur.fr/en/member/veronique-hourdel/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact",
                        "Support"
                    ],
                    "name": "Marie-Agnès Dillies",
                    "email": "marie-agnes.dillies@pasteur.fr",
                    "url": "https://research.pasteur.fr/en/member/marie-agnes-dillies/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact",
                        "Support"
                    ],
                    "name": "Sébastien Brier",
                    "email": "sbrier@pasteur.fr",
                    "url": "https://research.pasteur.fr/en/member/sebastien-brier/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact",
                        "Maintainer"
                    ],
                    "name": "Stevenn Volant",
                    "email": "svolant@pasteur.fr",
                    "url": "https://research.pasteur.fr/en/member/stevenn-volant/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Provider"
                    ],
                    "name": "Structural Mass Spectrometry and Proteomics",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/team/structural-mass-spectrometry-and-proteomics/",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Division",
                    "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
                }
            ],
            "tool_licence": null,
            "documentation": "https://www.youtube.com/watch?v=WeCt1sVyHio&feature=youtu.be",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": 833,
            "citations": null,
            "annual_visits": 1524,
            "last_update": "2024-11-25T14:14:10.281449Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": null
        },
        {
            "id": 196,
            "name": "Viral Host Range database",
            "description": "The Viral Host Range database represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the years, countless host range experiments have been performed in many laboratories. However, these data are not readily available to the community and are therefore underexploited.\n\nThe VHRdb is an online resource that centralizes experimental data related to the host range of viruses. While it originates from bacteriophages and bacteria interaction studies, its design is compatible with viruses infecting all living forms. Users can browse publicly available data to find which host is infected by a virus, and vice versa. Users can also upload their own data while keeping it private or making it public, analyze results across independent sets of data, generate and visualize outputs. Data implemented in the VHRdb are linked to users and, if available, to publications and sequence identifiers.",
            "homepage": "https://viralhostrangedb.pasteur.cloud/",
            "biotoolsID": "VHRdb",
            "biotoolsCURIE": "biotools:VHRdb",
            "tool_type": [
                "Database portal",
                "Web API",
                "Web application"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3489",
                "http://edamontology.org/topic_0781"
            ],
            "primary_publication": [
                "10.1093/bioinformatics/btab070"
            ],
            "operating_system": [
                "Mac",
                "Windows",
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Contributor",
                        "Developer"
                    ],
                    "name": "LAMY-BESNIER Quentin",
                    "email": null,
                    "url": "https://research.pasteur.fr/fr/member/fr-quentin-lamy-besnier/",
                    "orcidid": "https://orcid.org/0000-0002-7141-6340",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Documentor"
                    ],
                    "name": "MÉNAGER Hervé",
                    "email": null,
                    "url": "https://research.pasteur.fr/fr/member/herve-menager/",
                    "orcidid": "https://orcid.org/0000-0002-7552-1009",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                },
                {
                    "type_role": [
                        "Maintainer"
                    ],
                    "name": "Institut Pasteur",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": "grid.428999.7",
                    "typeEntity": "Institute",
                    "note": null
                },
                {
                    "type_role": [
                        "Maintainer",
                        "Developer"
                    ],
                    "name": "Bryan Brancotte",
                    "email": null,
                    "url": "https://research.pasteur.fr/en/member/bryan-brancotte",
                    "orcidid": "https://orcid.org/0000-0001-8669-5525",
                    "gridid": null,
                    "typeEntity": null,
                    "note": null
                },
                {
                    "type_role": [
                        "Primary contact"
                    ],
                    "name": "DEBARBIEUX Laurent",
                    "email": null,
                    "url": "https://research.pasteur.fr/fr/member/laurent-debarbieux/",
                    "orcidid": "https://orcid.org/0000-0001-6875-5758",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": null
                }
            ],
            "tool_licence": null,
            "documentation": "https://hub.pages.pasteur.fr/viralhostrangedb/",
            "maturity": "Mature",
            "cost": null,
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2022-06-24T08:58:13.476714Z",
            "teams": [
                "Pasteur HUB"
            ],
            "source_repository": "https://gitlab.pasteur.fr/hub/viralhostrangedb/"
        },
        {
            "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": 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": 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": 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": 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
        }
    ]
}