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            "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/",
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                "fr"
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                "http://edamontology.org/topic_3301",
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                "http://edamontology.org/topic_0219"
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                "10.1093/nar/gkw1101",
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            "id": 88,
            "name": "MetExplore",
            "description": "Metabolic network curation, visualisation and omics data analysis. It is possible to curate and annotate metabolic networks in a collaborative environment. Several tools are available for metabolomics data mapping in networks and visualisation.",
            "homepage": "http://www.metexplore.fr/",
            "biotoolsID": "metexplore",
            "biotoolsCURIE": "biotools:metexplore",
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                "Windows",
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            ],
            "tool_credit": [
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                    "name": "MetaboHub",
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                    "url": null,
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                },
                {
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                    "name": null,
                    "email": "ludovic.cottret@inra.fr",
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                },
                {
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                    ],
                    "name": "Fabien JOURDAN",
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                    "url": "https://sites.google.com/site/fabienjourdan/",
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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"
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            "scientific_topics": [
                "http://edamontology.org/topic_2259",
                "http://edamontology.org/topic_0602",
                "http://edamontology.org/topic_0204"
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                "Mac"
            ],
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                {
                    "type_role": [
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                        "Developer"
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                    "name": null,
                    "email": null,
                    "url": "http://ginsim.org/contact",
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            "tool_licence": "GPL-3.0",
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            "source_repository": "http://ginsim.org/models_repository"
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        {
            "id": 176,
            "name": "Galaxy",
            "description": "Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.",
            "homepage": "https://galaxyproject.org/",
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            "biotoolsCURIE": "biotools:galaxy",
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                "Bioinformatics portal",
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                "Web API"
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                "Linux",
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                "Mac"
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                    "type_role": [
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                    "name": "Galaxy support",
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                    "url": "https://biostar.usegalaxy.org/",
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                    "name": "Galaxy Community",
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                    "orcidid": null,
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                }
            ],
            "tool_licence": "AFL-3.0",
            "documentation": "https://usegalaxy.org/api/docs",
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            "teams": [
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                "South Green"
            ],
            "source_repository": "https://github.com/galaxyproject/galaxy"
        },
        {
            "id": 178,
            "name": "NGS-QC Generator",
            "description": "Comparative analysis between ChIP-seq and other enrichment-related NGS datasets requires prior characterization of their degree of technical similarity. The Galaxy tool NGS-QC Generator is a computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies to improve the quality of sample-derived datasets.",
            "homepage": "http://www.ngs-qc.org/",
            "biotoolsID": "ngs-qc_generator",
            "biotoolsCURIE": "biotools:ngs-qc_generator",
            "tool_type": [
                "Web application"
            ],
            "collection": [
                "Animal and Crop Genomics"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3572",
                "http://edamontology.org/topic_3169"
            ],
            "primary_publication": [
                "10.1007/978-1-4939-3578-9_13"
            ],
            "operating_system": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
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                        "Primary contact"
                    ],
                    "name": null,
                    "email": "contact@ngs-qc.org",
                    "url": null,
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            ],
            "tool_licence": "GPL-2.0",
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            "last_update": "2024-11-25T14:05:15.865852Z",
            "teams": [
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            ],
            "source_repository": null
        },
        {
            "id": 119,
            "name": "RSAT suite",
            "description": "Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows.",
            "homepage": "http://rsat.eu",
            "biotoolsID": "rsat",
            "biotoolsCURIE": "biotools:rsat",
            "tool_type": [
                "Web application",
                "Suite"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "Animal and Crop Genomics"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0621",
                "http://edamontology.org/topic_0749",
                "http://edamontology.org/topic_0203",
                "http://edamontology.org/topic_3512",
                "http://edamontology.org/topic_3125"
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            "primary_publication": [],
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                "Windows",
                "Mac"
            ],
            "tool_credit": [
                {
                    "type_role": [
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                    ],
                    "name": "Jacques van Helden",
                    "email": "Jacques.van-Helden@univ-amu.fr",
                    "url": null,
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            ],
            "tool_licence": "Other",
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            "last_update": "2024-11-25T14:00:33.330732Z",
            "teams": [
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            ],
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        },
        {
            "id": 87,
            "name": "Genetic and Genomic Information System (GnpIS)",
            "description": "A multispecies integrative information system dedicated to plant and fungi pests.. It allows researchers to access genetic, phenotypic and genomic data. It is used by both large international projects and the French National Research Institute for Agriculture, Food and Environment",
            "homepage": "https://urgi.versailles.inrae.fr/gnpis",
            "biotoolsID": "gnpis",
            "biotoolsCURIE": "biotools:gnpis",
            "tool_type": [
                "Database portal",
                "Web application"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "Animal and Crop Genomics"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_0622",
                "http://edamontology.org/topic_0780",
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                "10.3835/plantgenome2015.06.0038"
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            ],
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                    ],
                    "name": null,
                    "email": "urgi-contact@versailles.inra.fr",
                    "url": null,
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                }
            ],
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            "documentation": "https://urgi.versailles.inra.fr/gnpis/",
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            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2025-07-29T13:42:38.871501Z",
            "teams": [
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            ],
            "source_repository": null
        },
        {
            "id": 86,
            "name": "BIII (BioImage Informatics Index, biii.eu)",
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            "homepage": "https://biii.eu",
            "biotoolsID": "BISE",
            "biotoolsCURIE": "biotools:BISE",
            "tool_type": [
                "Database portal",
                "Bioinformatics portal",
                "Web application"
            ],
            "collection": [
                "elixir-fr-sdp-2019",
                "NEUBIAS"
            ],
            "scientific_topics": [
                "http://edamontology.org/topic_3063",
                "http://edamontology.org/topic_0091",
                "http://edamontology.org/topic_0769",
                "http://edamontology.org/topic_3298",
                "http://edamontology.org/topic_3382"
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            "primary_publication": [],
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                    "name": "NEUBIAS Network of Bioimage Analysts",
                    "email": null,
                    "url": "https://neubias.eu",
                    "orcidid": null,
                    "gridid": null,
                    "typeEntity": "Consortium",
                    "note": "COST action having supported the creation and curation of this database"
                },
                {
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                    ],
                    "name": "Perrine Paul-Gilloteaux",
                    "email": "perrine.paul-gilloteaux@univ-nantes.fr",
                    "url": null,
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                    "note": "Leader of the project"
                },
                {
                    "type_role": [
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                    ],
                    "name": "Taggers",
                    "email": null,
                    "url": "http://biii.eu/show-taggers",
                    "orcidid": null,
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                },
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                    ],
                    "name": "Matúš Kalaš",
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                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-1509-4981",
                    "gridid": null,
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                    "note": "Coordinator of the EDAM-bioimaging ontology development"
                },
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                    "name": "Leandro Scholz",
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                    "url": null,
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                    ],
                    "name": "Kota Miura",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-6926-191X",
                    "gridid": null,
                    "typeEntity": "Person",
                    "note": "Main technical support and one of the founders of the project"
                },
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                    "name": "Chong Zhang",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
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                    "note": "Co-leader of the developement"
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                    "url": null,
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                    "gridid": null,
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                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-3597-8557",
                    "gridid": null,
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        {
            "id": 85,
            "name": "ARIA",
            "description": "A software for automated NOE assignment and NMR structure calculation.",
            "homepage": "http://aria.pasteur.fr/",
            "biotoolsID": "aria",
            "biotoolsCURIE": "biotools:aria",
            "tool_type": [
                "Command-line tool"
            ],
            "collection": [
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                "Institut Pasteur",
                "FR"
            ],
            "scientific_topics": [
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                "http://edamontology.org/topic_0593",
                "http://edamontology.org/topic_0176",
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                "http://edamontology.org/topic_3332",
                "http://edamontology.org/topic_2275",
                "http://edamontology.org/topic_0081",
                "http://edamontology.org/topic_0078"
            ],
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            ],
            "operating_system": [
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            ],
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                    "type_role": [
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                    ],
                    "name": "Michael Nilges",
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                    "url": null,
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                },
                {
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                    ],
                    "name": "Benjamin Bardiaux",
                    "email": "benjamin.bardiaux@pasteur.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
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                    "note": null
                },
                {
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                    "name": "Institut Pasteur",
                    "email": null,
                    "url": "http://aria.pasteur.fr/contact-info",
                    "orcidid": null,
                    "gridid": null,
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                }
            ],
            "tool_licence": "MIT",
            "documentation": "http://aria.pasteur.fr/documentation",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2024-11-24T20:37:34.670261Z",
            "teams": [],
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        },
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            "id": 110,
            "name": "RSAT retrieve-ensembl-seq",
            "description": "Returns upstream, downstream, intronic, exonic, UTR, transcript, mRNA, CDS or gene sequences for a list of genes from the EnsEMBL database.\nMulti-genome queries are supported: automatic retrieval of sequences for all the orthologs of the query genes, at a given taxonomical level.",
            "homepage": "http://rsat.sb-roscoff.fr/retrieve-ensembl-seq_form.cgi",
            "biotoolsID": "rsat-retrieve-ensembl-seq",
            "biotoolsCURIE": "biotools:rsat-retrieve-ensembl-seq",
            "tool_type": [
                "Web service",
                "Web application",
                "Command-line tool"
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            "collection": [
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                    "url": "https://www.ulb.be/",
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                    ],
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                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-2608-476X",
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                },
                {
                    "type_role": [
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                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-1465-1640",
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                }
            ],
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            "documentation": "https://rsat-doc.github.io/using-RSAT/",
            "maturity": "Mature",
            "cost": "Free of charge",
            "unique_visits": null,
            "citations": null,
            "annual_visits": null,
            "last_update": "2020-06-16T10:55:27Z",
            "teams": [],
            "source_repository": "https://github.com/rsat-doc"
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            "id": 109,
            "name": "RSAT dyad-analysis",
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