{"count":395,"next":"https://catalogue.france-bioinformatique.fr/api/training/?format=json&limit=20&offset=380&ordering=-personalised","previous":"https://catalogue.france-bioinformatique.fr/api/training/?format=json&limit=20&offset=340&ordering=-personalised","results":[{"id":316,"name":"IMGT® standards, databases, tools and web resources","shortName":"IMGT workshop","description":"Presentation of IMGT® patterns and resources for the study of genes, expressed repertoires and three-dimensional structures of immunoglobulins (antibodies) and T cell receptors.","homepage":"https://www.imgt.org/","is_draft":false,"costs":[],"topics":["http://edamontology.org/topic_3930","http://edamontology.org/topic_3948"],"keywords":["Protein structures","Immune repertoire analysis","Monoclonal antibody","Immunology"],"prerequisites":[],"openTo":"Everyone","accessConditions":"","maxParticipants":10,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/339/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[],"organisedByTeams":[],"logo_url":null,"updated_at":"2022-06-02T11:50:50.812642Z","audienceTypes":[],"audienceRoles":["Researchers","Biologists","Bioinformaticians"],"difficultyLevel":"","trainingMaterials":[],"learningOutcomes":"","hoursPresentations":null,"hoursHandsOn":null,"hoursTotal":6,"personalised":true,"event_set":["https://catalogue.france-bioinformatique.fr/api/event/485/?format=json"]},{"id":413,"name":"Galaxy Beyond Basics: Mastering Workflows, Automation, and Scalability","shortName":"Galaxy avancée","description":"Join us for an intensive, week-long, in-person training designed to elevate your Galaxy expertise to new heights. This workshop is tailored for data scientists, advanced Galaxy users, and team leaders who need to scale, automate, and publish their data analysis workflows for batch processing and production-level applications.\r\n\r\nOver five days, you’ll embark on a comprehensive journey through Galaxy’s advanced capabilities:\r\n\r\nMonday: Introduction & Workflow Development\r\n\r\nStart with a welcome and icebreaker to foster collaboration, followed by a brief overview of Galaxy and its workflow features. Dive into hands-on workflow development, where you’ll learn to design clean, efficient workflows, customize them with parameters, and generate user-friendly workflow reports—combining theory with practical application.\r\n\r\nTuesday: Workflow FAIRification, Documentation, and Export\r\n\r\nBegin with a recap of Day 1, then explore UseGalaxy.fr and its unique features. 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\nLearning Objectives\r\nAt the end of the workshop, you will be able to:\r\n\r\nWorkflow development\r\n    Understand the key aspects of workflows by identifying their core components and purpose.\r\n    Create clean, non-repetitive workflows by applying best practices for process design.\r\n    Use workflow parameters to customize and optimize workflows for specific tasks.\r\n    Generate user-friendly workflow reports to display workflow results in a structured way.\r\nWorkflow FAIRyfication\r\n    Annotate a Galaxy workflow with essential metadata to ensure it is findable and reusable.\r\n    Apply best practices to data analysis workflows to improve consistency and interoperability.\r\n    Implement robust tests to validate workflow reliability and accuracy.\r\n    Publish a Galaxy workflow on WorkflowHub and Dockstore via its integration into the IWC, demonstrating enhanced findability,accessibility, interroperability and usability for the scientific community.\r\nWorkflow Documentation\r\n    Design a high-resolution workflow image optimized for documentation and presentations.\r\n    Develop a hands-on tutorial with a “Choose Your Own Tutorial” approach, including:\r\n        A step-by-step tutorial with skeleton generation from the workflow.\r\n        A real-time tutorial that runs and explains the workflow interactively.\r\n    Produce a final documentation package that includes both tutorial formats and high-resolution visuals.\r\nWorkflow Export\r\n    Apply the process of creating a Galaxy Workflow Run RO-Crate by packaging a workflow with its metadata, inputs, and outputs, ensuring it is reproducible and FAIR-compliant.\r\n    Evaluate the completeness and accuracy of a Galaxy Workflow Run RO-Crate by reviewing its structure, metadata, and included files for adherence to best practices.\r\n    Submit a workflow to LifeMonitor, analyzing the platform’s feedback to assess workflow performance and improve its reliability for future use.\r\nWorkflow Scaling using command-line\r\nExecute workflows from the command line using the Planemo run subcommand, demonstrating the ability to run and monitor workflows outside the Galaxy interface.\r\nDevelop simple shell scripts to automate the execution of multiple workflows concurrently or sequentially, optimizing efficiency and scalability.\r\nAnalyze the performance and resource usage of workflows run via shell scripts, evaluating the effectiveness of scaling strategies for large-scale data processing.\r\nScaling Galaxy Use with the API and BioBlend\r\nUtilize the BioBlend library to programmatically interact with Galaxy, executing workflows, managing datasets, and automating repetitive tasks.\r\nDesign a Python script using BioBlend to scale Galaxy workflows for batch processing, ensuring efficient resource use and reproducibility.\r\nEvaluate the performance and scalability of workflows executed via BioBlend, comparing results with manual Galaxy interactions to identify improvements.\r\n“Bring Your Own Work”\r\nApply the concepts and tools learned during the training to develop or refine your own workflows using your personal data, with guidance from trainers.\r\nTroubleshoot challenges in your workflow or data analysis, implementing solutions with the support of trainers and peers.\r\nDemonstrate progress in your project by documenting your workflow, results, and any optimizations made during the sessions.\r\n\r\nRequirements\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 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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":"2026-04-23T08:22:23.122272Z","audienceTypes":["Professional (continued)"],"audienceRoles":["Computer scientists","Bioinformaticians","All"],"difficultyLevel":"","trainingMaterials":[],"learningOutcomes":"At the end of the workshop, you will be able to:\r\n\r\nWorkflow development\r\nUnderstand the key aspects of workflows by identifying their core components and purpose.\r\nCreate clean, non-repetitive workflows by applying best practices for process design.\r\nUse workflow parameters to customize and optimize workflows for specific tasks.\r\nGenerate user-friendly workflow reports to display workflow results in a structured way.\r\nWorkflow FAIRyfication\r\nAnnotate a Galaxy workflow with essential metadata to ensure it is findable and reusable.\r\nApply best practices to data analysis workflows to improve consistency and interoperability.\r\nImplement robust tests to validate workflow reliability and accuracy.\r\nPublish a Galaxy workflow on WorkflowHub and Dockstore via its integration into the IWC, demonstrating enhanced findability, accessibility, interroperability and usability for the scientific community.\r\nWorkflow Documentation\r\nDesign a high-resolution workflow image optimized for documentation and presentations.\r\nDevelop a hands-on tutorial with a “Choose Your Own Tutorial” approach, including:\r\nA step-by-step tutorial with skeleton generation from the workflow.\r\nA real-time tutorial that runs and explains the workflow interactively.\r\nProduce a final documentation package that includes both tutorial formats and high-resolution visuals.\r\nWorkflow Export\r\nApply the process of creating a Galaxy Workflow Run RO-Crate by packaging a workflow with its metadata, inputs, and outputs, ensuring it is reproducible and FAIR-compliant.\r\nEvaluate the completeness and accuracy of a Galaxy Workflow Run RO-Crate by reviewing its structure, metadata, and included files for adherence to best practices.\r\nSubmit a workflow to LifeMonitor, analyzing the platform’s feedback to assess workflow performance and improve its reliability for future use.\r\nWorkflow Scaling using command-line\r\nExecute workflows from the command line using the Planemo run subcommand, demonstrating the ability to run and monitor workflows outside the Galaxy interface.\r\nDevelop simple shell scripts to automate the execution of multiple workflows concurrently or sequentially, optimizing efficiency and scalability.\r\nAnalyze the performance and resource usage of workflows run via shell scripts, evaluating the effectiveness of scaling strategies for large-scale data processing.\r\nScaling Galaxy Use with the API and BioBlend\r\nUtilize the BioBlend library to programmatically interact with Galaxy, executing workflows, managing datasets, and automating repetitive tasks.\r\nDesign a Python script using BioBlend to scale Galaxy workflows for batch processing, ensuring efficient resource use and reproducibility.\r\nEvaluate the performance and scalability of workflows executed via BioBlend, comparing results with manual Galaxy interactions to identify improvements.\r\n“Bring Your Own Work”\r\nApply the concepts and tools learned during the training to develop or refine your own workflows using your personal data, with guidance from trainers.\r\nTroubleshoot challenges in your workflow or data analysis, implementing solutions with the support of trainers and peers.\r\nDemonstrate progress in your project by documenting your workflow, results, and any optimizations made during the sessions.","hoursPresentations":null,"hoursHandsOn":null,"hoursTotal":null,"personalised":true,"event_set":["https://catalogue.france-bioinformatique.fr/api/event/802/?format=json","https://catalogue.france-bioinformatique.fr/api/event/803/?format=json"]},{"id":317,"name":"Datathon AGENT - FAIRDOM","shortName":"FAIRDOM","description":"Datathon on experimental phenotypic data management using the FAIRDOM platform, and submission workflow using curation & validation tools.","homepage":"","is_draft":false,"costs":["Free"],"topics":["http://edamontology.org/topic_3365","http://edamontology.org/topic_3571","http://edamontology.org/topic_3366","http://edamontology.org/topic_3572","http://edamontology.org/topic_0625","http://edamontology.org/topic_0780","http://edamontology.org/topic_0091"],"keywords":["Données"],"prerequisites":["Attendees will bring their own data"],"openTo":"Internal personnel","accessConditions":"For H2020-AGENT project members only","maxParticipants":null,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/504/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/8/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[{"id":21,"name":"H2020-AGENT","url":"https://catalogue.france-bioinformatique.fr/api/eventsponsor/H2020-AGENT/?format=json"}],"organisedByOrganisations":[{"id":39,"name":"URGI - US1164","url":"https://catalogue.france-bioinformatique.fr/api/organisation/URGI%20-%20US1164/?format=json"},{"id":82,"name":"INRAE","url":"https://catalogue.france-bioinformatique.fr/api/organisation/INRAE/?format=json"}],"organisedByTeams":[{"id":26,"name":"URGI","url":"https://catalogue.france-bioinformatique.fr/api/team/URGI/?format=json"}],"logo_url":"https://urgi.versailles.inra.fr/extension/inra/design/urgi/images/logoURGI_res72_2-82X1-98.png","updated_at":"2025-09-13T13:27:42.544621Z","audienceTypes":["Graduate","Professional (initial)","Professional (continued)"],"audienceRoles":["All"],"difficultyLevel":"Novice","trainingMaterials":[],"learningOutcomes":"","hoursPresentations":null,"hoursHandsOn":null,"hoursTotal":null,"personalised":true,"event_set":["https://catalogue.france-bioinformatique.fr/api/event/737/?format=json","https://catalogue.france-bioinformatique.fr/api/event/735/?format=json"]},{"id":306,"name":"Molecular Phylogeny - Level 1","shortName":"Phylogénie moléculaire - Niveau 1","description":"OBJECTIF\r\n- Savoir inférer un arbre phylogénétique et l'interpréter\r\n\r\nPRÉREQUIS\r\n- Savoir ce à quoi correspondent des séquences génétiques homologues\r\n- Avoir déjà utilisé les logiciels de base en bioinformatique\r\n- Connaître les notions de base en statistiques (tests, lois probabilistes usuelles, méthodes simples d'estimation de paramètres)\r\n- Avoir des notions de programmation\r\n\r\nPROGRAMME\r\n- Lignes de commandes Linux\r\n- Le format Newick\r\n- Dessin d'arbres\r\n- Alignements multiples et nettoyage\r\n- Modèles d'évolution\r\n- Choix de modèles\r\n- Définitions et propriétés des arbres\r\n- Méthodes de parcimonie\r\n- Méthodes de distance\r\n- Maximum de vraisemblance\r\n- Reconstruction phylogénétique Bayésienne\r\n- Bootstraps et autres supports de branches","homepage":"","is_draft":false,"costs":["1200 €"],"topics":["http://edamontology.org/topic_3299","http://edamontology.org/topic_0084","http://edamontology.org/topic_3293"],"keywords":[],"prerequisites":[],"openTo":"Everyone","accessConditions":"","maxParticipants":12,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/241/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[{"id":1,"name":"CNRS formation entreprises","url":"https://catalogue.france-bioinformatique.fr/api/organisation/CNRS%20formation%20entreprises/?format=json"}],"organisedByTeams":[{"id":7,"name":"ATGC","url":"https://catalogue.france-bioinformatique.fr/api/team/ATGC/?format=json"}],"logo_url":"https://ressources.france-bioinformatique.fr/sites/default/files/ATGClogox120_0.png","updated_at":"2023-01-24T10:44:55.936489Z","audienceTypes":["Professional (continued)"],"audienceRoles":[],"difficultyLevel":"Novice","trainingMaterials":[],"learningOutcomes":"To know how to infer a phylogenetic tree and interpret it.","hoursPresentations":null,"hoursHandsOn":null,"hoursTotal":null,"personalised":true,"event_set":["https://catalogue.france-bioinformatique.fr/api/event/460/?format=json","https://catalogue.france-bioinformatique.fr/api/event/509/?format=json"]},{"id":309,"name":"EBAII A&A - Ecole EBAII Assemblage & Annotation / Assembly & Annotation EBAII school","shortName":"EBAII Assemblage & Annotation / Assembly & Annotation EBAii school","description":"Objectifs\r\nLa formation s’adresse à des biologistes directement impliqués dans des projets “Next Generation Sequencing” (NGS), pour l'assemblage et l'annotation de novo de génomes. Cette édition de l’école aborde les nouveaux enjeux technologiques: elle s’articulera autour des différentes étapes qui mèneront à l’obtention d’un génome annoté à partir de données “long reads” et “hybride” : contrôle qualité des données, assemblage, scaffolding, polishing, annotation structurale et fonctionnelle (en session parallèle pour les procaryotes et les eucaryotes). \r\nL’école vise à introduire les concepts, à manipuler les outils informatiques et à en interpréter les résultats. Elle est basée sur une alternance de courtes sessions théoriques et d’ateliers pratiques. Les participants bénéficieront d’un tutorat personnalisé pour élaborer leur plan d’analyse, et effectuer les premières étapes de traitement de leurs propres données ou de celles de leur équipe.\r\nAttention : le tutorat n'a pas pour vocation de réaliser l’analyse complète des données des participants.\r\nPublic visé\r\nCette formation est destinée aux biologistes (ingénieurs, doctorants, chercheurs, enseignants-chercheurs, praticiens…) confrontés à l’analyse de données NGS, et qui ne disposent pas des compétences bioinformatiques suffisantes.","homepage":"https://www.france-bioinformatique.fr/formation/ebaii2022_genomique/","is_draft":false,"costs":[],"topics":[],"keywords":[],"prerequisites":[],"openTo":"Everyone","accessConditions":"","maxParticipants":40,"contacts":[],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[],"organisedByTeams":[],"logo_url":"https://cvt.aviesan.fr/wp-content/themes/cvtaviesan/images/logo_cvt.png","updated_at":"2024-12-05T09:11:55.721141Z","audienceTypes":[],"audienceRoles":[],"difficultyLevel":"Novice","trainingMaterials":[],"learningOutcomes":"Initiation au traitement des données de génomique obtenues par séquençage à haut débit\r\nAssemblage et annotation de novo de génomes\r\nL’école vise à introduire les concepts, à manipuler les outils informatiques et à en interpréter les résultats. Elle est basée sur une alternance de courtes sessions théoriques et d’ateliers pratiques. Les participants bénéficieront d’un tutorat personnalisé pour élaborer leur plan d’analyse, et effectuer les premières étapes de traitement de leurs propres données ou de celles de leur équipe.","hoursPresentations":null,"hoursHandsOn":null,"hoursTotal":null,"personalised":true,"event_set":["https://catalogue.france-bioinformatique.fr/api/event/463/?format=json"]},{"id":310,"name":"Diplôme Universitaire en Bioinformatique Intégrative / University Diploma in Integrative Bioinformatics","shortName":"DUBii","description":"La bioinformatique est devenue une compétence incontournable pour l'analyse de données de natures diverses : génomes, transcriptomes, protéomes, métabolomes, structures macromoléculaires, réseaux d'interactions. L'appropriation par les biologistes des méthodes et des outils de biostatistique et bioinformatique intégrative est un enjeu majeur pour la montée en compétence des équipes de recherche et des plateformes de service.\r\n\r\nL'université de Paris propose en partenariat avec l'Institut Français de Bioinformatique (IFB) la troisième édition du Diplôme Universitaire en Bioinformatique intégrative (DUBii). Cette formation s’adresse en priorité à des biologistes ou à des médecins souhaitant évoluer en compétences ou envisager une reconversion professionnelle et 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). \r\n\r\nLe DUBii fournira une formation théorique et pratique, complétée par une période d'immersion de 20 jours 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. 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