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Chaque session sera également suivie d’un cours optionnel sur l’analyse et le traitement des images.\nPour plus d’information, ainsi que pour les inscriptions au module optionnel et les demandes d’exemption, rendez-vous sur la page du cours : https://c3bi.pasteur.fr/introduction-to-data-analysis-2018-19/\nThèmes abordés\nLe module d’analyse de données couvrira un large champ de notions nécessaires aux étudiants pour planifier leurs expériences, analyser et explorer leurs données, interpréter les résultats et générer des figures à des fins de publication. Il abordera des notions de base en statistique, dont les analyses uni- et multivariées, les analyses descriptives, les distributions statistiques usuelles utilisées en biologie, ainsi que les tests d’hypothèses. Les exercices et travaux pratiques seront réalisés avec R et RStudio. 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Learn to annotate workflows with metadata, apply best practices for FAIR compliance, and implement tests to ensure reliability. Publish your workflows to WorkflowHub and Dockstore via the IWC. Develop high-resolution workflow visualizations and create interactive tutorials using a “Choose Your Own Tutorial” approach. Finally, master workflow export by creating RO-Crates for reproducibility and submitting workflows to LifeMonitor for performance tracking.\r\n\r\nWednesday: Scaling Workflows & Galaxy Using Command-Line and API\r\n\r\nStart with a recap and real-world examples of large-scale Galaxy projects. Learn to execute workflows from the command line using Planemo, automate batch processing with shell scripts, and analyze performance for efficiency. Discover how to scale Galaxy use with BioBlend, designing Python scripts for batch workflow execution and evaluating scalability. The day concludes with an introduction to the “Bring Your Own Work” session.\r\n\r\nThursday: Bring Your Own Work (BYOW)\r\n\r\nDedicate the day to applying your new skills to your own projects. With guidance from trainers, refine your workflows, troubleshoot challenges, and implement solutions using your personal data. Collaborate with peers, document your progress, and optimize your workflows to leave with actionable results for your research.\r\n\r\nFriday: Storage, Data Management, Recap, and Closing\r\n\r\nThe final half-day begins with a recap of the week’s progress, followed by a session on “Bring Your Own Storage”, exploring how to integrate personal or institutional storage with Galaxy. Learn about managing databases in Galaxy and the IDC (Intergalactic Data Commission) effort for efficient data organization. The workshop concludes with a general recap, supplementary exercises, and feedback and closing remarks, ensuring you leave with a comprehensive understanding and resources for continued success.\r\n\r\nThis training will be conducted in French, while the materials (slides) will be in English.\r\n\r\nRequirements\r\n\r\nPrior knowledge and experience using Galaxy\r\nPrior knowledge and experience using command line\r\nFluent in French (materials will be in English and discussions will happen in French)\r\nYour own computer\r\nOptional but encouraged: your own workflow and dataset for the Bring Your Own Work (BYOW) session. The workflow and the dataset must be shareable and non-sensitive (i.e., they must not contain any patient-related information or confidential data). The dataset size must be small.","homepage":"https://training.galaxyproject.org/training-material/events/2026-10-12-Advanced-Galaxy-Training.html#overview","is_draft":false,"costs":["700 euros HT"],"topics":["http://edamontology.org/topic_3316","http://edamontology.org/topic_0769","http://edamontology.org/topic_0091"],"keywords":["Reproducibility","Galaxy","Workflow development"],"prerequisites":[],"openTo":"Everyone","accessConditions":"NA","maxParticipants":20,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/810/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/762/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/116/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[{"id":3,"name":"IFB","url":"https://catalogue.france-bioinformatique.fr/api/eventsponsor/IFB/?format=json"}],"organisedByOrganisations":[{"id":43,"name":"IFB-core","url":"https://catalogue.france-bioinformatique.fr/api/organisation/IFB-core/?format=json"}],"organisedByTeams":[{"id":29,"name":"IFB Core","url":"https://catalogue.france-bioinformatique.fr/api/team/IFB%20Core/?format=json"}],"logo_url":"https://training.galaxyproject.org/training-material/assets/images/GTN.png","updated_at":"2026-06-16T15:50:42.378756Z","type":"Training course","start_date":"2026-10-12","end_date":"2026-10-16","venue":"","city":"Paris","country":"France","geographical_range":"National","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"future","registration_opening":"2026-04-22","registration_closing":"2026-07-03","registration_status":"closed","courseMode":"Onsite"},{"id":664,"name":"Les langages de workflows pour une analyse bioinformatique reproductible / Workflow languages for reproducible bioinformatics analysis","shortName":"WF4bioinfo","description":"L’Institut Français de Bioinformatique (IFB) organise en partenariat avec iPOP-UP (représenté par EDC) une formation sur les langages de workflows en bioinformatique à destination des bioinformaticien·ne·s et des bioanalystes. La formation abordera les fondamentaux et les fonctionnalités avancées des deux langages Snakemake et Nextflow. Ces outils sont en effet devenus indispensables pour assurer la reproductibilité et l’efficacité des analyses bioinformatiques. La formation sera structurée en deux séquences :\r\n- une journée commune qui abordera les grands principes des gestionnaires de workflow, en particulier dans le domaine de la bioinformatique et en lien avec les infrastructures de calcul de type cluster et cloud proposés au sein de l’IFB \r\n- une  journée de session pratique  avec 1 atelier snakemake et 1 atelier nextflow en parallèle au choix des participants. Nous proposons aux participants qui le souhaitent de travailler sur leur propre workflow dans une approche “Bring your own script” avec l’aide de l’équipe pédagogique.","homepage":"https://moodle.france-bioinformatique.fr/course/view.php?id=36","is_draft":false,"costs":[],"topics":["http://edamontology.org/topic_0769","http://edamontology.org/topic_0091"],"keywords":["FAIR","Reproducibility","Nextflow","Snakemake"],"prerequisites":["Linux - Basic Knowledge"],"openTo":"Everyone","accessConditions":"","maxParticipants":20,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/116/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/326/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/804/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[{"id":4,"name":"IFB - ELIXIR-FR","url":"https://catalogue.france-bioinformatique.fr/api/organisation/IFB%20-%20ELIXIR-FR/?format=json"}],"organisedByTeams":[{"id":38,"name":"PB-IBENS","url":"https://catalogue.france-bioinformatique.fr/api/team/PB-IBENS/?format=json"}],"logo_url":"https://moodle.france-bioinformatique.fr/pluginfile.php/1/core_admin/logocompact/300x300/1654772049/IFB-HAUT-COULEUR-PETIT.png","updated_at":"2025-09-23T09:21:52.846631Z","type":"Training course","start_date":"2025-09-29","end_date":"2025-10-01","venue":"","city":"Paris","country":"France","geographical_range":"","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":null,"registration_closing":null,"registration_status":"unknown","courseMode":"Onsite"},{"id":601,"name":"Introduction to Linux","shortName":"Introduction to Linux - BiRD","description":"Objectives\r\n- Understand the principles and advantages of the Linux system\r\n- Know and use the main bash commands. Ability to chain multiple commands using pipes\r\n- Launch programs with arguments\r\n- Gain independence to perform command line analyses\r\n\r\nPedagogical Content\r\n- Introduction to the Linux system.\r\n- File system: directory structure, paths, home directory, file and directory management.\r\n- Principle of protections: reading file attributes, access rights, management of user groups.\r\n- Shell usage: command reminders, input/output redirection, history, completion, launching programs with arguments.\r\n- Commands relevant to bioinformatics: grep, cut, sed, sort, more, etc.\r\n- Connection (ssh) - how to start a session from Linux or Windows PowerShell","homepage":"https://pf-bird.univ-nantes.fr/training/","is_draft":false,"costs":["Priced"],"topics":["http://edamontology.org/topic_0605"],"keywords":[],"prerequisites":[],"openTo":"Everyone","accessConditions":"","maxParticipants":12,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/596/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[],"organisedByTeams":[{"id":16,"name":"BiRD","url":"https://catalogue.france-bioinformatique.fr/api/team/BiRD/?format=json"}],"logo_url":"https://bird.univ-nantes.io/website/images/logo/logo.svg","updated_at":"2024-02-19T09:37:34.209594Z","type":"Training course","start_date":"2024-03-18","end_date":"2024-03-18","venue":"Faculté de Pharmacie - Salle 450, 4ème étage","city":"Nantes","country":"","geographical_range":"National","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2024-02-08","registration_closing":"2024-03-15","registration_status":"closed","courseMode":"Onsite"},{"id":497,"name":"Linux Avancé / Advanced Linux - 2022 Session2","shortName":"Advanced Linux - 2022 Session 2","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/training/courses","is_draft":false,"costs":["Free"],"topics":["http://edamontology.org/topic_3316"],"keywords":[],"prerequisites":["Linux - Basic Knowledge"],"openTo":"Everyone","accessConditions":"","maxParticipants":18,"contacts":[],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[{"id":65,"name":"SBR - Roscoff Marine Station","url":"https://catalogue.france-bioinformatique.fr/api/organisation/SBR%20-%20Roscoff%20Marine%20Station/?format=json"}],"organisedByTeams":[{"id":4,"name":"ABiMS","url":"https://catalogue.france-bioinformatique.fr/api/team/ABiMS/?format=json"}],"logo_url":"https://abims.sb-roscoff.fr/sites/default/files/abims.png","updated_at":"2023-05-17T09:55:24.793130Z","type":"Training course","start_date":"2022-11-22","end_date":"2022-11-22","venue":"Station Biologique de Roscoff","city":"Roscoff","country":"France","geographical_range":"","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2022-10-07","registration_closing":"2022-11-06","registration_status":"closed","courseMode":"Onsite"},{"id":496,"name":"Initiation à Git / Git Initiation  - 2022 Session 2","shortName":"Git Initiation - 2022 Session 2","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":["Free"],"topics":["http://edamontology.org/topic_3372"],"keywords":[],"prerequisites":[],"openTo":"Everyone","accessConditions":"","maxParticipants":18,"contacts":[],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[],"organisedByTeams":[{"id":4,"name":"ABiMS","url":"https://catalogue.france-bioinformatique.fr/api/team/ABiMS/?format=json"}],"logo_url":"https://abims.sb-roscoff.fr/sites/default/files/abims.png","updated_at":"2023-05-17T09:55:45.294813Z","type":"Training course","start_date":"2022-11-25","end_date":"2022-11-25","venue":"Station Biologique de Roscoff","city":"Roscoff","country":"France","geographical_range":"","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2022-10-07","registration_closing":"2022-11-06","registration_status":"closed","courseMode":"Onsite"},{"id":209,"name":"Introduction to R Language","shortName":"","description":"","homepage":"","is_draft":false,"costs":[],"topics":[],"keywords":[],"prerequisites":[],"openTo":"Internal personnel","accessConditions":"","maxParticipants":null,"contacts":[],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[],"organisedByTeams":[],"logo_url":"https://ressources.france-bioinformatique.fr/sites/default/files/150x150.png","updated_at":"2022-06-02T11:50:50.627601Z","type":"Training course","start_date":"2019-05-20","end_date":null,"venue":"","city":"CBiB","country":"","geographical_range":"","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":null,"registration_closing":null,"registration_status":"unknown","courseMode":null},{"id":704,"name":"Mathematical and Computational Evolutionary Biology (MCEB)","shortName":"MCEB","description":"MCEB will take place in Granada, Spain for its 2025 edition. The meeting will put the emphasis on methods and models for phylogenomics and population genomics. Beyond this year's themes, general concepts, models, methods and algorithms will be presented and discussed, just as in the previous editions of MCEB. As usual, the meeting will bring together researchers originating from various disciplines: mathematics, statistics, computer science, phylogenetics, population genetics, molecular epidemiology, biodiversity and macroevolution... Keynote speakers will\r\nintroduce a field of research and discuss their own work in this field. Afternoon will be for short presentations and posters, with plenty of time for discussions. We will stop early every day, thus leaving time for other activities.\r\n\r\nKEYNOTES:\r\n** Sophie Abby - \"Evolution of biosynthetic pathways in Bacteria\"\r\n** Richard Durbin - \"Population genome variation – going beyond SNPs\"\r\n** Lisa Pokorny Montero - \"Genomic approaches to the study of plant evolution\"\r\n** Harald Ringbauer - \"Advanced ancient DNA analysis\"\r\n** Kristina Wicke - \"Inference of phylogenetic networks\"\r\n** Jaime Huerta-Cepas - \"Evolutionary significance of unknown microbial genes\"","homepage":"https://mceb2025.sciencesconf.org/","is_draft":false,"costs":["Priced"],"topics":["http://edamontology.org/topic_3056","http://edamontology.org/topic_3050","http://edamontology.org/topic_3293","http://edamontology.org/topic_2269"],"keywords":["Biostatistics","Biodiversity","Evolution and Phylogeny","Phylogenetics"],"prerequisites":[],"openTo":"Everyone","accessConditions":"PRACTICAL INFORMATION\r\n\r\n** Place: \"Carmen de la Victoria\" and \"Corrala de Santiago\", Granada, Spain.\r\n\r\n** Dates: May 12-16th, 2025. The conference will begin Monday evening and will\r\n  end at about 3pm on Friday.\r\n\r\n** Fees: Between 650€ to 850€. Fees will vary depending on the type of room,\r\n  shared (for students) or individual. They include accommodation for four nights\r\n  with breakfast, lunches, coffee breaks, two dinners and drinks around posters\r\n  from Monday night until Friday lunchtime included.\r\n\r\n** Deadline for abstract submission and pre-registration: February 21, 2025.\r\n\r\n** Notification of acceptance: March 15, 2025.","maxParticipants":60,"contacts":[],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[],"organisedByTeams":[{"id":7,"name":"ATGC","url":"https://catalogue.france-bioinformatique.fr/api/team/ATGC/?format=json"}],"logo_url":null,"updated_at":"2025-02-17T08:51:35.482439Z","type":"Meeting","start_date":"2025-05-12","end_date":"2025-05-16","venue":"Carmen de la Victoria\" and \"Corrala de Santiago\"","city":"Granada","country":"Spain","geographical_range":"International","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2025-02-01","registration_closing":"2025-05-05","registration_status":"closed","courseMode":"Onsite"}]}