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            "teams": [
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            "source_repository": "https://github.com/DyogenIBENS/FINSURF/"
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            "name": "Lifemap",
            "description": "Explorer of the entire tree of life. Lifemap allows visualizing the entire NCBI taxonomy on a single page with a deep zoom interface and performing easy search, mrca detection, subtree download, etc.",
            "homepage": "http://lifemap.univ-lyon1.fr",
            "biotoolsID": "Lifemap",
            "biotoolsCURIE": "biotools:Lifemap",
            "tool_type": [
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                "Web application"
            ],
            "collection": [
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            ],
            "scientific_topics": [
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            "primary_publication": [],
            "operating_system": [
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                "Windows",
                "Mac"
            ],
            "tool_credit": [],
            "tool_licence": "CC-BY-NC-4.0",
            "documentation": "http://lifemap.univ-lyon1.fr/help/",
            "maturity": "Legacy",
            "cost": "Free of charge",
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            "last_update": "2020-06-16T10:55:27Z",
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            "source_repository": "https://github.com/damiendevienne/Lifemap"
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            "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",
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            ],
            "primary_publication": [
                "10.1073/pnas.1523899113"
            ],
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                "Mac"
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                    "name": "Institut Pasteur",
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                    "url": "https://research.pasteur.fr",
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            "documentation": "http://shaman.c3bi.pasteur.fr/",
            "maturity": "Mature",
            "cost": "Free of charge",
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            "citations": null,
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            "last_update": "2025-10-23T10:46:59.953305Z",
            "teams": [
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            ],
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            "name": "FAIDARE",
            "description": "FAIDARE: FAIR Data-finder for Agronomic Research. \nThe purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.\n\nIt is based on the Breeding API (BrAPI) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface. It also provides a standard interface that can be accessed programatically through web services.\n\nIt is an extension of the generic DataDiscovery portal, a web portal that allows finding any type of data across several databases through a lightweight keyword based search. FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.",
            "homepage": "https://urgi.versailles.inrae.fr/faidare/",
            "biotoolsID": "faidare",
            "biotoolsCURIE": "biotools:faidare",
            "tool_type": [
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                "Web service",
                "Web API",
                "Web application"
            ],
            "collection": [
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                "URGI"
            ],
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            "operating_system": [
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            "tool_credit": [
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                    "name": "URGI support",
                    "email": "urgi-support@inrae.fr",
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            "tool_licence": "BSD-3-Clause",
            "documentation": "https://urgi.versailles.inrae.fr/faidare/help",
            "maturity": "Emerging",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-09-02T05:04:34.812991Z",
            "teams": [
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            ],
            "source_repository": "https://forgemia.inra.fr/urgi-is/faidare"
        },
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            "name": "DataDiscovery",
            "description": "DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters.\n\nThis tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.",
            "homepage": "https://urgi.versailles.inrae.fr/data-discovery/",
            "biotoolsID": "DataDiscovery",
            "biotoolsCURIE": "biotools:DataDiscovery",
            "tool_type": [
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                "Web service",
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            ],
            "collection": [
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            ],
            "scientific_topics": [
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                "http://edamontology.org/topic_0610",
                "http://edamontology.org/topic_3071",
                "http://edamontology.org/topic_3810"
            ],
            "primary_publication": [
                "10.3835/plantgenome2015.06.0038"
            ],
            "operating_system": [
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [
                        "Primary contact",
                        "Support"
                    ],
                    "name": "urgi-support",
                    "email": "urgi-support@inrae.fr",
                    "url": null,
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            "tool_licence": "BSD-3-Clause",
            "documentation": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md",
            "maturity": "Emerging",
            "cost": "Free of charge",
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            "citations": null,
            "annual_visits": null,
            "last_update": "2025-07-29T13:42:39.375595Z",
            "teams": [
                "URGI"
            ],
            "source_repository": "https://forgemia.inra.fr/urgi-is/data-discovery"
        },
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            "name": "Genetic and Genomic Information System (GnpIS)",
            "description": "GnpIS is an integrative and multi-species information system dedicated to plants, including forest trees. It handles various types of data, focusing on genetic resources and phenomics. It allows researchers from the Plant community to access and cross-reference genetic data (accessions, phenotypes, polymorphisms, markers and QTLs) and genomic data (sequences, physical maps, genome annotations) for species of agronomic and forestry interest.\nAccessible via a public web portal, GnpIS enables different types of data to be managed, browsed and retrieved via specialized search tools and web services.\nGnpIS is used by the French National Research Institute for Agriculture, Food and Environment (INRAE) and its partners in major national and international projects.",
            "homepage": "https://urgi.versailles.inrae.fr/gnpis",
            "biotoolsID": "gnpis",
            "biotoolsCURIE": "biotools:gnpis",
            "tool_type": [
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                "Web application"
            ],
            "collection": [
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                "Animal and Crop Genomics"
            ],
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            "last_update": "2025-12-19T17:15:16.754031Z",
            "teams": [
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            ],
            "source_repository": "https://forge.inrae.fr/urgi/is/gnpis"
        },
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            "name": "metagWGS",
            "description": "metagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.",
            "homepage": "https://forgemia.inra.fr/genotoul-bioinfo/metagwgs",
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            "tool_credit": [
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                    ],
                    "name": "Claire Hoede",
                    "email": "claire.hoede@inrae.fr",
                    "url": null,
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                    "name": "GenoToul bioinformatics facility",
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                    "url": "http://bioinfo.genotoul.fr/",
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            "tool_licence": null,
            "documentation": "https://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.html",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2025-12-11T14:51:44.804907Z",
            "teams": [
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            ],
            "source_repository": "https://forge.inrae.fr/genotoul-bioinfo/metagwgs"
        },
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            "id": 282,
            "name": "easy16S",
            "description": "Easy16S is designed to facilitate the exploration, visualization, and analysis of microbiome data.",
            "homepage": "https://easy16s.migale.inrae.fr/",
            "biotoolsID": "easy16s",
            "biotoolsCURIE": "biotools:easy16s",
            "tool_type": [],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_3174"
            ],
            "primary_publication": [
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            ],
            "operating_system": [
                "Mac",
                "Windows",
                "Linux"
            ],
            "tool_credit": [
                {
                    "type_role": [],
                    "name": "Cédric Midoux",
                    "email": "cedric.midoux@inrae.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-7964-0929",
                    "gridid": null,
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                }
            ],
            "tool_licence": null,
            "documentation": "https://easy16s.migale.inrae.fr/",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2025-12-11T14:36:21.065324Z",
            "teams": [
                "MIGALE"
            ],
            "source_repository": "https://doi.org/10.57745/ZN1HXQ"
        },
        {
            "id": 263,
            "name": "TrEMOLO",
            "description": "Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.",
            "homepage": "https://github.com/DrosophilaGenomeEvolution/TrEMOLO",
            "biotoolsID": "tremolo",
            "biotoolsCURIE": "biotools:tremolo",
            "tool_type": [
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                "Command-line tool"
            ],
            "collection": [],
            "scientific_topics": [
                "http://edamontology.org/topic_0798",
                "http://edamontology.org/topic_0196",
                "http://edamontology.org/topic_3168",
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            ],
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            ],
            "operating_system": [
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            ],
            "tool_credit": [
                {
                    "type_role": [],
                    "name": "Anna-Sophie Fiston-Lavier",
                    "email": "anna-sophie.fiston-lavier@umontpellier.fr",
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                },
                {
                    "type_role": [],
                    "name": "Séverine Chambeyron",
                    "email": "severine.chambeyron@igh.cnrs.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-2775-6556",
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            "last_update": "2024-11-24T14:41:13.039486Z",
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            "source_repository": "https://dataverse.ird.fr/dataverse/tremolo_data"
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            "id": 96,
            "name": "GINsim",
            "description": "Computer tool for the modeling and simulation of genetic regulatory networks.",
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            "biotoolsCURIE": "biotools:ginsim",
            "tool_type": [
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            ],
            "collection": [
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                "FR",
                "EBI Training Tools",
                "PerMedCoE"
            ],
            "scientific_topics": [
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                "http://edamontology.org/topic_0602",
                "http://edamontology.org/topic_0204"
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            "operating_system": [
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                "Mac"
            ],
            "tool_credit": [
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                    "name": null,
                    "email": null,
                    "url": "http://ginsim.org/contact",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Project",
                    "note": null
                }
            ],
            "tool_licence": "GPL-3.0",
            "documentation": "http://ginsim.org/documentation",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
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            "last_update": "2024-11-24T20:09:51.625867Z",
            "teams": [],
            "source_repository": "http://ginsim.org/models_repository"
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        {
            "id": 9,
            "name": "remap",
            "description": "Display restriction enzyme binding sites in a nucleotide sequence.",
            "homepage": "http://emboss.open-bio.org/rel/rel6/apps/remap.html",
            "biotoolsID": "remap",
            "biotoolsCURIE": "biotools:remap",
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