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            "name": "Introduction to Linux",
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            "description": "La bioinformatique est devenue une compétence incontournable pour l'analyse de données de nature diverse : génomes, transcriptomes, protéomes, métabolomes, structures macromoléculaires, réseaux d'interactions. L'appropriation par les biologistes des méthodes et outils de biostatistique et bioinformatique intégrative est un enjeu majeur pour la montée en compétence des équipes de recherche et des plateformes de service. L'université Paris Diderot propose en partenariat avec l'Institut Français de Bioinformatique (IFB) la deuxième édition du Diplôme Universitaire en Bioinformatique intégrative (DU-Bii). Cette formation s’adresse en priorité à des biologistes en demande d'évolution ou de reconversion professionnelle ayant déjà acquis des compétences (formation courte, autoapprentissage, expérience de terrain) en informatique ou bioinformatique/biostatistique (environnement Unix, Python ou R ou autre langage de programmation). Les prérequis sont décrits sur le portail “DU” de l’université Paris Diderot, qui présente le DU-Bii et le DU complémentaire \"Création, Analyse et Valorisation de données omiques\" (DUO) : voir la page dédiée. Le DU-Bii fournira une formation théorique et pratique, complétée par une période d'immersion sur l'une des plateformes régionales de l'IFB, qui mobilisera, dans le cadre d'un projet tutoré, l'ensemble des méthodes et outils appris durant les cours pour réaliser un projet personnel de bioinformatique intégrative. Ce projet combinera des données propres à chaque participant produites dans son laboratoire (principe BYOD : “Bring Your Own Data”) ou collectées à partir de bases de données publiques. Cette formation se déroulera pendant 8 semaines réparties entre : Les cours : 4 semaines à raison de 4 jours/semaine en présentiel (96h) du 2 mars au 2 avril 2020 avec 1 semaine de césure la semaine 12). Le projet tutoré : 20 jours sur l'une des plateformes bioinformatique de l'IFB, à répartir entre le 6 avril et le 19 juin 2020.\r\nRenseignements et candidatures : fcsdv@univ-paris-diderot.fr\r\nInscriptions : voir la page page du DU-Bii de l'Université Paris Diderot\r\nContacts Paris-Diderot : Bertrand.Cosson@univ-paris-diderot.fr \r\nContacts IFB : Helene.Chiapello@inra.fr, Jacques.van-Helden@univ-amu.fr",
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            "name": "4th Workshop Single-Cell / SincellTE 2022 / Single-Cell : Transcriptomics, Spatial and Multi-Omics",
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            "description": "This workshop focuses on the large-scale study of heterogeneity across individual cells from a genomic, transcriptomic and epigenomic point of view. New technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce raise novel methodological challenges for the analysis. In this regard, dedicated bioinformatics and statistical methods have been developed in order to extract robust information.\r\n\r\nThe workshop aims to provide such methods for engineers and researchers directly involved in functional genomics projects making use of single-cell technologies. A wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. For this edition, new courses/practicals will focus on spatial transcriptomics, cell phenotyping and additional multi-omics.\r\n\r\nA wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. For this edition, new courses/practicals will focus on spatial transcriptomics, cell phenotyping and additional multi-omics.\r\n\r\nRequirements : Participants must have prior experience on NGS data analysis  with everyday use of R and good knowledge of Unix command line. Before the training, participants will be asked to familiarize themselves with the processing and primary analyses steps of scRNA-seq datasets with provided pedagogic material.\r\n\r\nIt is not necessary to have personal single-cell data to analyse.",
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            "updated_at": "2022-09-15T13:10:14.790898Z",
            "type": "Training course",
            "start_date": "2022-01-09",
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            "name": "LINUX - session 11 March 2025",
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            "description": "This training session is organized by the Genotoul bioinfo platform and aims at learning sequence analysis. This training session has been designed to familiarize yourself with the platform resources and its organization. You will learn to access the platform from your work station, what is an Linux environment and how to use it, how to create and manipulate files, how to transfer them from and to your personal computer.\r\n\r\nThis training is focused on practice. It consists of 3 modules with a large variety of exercises:\r\n\r\n- Connect to « genotoul » server (09:00 am to 10:30 am): Platform presentation, Linux basics, opening an user account, Putty installation, first connection.\r\n- Files and basics commands  (10:45 am to 12:00 pm): types of files and secure access, file manipulation commands, text editors and viewers, disk space management .\r\n- Transfers and file manipulation (14:00 pm to 17:00 pm): download/transfer, compress/uncompress, utility commands and data extraction, output redirections.",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/linux-2-2/",
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            "city": "castanet-tolosan",
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            "name": "New session of Molecular Phylogeny - Level 1",
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            "updated_at": "2023-10-05T12:37:00.397895Z",
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            "name": "Linux - Initiation / Linux for Beginners - 2022 Session 2",
            "shortName": "Linux Init - 2022 Session 2",
            "description": "Objectifs :\r\n- Être capable de se connecter à une machine Linux\r\n- Être capable de transférer des fichiers à partir de/vers une machine Linux\r\n- Être capable de naviguer dans le système de fichiers\r\n- Être capable d’examiner le contenu d’un fichier et de gérer l’espace disque\r\n- Être capable de gérer les droits d’accès aux répertoires et aux fichiers.\r\n- Être capable de gérer le lancement, l’interruption et l’arrêt de processus",
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            "updated_at": "2023-05-17T09:55:01.623771Z",
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            "name": "New session of Molecular Phylogeny - Level 2",
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            "name": "Principes FAIR dans un projet de bioinformatique - Session 2023",
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            "description": "L’Institut Français de Bioinformatique (IFB) organise en partenariat avec l’Institut de Biologie Intégrative de la Cellule (I2BC) une formation à destination des bioinformaticiens et biostatisticiens souhaitant mettre en oeuvre les principes “FAIR” (Facile à trouver, Accessible, Interopérable, Réutilisable) dans leurs projets d’analyse et de développement. Les concepts FAIR, initialement définis dans le contexte d’ouverture des données de la recherche, seront ici adaptés pour cadrer avec un projet type de développement et/ou analyse bioinformatique/biostatistique. Ainsi, la formation n’abordera pas les aspects “FAIR” spécifiques aux données mais introduira plusieurs outils permettant d’améliorer la reproductibilité des analyses.",
            "homepage": "https://moodle.france-bioinformatique.fr/course/view.php?id=19",
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                "NGS Sequencing Data Analysis",
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            ],
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                    "id": 64,
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            "type": "Training course",
            "start_date": "2023-10-09",
            "end_date": "2023-10-11",
            "venue": "Institut des Systèmes Complexes",
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            "homepage": "https://abims.sb-roscoff.fr/training/courses",
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            "type": "Training course",
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            "end_date": "2022-11-23",
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            "city": "Roscoff",
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            "registration_closing": "2022-11-06",
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            "description": "This training session is organized by the Genotoul bioinfo platform and aims at learning sequence analysis. This training session has been designed to familiarize yourself with the platform resources and its organization. You will learn to access the platform from your work station, what is an Linux environment and how to use it, how to create and manipulate files, how to transfer them from and to your personal computer.\r\n\r\nThis training is focused on practice. It consists of 3 modules with a large variety of exercises:\r\n\r\n- Connect to « genotoul » server (09:00 am to 10:30 am): Platform presentation, Linux basics, opening an user account, Putty installation, first connection.\r\n- Files and basics commands  (10:45 am to 12:00 pm): types of files and secure access, file manipulation commands, text editors and viewers, disk space management .\r\n- Transfers and file manipulation (14:00 pm to 17:00 pm): download/transfer, compress/uncompress, utility commands and data extraction, output redirections.",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/linux-2-2/",
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                "Non-academic: 550€ + 20% taxes (TVA)",
                "Academic but non-INRAE: 170 € + 20% taxes (TVA)",
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                }
            ],
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            "updated_at": "2022-06-02T11:50:50.627601Z",
            "type": "Training course",
            "start_date": "2022-03-14",
            "end_date": "2022-03-14",
            "venue": "INRAE Occitanie Toulouse 24 Chemin de Borde Rouge – Auzeville CS 52627 31326 Castanet Tolosan cedex",
            "city": "Toulouse",
            "country": "France",
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        },
        {
            "id": 649,
            "name": "Analyses NGS avec R",
            "shortName": "",
            "description": "Cette formation introduira les paquetages Bioconductor permettant l'analyse de données issues du séquençage nouvelle génération.\r\n\r\n- Rappels des concepts du séquençage NGS\r\n- Les outils d'annotation et de conversion d'identifiants\r\n- L'analyse des reads et du résultat d'alignement\r\n- L'analyse d'expression différentielle en RNA-seq\r\n- Les techniques d'enrichissement\r\n- Les outils de visualisation pour les NGS\r\n\r\nLa fin du stage (2 h) sera consacrée à un atelier pédagogique d'analyse et de réflexion sur les données apportées par les stagiaires.",
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            ],
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                "Gene expression differential analysis",
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            ],
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            ],
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            ],
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            ],
            "logo_url": "https://services.cbib.u-bordeaux.fr/utils/logo_cbib.png",
            "updated_at": "2024-12-04T10:38:10.103074Z",
            "type": "Training course",
            "start_date": "2025-05-15",
            "end_date": "2025-05-16",
            "venue": "",
            "city": "Bordeaux",
            "country": "France",
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        },
        {
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            "name": "Analyses Single Cell RNA-seq (ScRNA-seq) avec R",
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            "homepage": "https://cnrsformation.cnrs.fr/analyses-single-cell-rna-seq-scrna-seq-avec-r?axe=176",
            "is_draft": false,
            "costs": [],
            "topics": [],
            "keywords": [
                "Bioinformatics & Biomedical",
                "R Language",
                "R",
                "NGS Sequencing Data Analysis"
            ],
            "prerequisites": [
                "Basic knowledge of R",
                "R programming"
            ],
            "openTo": "Everyone",
            "accessConditions": "Maîtrise du langage R\r\nAvoir suivi le stage \"Langage R : introduction\" ou niveau équivalent.\r\nAfin de vérifier que votre maîtrise du langage R est suffisante pour pouvoir suivre ce stage, nous vous invitons à effectuer et à renvoyer le test téléchargeable\r\nhttps://cnrsformation.cnrs.fr/data/STG_23294_55153.docx",
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            ],
            "logo_url": "https://services.cbib.u-bordeaux.fr/utils/logo_cbib.png",
            "updated_at": "2024-12-04T10:38:18.342890Z",
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            "end_date": "2025-06-04",
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            "name": "LINUX - session 07/10/2024",
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            "description": "This training session is organized by the Genotoul bioinfo platform and aims at learning sequence analysis. This training session has been designed to familiarize yourself with the platform resources and its organization. You will learn to access the platform from your work station, what is an Linux environment and how to use it, how to create and manipulate files, how to transfer them from and to your personal computer.\r\n\r\nThis training is focused on practice. It consists of 3 modules with a large variety of exercises:\r\n\r\n- Connect to « genotoul » server (09:00 am to 10:30 am): Platform presentation, Linux basics, opening an user account, Putty installation, first connection.\r\n- Files and basics commands  (10:45 am to 12:00 pm): types of files and secure access, file manipulation commands, text editors and viewers, disk space management .\r\n- Transfers and file manipulation (14:00 pm to 17:00 pm): download/transfer, compress/uncompress, utility commands and data extraction, output redirections.",
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            "is_draft": false,
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                "Academic but non-INRAE: 170 € + 20% taxes (TVA)",
                "For INRAE's staff: 150 € no VAT charged;"
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            "keywords": [],
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            ],
            "logo_url": "http://bioinfo.genotoul.fr/wp-content/uploads/bioinfo_logo-rvb-petit.png",
            "updated_at": "2024-06-05T09:15:55.325587Z",
            "type": "Training course",
            "start_date": "2024-10-07",
            "end_date": "2024-10-07",
            "venue": "",
            "city": "castanet-tolosan",
            "country": "France",
            "geographical_range": "National",
            "trainers": [
                "https://catalogue.france-bioinformatique.fr/api/userprofile/344/?format=api",
                "https://catalogue.france-bioinformatique.fr/api/userprofile/739/?format=api"
            ],
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                    "id": 137,
                    "name": "Linux slides",
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                },
                {
                    "id": 138,
                    "name": "Linux TP",
                    "url": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/Linux%20TP/?format=api"
                }
            ],
            "computingFacilities": [],
            "realisation_status": "past",
            "registration_opening": "2024-06-05",
            "registration_closing": "2024-10-01",
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        },
        {
            "id": 528,
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            "shortName": "",
            "description": "This training session is organized by the Genotoul bioinfo platform and aims at learning sequence analysis. This training session has been designed to familiarize yourself with the platform resources and its organization. You will learn to access the platform from your work station, what is an Linux environment and how to use it, how to create and manipulate files, how to transfer them from and to your personal computer.\r\n\r\nThis training is focused on practice. It consists of 3 modules with a large variety of exercises:\r\n\r\n- Connect to « genotoul » server (09:00 am to 10:30 am): Platform presentation, Linux basics, opening an user account, Putty installation, first connection.\r\n- Files and basics commands  (10:45 am to 12:00 pm): types of files and secure access, file manipulation commands, text editors and viewers, disk space management .\r\n- Transfers and file manipulation (14:00 pm to 17:00 pm): download/transfer, compress/uncompress, utility commands and data extraction, output redirections.",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/linux-2-2/",
            "is_draft": false,
            "costs": [
                "Non-academic: 550€ + 20% taxes (TVA)",
                "Academic but non-INRAE: 170 € + 20% taxes (TVA)",
                "For INRAE's staff: 150 € no VAT charged;"
            ],
            "topics": [
                "http://edamontology.org/topic_3316"
            ],
            "keywords": [],
            "prerequisites": [
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            ],
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                    "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api"
                }
            ],
            "logo_url": "http://bioinfo.genotoul.fr/wp-content/uploads/bioinfo_logo-rvb-petit.png",
            "updated_at": "2023-05-17T10:04:05.719947Z",
            "type": "Training course",
            "start_date": "2023-04-17",
            "end_date": "2023-04-17",
            "venue": "",
            "city": "",
            "country": "",
            "geographical_range": "",
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            "realisation_status": "past",
            "registration_opening": "2023-04-04",
            "registration_closing": "2023-04-12",
            "registration_status": "closed",
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        },
        {
            "id": 602,
            "name": "Environments and best practices for using the BiRD cluster",
            "shortName": "Best practices BiRD cluster",
            "description": "Objectives\r\n- Understand and implement the principles of reproducible science in analysis and development projects\r\n- Acquire basic commands necessary for optimal use of the cluster\r\n\r\nPedagogical Content\r\n- Introduction to reproducibility\r\n- Best practices on code history and sharing: Git\r\n- Conda environment\r\n- Presentation of the computing cluster\r\n- Introduction to workflows using Snakemake",
            "homepage": "https://pf-bird.univ-nantes.fr/training/cluster/",
            "is_draft": false,
            "costs": [
                "Free"
            ],
            "topics": [],
            "keywords": [],
            "prerequisites": [
                "Linux - Basic Knowledge"
            ],
            "openTo": "Everyone",
            "accessConditions": "Have an account on the BiRD cluster.",
            "maxParticipants": 20,
            "contacts": [
                "https://catalogue.france-bioinformatique.fr/api/userprofile/596/?format=api"
            ],
            "elixirPlatforms": [],
            "communities": [],
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            "organisedByTeams": [
                {
                    "id": 16,
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                }
            ],
            "logo_url": "https://bird.univ-nantes.io/website/images/logo/logo.svg",
            "updated_at": "2024-02-19T09:37:24.789207Z",
            "type": "Training course",
            "start_date": "2024-03-19",
            "end_date": "2024-03-19",
            "venue": "",
            "city": "Nantes",
            "country": "",
            "geographical_range": "",
            "trainers": [],
            "trainingMaterials": [],
            "computingFacilities": [],
            "realisation_status": "past",
            "registration_opening": "2024-02-08",
            "registration_closing": "2024-03-18",
            "registration_status": "closed",
            "courseMode": "Onsite"
        },
        {
            "id": 676,
            "name": "Initiation à Galaxy - session Février 2024",
            "shortName": "",
            "description": "Bilille organise régulièrement des formations d'initiation à l'outil Galaxy d'une journée, destinée aux biologistes et médecins désirant découvrir le traitement bioinformatique de données via une interface conviviale.\r\n\r\nGalaxy est très répandu pour l’analyse de données omiques, telles que données de séquençage ou données de puces à ADN. \r\nC'est l'environnement qui est utilisé lors du cycle de formation “Analyse de données de séquençage à haut-débit”.",
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