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            "description": "Objectifs\r\n- Savoir utiliser des commandes linux pour traiter de grosses quantités de données : fichiers\r\nvolumineux et/ou en grands nombres : recherche, comptage, tri, fusion, …\r\nProgramme\r\n- Introduction\r\n- Décrire (wc, grep)\r\n- Manipuler des fichiers tabulés (cut, sort)\r\n- Rechercher (grep)\r\n- Redirection / Pipeline (stdin, stdout, stderr, >, 2>, &&, |)\r\n- Recherche avancée : notion d’expression régulière (egrep)\r\n- Rechercher/Remplacer haut débit (tr, sed)\r\n- Manipulation de fichier tabulé – mode avancé (awk)\r\n- Traitement séquentiel de nombreux fichiers (for)",
            "homepage": "https://abims.sb-roscoff.fr/ateliers/2025",
            "is_draft": false,
            "costs": [
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            ],
            "topics": [
                "http://edamontology.org/topic_3316"
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                "Linux - Basic Knowledge"
            ],
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                    "name": "SBR - Roscoff Marine Station",
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            "updated_at": "2025-02-21T08:52:39.134624Z",
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            "end_date": "2025-05-15",
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        {
            "id": 636,
            "name": "How To Run a NF-Core Nextflow Workflow On Genotoul ? - session 12/11/2024",
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            "description": "This training session is organized by the Genotoul bioinfo platform and aims at learning nf-core workflow submission, error understanding, resuming jobs and ressource reservation. We will present and practice:\r\n\r\nthe Nextflow software\r\nthe nf-core community and pipelines\r\nWhat is a singularity image ?\r\nWhere are installed the nf-core workflows ? Which version do I use ?\r\nHow to run a workflow and which config file is used ?\r\nWhich kind of error I can get ?\r\nHow to resume failed jobs?\r\nHow to handle genome indexes ?\r\nHow to monitor my process and then well configure my workflow ?\r\nHow do you best adjust CPU and RAM reservations?\r\nThis is NOT a bioinformatic training on a particular workflow or a training on how to develop a workflow.\r\n\r\nThis training is focused on practice. It consists of several modules with a large variety of exercises:\r\n\r\nStart at 09:00 am\r\nEnd at 17:00 pm",
            "homepage": "https://bioinfo.genotoul.fr/index.php/events/how-to-run-a-nf-core-nextflow-workflow-on-genotoul-2/",
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            "costs": [
                "Non-academic: 550€ + 20% taxes (TVA)",
                "Academic but non-INRAE: 170 € + 20% taxes (TVA)",
                "For INRAE's staff: 150 € no VAT charged;"
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            "topics": [
                "http://edamontology.org/topic_0769"
            ],
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            "logo_url": "http://bioinfo.genotoul.fr/wp-content/uploads/bioinfo_logo-rvb-petit.png",
            "updated_at": "2024-06-10T12:38:11.016801Z",
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            "registration_closing": "2024-11-06",
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            "id": 463,
            "name": "École EBAii Assemblage & Annotation / Assembly & Annotation EBAii school - Session 2022",
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            "end_date": "2022-09-30",
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                "Non-academic: 550€ + 20% taxes (TVA)",
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            ],
            "logo_url": "http://bioinfo.genotoul.fr/wp-content/uploads/bioinfo_logo-rvb-petit.png",
            "updated_at": "2024-06-04T07:39:04.387849Z",
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            "end_date": "2024-10-03",
            "venue": "",
            "city": "castanet-tolosan",
            "country": "France",
            "geographical_range": "National",
            "trainers": [
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            "registration_opening": "2024-06-04",
            "registration_closing": null,
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            "id": 750,
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            "homepage": "https://mesocentre.uca.fr/",
            "is_draft": false,
            "costs": [
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            ],
            "topics": [
                "http://edamontology.org/topic_0605",
                "http://edamontology.org/topic_0091"
            ],
            "keywords": [],
            "prerequisites": [
                "Licence"
            ],
            "openTo": "Everyone",
            "accessConditions": "Have an account on the Mesocentre UCA computing cluster (make a request if necessary on the site https://hub.mesocentre.uca.fr)\r\nAlternation of theoretical courses and practical work.\r\nCOME WITH A LAPTOP with an operational Eduroam connection.\r\nThe training is in French.",
            "maxParticipants": 10,
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                "https://catalogue.france-bioinformatique.fr/api/userprofile/261/?format=api"
            ],
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            ],
            "logo_url": "https://mesocentre.uca.fr/medias/photo/logoaubi-2019minus_1553844844490-jpg?ID_FICHE=41175",
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            "end_date": "2026-02-25",
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            "city": "Clermont-Ferrand",
            "country": "France",
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        },
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            "id": 696,
            "name": "Annotation et comparaison de génomes bactériens : 2025",
            "shortName": "Annotation et comparaison de génomes bactériens",
            "description": "Objectifs pédagogiques\r\nConnaître les concepts et les principales méthodes bioinformatiques pour comparer un jeu de données de génomes microbiens. Construire et évaluer la qualité d’un jeu de données. Savoir mettre en œuvre une comparaison de génomes et en interpréter les résultats.\r\n\r\nProgramme\r\n* Construction d’un jeu de données :\r\n* Téléchargement de données publiques\r\n* Evaluation de la qualité\r\n* Caractérisation de la diversité génomique\r\n* Stratégies de comparaison :\r\n* Construction de famille de protéines\r\n* Alignement de génomes complets\r\n* Analyse des résultats :\r\n   o Notion de core et pan-génome\r\n   o Notions élémentaires de phylogénomique\r\n   o Visualisation et interprétation des résultats\r\n* Mise en pratique sur un jeu de données bactériens, utilisation des logiciels dRep et Roary sous Galaxy.",
            "homepage": "https://documents.migale.inrae.fr/trainings.html",
            "is_draft": false,
            "costs": [
                "Priced"
            ],
            "topics": [
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                "http://edamontology.org/topic_0622"
            ],
            "keywords": [
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            "prerequisites": [],
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            "accessConditions": "",
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                    "id": 88,
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            ],
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            ],
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            "updated_at": "2025-01-29T11:32:53.505947Z",
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            "start_date": "2025-05-19",
            "end_date": "2025-05-20",
            "venue": "",
            "city": "Jouy-en-Josas",
            "country": "France",
            "geographical_range": "",
            "trainers": [],
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            "registration_opening": "2025-01-22",
            "registration_closing": "2025-05-04",
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        },
        {
            "id": 790,
            "name": "Initiation à l’utilisation de Galaxy",
            "shortName": "Initiation Galaxy",
            "description": "Objectifs pédagogiques :\r\nCette formation propose une introduction sur l’interface utilisateur et les fonctionnalités générales d’une plateforme Galaxy.\r\nA l’issue de la formation, les apprenants seront en mesure de :\r\n* connaître les caractéristiques et le fonctionnement d’un portail Galaxy,\r\n* appliquer sur des cas concrets en bioinformatique,\r\n* être autonome dans le traitement de fichiers et l’exécution d’outils.\r\n\r\nProgramme :\r\n* Prise en main d’un portail Galaxy\r\n* Utilisation de l’historique\r\n* Téléchargement des données à traiter\r\n* Manipulation de fichiers\r\n* Paramétrage et exécution d’outils\r\n* Récupération et visualisation de résultats",
            "homepage": "https://documents.migale.inrae.fr/trainings.html",
            "is_draft": false,
            "costs": [
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            ],
            "topics": [
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            ],
            "keywords": [
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            ],
            "prerequisites": [],
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            "accessConditions": "",
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                    "id": 88,
                    "name": "BioinfOmics",
                    "url": "https://catalogue.france-bioinformatique.fr/api/organisation/BioinfOmics/?format=api"
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            ],
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            ],
            "logo_url": "https://migale.inrae.fr/sites/default/files/migale-orange_0.png",
            "updated_at": "2026-02-12T10:34:28.195643Z",
            "type": "Training course",
            "start_date": "2026-03-25",
            "end_date": "2026-03-25",
            "venue": "",
            "city": "Jouy-en-Josas",
            "country": "France",
            "geographical_range": "",
            "trainers": [],
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            "computingFacilities": [],
            "realisation_status": "past",
            "registration_opening": null,
            "registration_closing": "2026-03-11",
            "registration_status": "closed",
            "courseMode": "Onsite"
        },
        {
            "id": 626,
            "name": "Initiation à Git / Git Initiation - 2024",
            "shortName": "Git Initiation - 2024",
            "description": "Objectifs\r\n- Savoir définir ce qu’est un outil de gestion de version\r\n- Être capable d’initialiser un entrepôt Git pour un projet\r\n- Être capable de définir quels fichiers inclure/exclure d’un projet\r\n- Savoir enregistrer localement une nouvelle version pour un projet\r\n- Savoir partager des modifications locales avec tous les contributeurs d’un projet\r\n- Savoir gérer des modifications en parallèle en utilisant les branches.\r\n- Connaître les bonnes pratiques pour contribuer à projet tiers\r\nProgramme :\r\n- Présentation des avantages de la gestion de versions (projets individuels & projets collaboratifs)\r\n- Présentation des principes de fonctionnement de Git\r\n- Présentation et mise en œuvre des commandes principales de Git (clone, checkout, add, rm, commit, merge,\r\npush, pull) ; en ligne de commande ou en utilisant une interface graphique (GitHub et GitLab)",
            "homepage": "https://abims.sb-roscoff.fr/training/courses",
            "is_draft": false,
            "costs": [
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            ],
            "topics": [
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            "accessConditions": "",
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            ],
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            "updated_at": "2025-01-23T13:48:53.713733Z",
            "type": "Training course",
            "start_date": "2024-05-31",
            "end_date": "2024-05-31",
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            "city": "Roscoff",
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            "geographical_range": "",
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            "registration_closing": "2024-04-21",
            "registration_status": "closed",
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        },
        {
            "id": 693,
            "name": "Introduction aux bonnes pratiques pour des analyses reproductibles : 2025",
            "shortName": "Good practices for better reproducibility of analyses :2025",
            "description": "Objectifs pédagogiques\r\n\r\nL’objectif de cette formation est d’initier les apprenants aux bonnes pratiques pour la reproductibilité des analyses. Ils apprendront à rédiger des rapports d’analyse en R Markdown et à les déposer sur un dépôt GitHub. Les principes FAIR (faciles à trouver, accessibles, interopérables et réutilisables) et les bases de la rédaction de PGD (plans de gestion de données) seront également présentés. Durant la formation, nous utiliserons RStudio et GitHub.\r\n\r\nProgramme\r\n\r\nPrincipes et enjeux de la recherche reproductible\r\nUtilisation de GitHub\r\nGestion des versions d’un document\r\nRédaction de document computationnel\r\nPartage d’un rapport avec ses collaborateurs\r\nPrincipes FAIR et PGD",
            "homepage": "https://documents.migale.inrae.fr/trainings.html",
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                    "id": 88,
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            "updated_at": "2025-01-23T15:36:00.927981Z",
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            "start_date": "2025-04-04",
            "end_date": "2025-04-04",
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        {
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            "name": "Annotation et comparaison de génomes bactériens - 2026",
            "shortName": "Annotation et comparaison de génomes bactériens 2026",
            "description": "Connaître les concepts et les principales méthodes bioinformatiques pour annoter automatiquement et comparer un jeu de données de génomes bactériens. Construire et évaluer la qualité d’un jeu de données publiques. Évaluer la qualité et annoter automatiquement un jeu de données. Savoir mettre en oeuvre une comparaison de génomes et en interpréter les résultats.\r\n\r\nProgramme :\r\n\r\n* Construction d’un jeu de données :\r\n        Téléchargement de données publiques\r\n        Evaluation de la qualité d’un jeu de données\r\n\r\n* Principes et mise en œuvre d’une annotation automatique d’un génome bactérien\r\n\r\n * Caractérisation de la diversité génomique\r\n\r\n * Construction de pangénomes\r\n\r\n * Analyse des résultats :\r\n        Résultats et métriques d’un pangénome\r\n        Notions élémentaires de phylogénomique\r\n        Visualisation et interprétation des résultats\r\n\r\n * Mise en pratique sur un jeu de données bactériens, utilisation des logiciels dRep, Quast, Bakta et PPanGGOLiN sous Galaxy.",
            "homepage": "https://documents.migale.inrae.fr/trainings.html",
            "is_draft": false,
            "costs": [
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            ],
            "topics": [
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                "http://edamontology.org/topic_0797",
                "http://edamontology.org/topic_0622"
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            "keywords": [
                "Genome annotation",
                "Comparative genomics"
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            "updated_at": "2026-02-12T10:46:56.602216Z",
            "type": "Training course",
            "start_date": "2026-03-19",
            "end_date": "2026-03-20",
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            "id": 634,
            "name": "Short-Read Alignment And Small Size Variants Calling - session 9/10/2024 - 10/10/2024",
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            "description": "This training session, organized jointly with the Sigenae platform, is designed to introduce NGS data, in particular Illumina Solexa technologies with command line. You will discover the new sequence formats, the assembly formats and the known biases of these technologies. You will use mapping on reference genome software, polymorphisms detection with the GATK pipeline and alignment visualization software.\r\n\r\nThis training is focused on the practice. It consists of modules with a large variety of exercises:\r\n\r\nDay 1 (09:00 am to 12:30 am): Fastq format / Sequence quality. Read mapping.\r\nDay 1 (14:00 pm to 17:00 pm): SAM format. Visualisation.\r\nDay 2 (09:00 am to 17:00 am): Variant calling. VCF format. Variant annotation (SNPeff / SNPsift).\r\n \r\nThe session will take place in the room ‘salle de formation’ at INRAE center of Toulouse-Auzeville.\r\n\r\nPrerequisites: ability to use a Unix environment (see Unix training) and Cluster (see Cluster training).\r\n \r\nTool box: FastQC, BWA, Samtools, Picard tools, GATK, SnpSift / SnpEff, IGV.",
            "homepage": "https://bioinfo.genotoul.fr/index.php/events/alignment-and-small-size-variants-calling/",
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                "Academic but non-INRAE: 170 € + 20% taxes (TVA)",
                "For INRAE's staff: 150 € no VAT charged;"
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                "http://edamontology.org/topic_0102"
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            ],
            "logo_url": "https://bioinfo.genotoul.fr/wp-content/uploads/sigenae-text-black-1.png",
            "updated_at": "2024-06-10T12:36:32.603065Z",
            "type": "Training course",
            "start_date": "2024-10-09",
            "end_date": "2024-10-10",
            "venue": "",
            "city": "castanet-tolosan",
            "country": "France",
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