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No specific bioinformatics skill is required: detailed instruction on the algorithm developed in each annotation methods can be found in specific training courses on «Genomic sequences analysis». Here we focus on the general idea behind each method and, above all, the way you can interpret the corresponding results and combine them with other evidences in order to change or correct the current automatic functional annotation of a given gene, if necessary.\r\n\r\nThis course will also describe how to perform effective searches and analysis of procaryotic data using the graphical functionalities of the MaGe’s interfaces. Because of the numerous pre-computation available in our system (results of “common” annotation tools, synteny with all complete bacterial genomes, metabolic pathway reconstruction, fusion/fission events, genomic islands, …), many practical exercises allow attendees to get familiar with the use the MaGe graphical interfaces in order to efficiently explore these sets of results.","homepage":"https://labgem.genoscope.cns.fr/professional-trainings/microscope-professional-trainings/training-annotation-analysis-of-prokaryotic-genomes-using-the-microscope-platform/","is_draft":false,"costs":["2500 € for private companies","1350 € for academics","945 € for students"],"topics":["http://edamontology.org/topic_0085","http://edamontology.org/topic_3301","http://edamontology.org/topic_0797"],"keywords":["Genome analysis","Sequence annotation"],"prerequisites":["Licence"],"openTo":"Everyone","accessConditions":"External training sessions can also be scheduled on demand, in France or abroad. 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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.\r\n\r\nAll the classes will be taught in English","homepage":"https://moodle.france-bioinformatique.fr/course/view.php?id=27","is_draft":false,"costs":["Priced"],"topics":[],"keywords":["Single-Cell Sequencing","long read sequencing","spatial transcriptomics"],"prerequisites":["Master","Autre (Diplôme universitaire, école d'ingénieur ...)"],"openTo":"Everyone","accessConditions":"Participants must have prior experience on NGS data analysis with everyday use of R and/or Python and good knowledge of Unix command line. Before the training, participants are advised to familiarize themselves with the processing and primary analyses steps of scRNA-seq datasets. \r\nIt is not necessary to have personal single-cell data to analyse.","maxParticipants":30,"contacts":[],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[{"id":48,"name":"Institut Pasteur","url":"https://catalogue.france-bioinformatique.fr/api/organisation/Institut%20Pasteur/?format=json"},{"id":4,"name":"IFB - ELIXIR-FR","url":"https://catalogue.france-bioinformatique.fr/api/organisation/IFB%20-%20ELIXIR-FR/?format=json"}],"organisedByTeams":[],"logo_url":"https://github.com/IFB-ElixirFr/Training/blob/main/logo_sincellte.png?raw=true","updated_at":"2024-03-20T16:00:20.423462Z","type":"Training course","start_date":"2024-10-20","end_date":"2024-10-25","venue":"Station Biologique","city":"Roscoff","country":"France","geographical_range":"International","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2024-03-12","registration_closing":"2024-05-07","registration_status":"closed","courseMode":"Onsite"},{"id":613,"name":"Les langages de workflows pour une analyse bioinformatique reproductible - session 2024 / Workflow languages for reproducible bioinformatics analysis -2024 session","shortName":"WF4bioinfo 2024","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=29","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":"2024-03-28T10:04:12.722566Z","type":"Training course","start_date":"2024-10-14","end_date":"2024-10-16","venue":"","city":"Paris","country":"France","geographical_range":"National","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2024-03-01","registration_closing":"2024-06-30","registration_status":"closed","courseMode":"Onsite"},{"id":571,"name":"Développement d’une application avec R Shiny (session 2024)","shortName":"Shiny application development (2024)","description":"Objectifs pédagogiques\r\n\r\nÀ l’issue de la formation, les stagiaires connaîtront les principes de bases et le fonctionnement du package “Shiny”. Ils et elles seront capables de créer leurs premières applications web interactives à partir de scripts R. Les solutions de déploiement d’applications Shiny seront également abordées.\r\n\r\nProgramme\r\n\r\nPrincipes généraux et fonctionnement d’une application Shiny\r\nDéveloppement d’applications Shiny\r\nDéploiement d’applications Shiny","homepage":"https://documents.migale.inrae.fr/trainings.html","is_draft":false,"costs":["Priced"],"topics":["http://edamontology.org/topic_0605"],"keywords":["Shiny"],"prerequisites":["Basic knowledge of R"],"openTo":"Everyone","accessConditions":"","maxParticipants":10,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/769/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[{"id":88,"name":"BioinfOmics","url":"https://catalogue.france-bioinformatique.fr/api/organisation/BioinfOmics/?format=json"}],"organisedByTeams":[{"id":10,"name":"MIGALE","url":"https://catalogue.france-bioinformatique.fr/api/team/MIGALE/?format=json"}],"logo_url":"https://migale.inrae.fr/sites/default/files/migale-orange_0.png","updated_at":"2024-01-17T10:46:26.358781Z","type":"Training course","start_date":"2024-03-14","end_date":"2024-03-14","venue":"https://migale.inrae.fr/how-to-come","city":"Jouy-en-Josas","country":"France","geographical_range":"","trainers":["https://catalogue.france-bioinformatique.fr/api/userprofile/415/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/175/?format=json","https://catalogue.france-bioinformatique.fr/api/userprofile/743/?format=json"],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2024-01-08","registration_closing":"2024-02-29","registration_status":"closed","courseMode":"Onsite"},{"id":477,"name":"Cluster - session 2022/10/11","shortName":"","description":"This training session is designed to help you deal with the platform compute cluster and data banks. You will launch your first processing batch on the cluster and will learn how to track and manage them. Organized jointly by the Sigenae and bioinfo genotoul platforms.","homepage":"http://bioinfo.genotoul.fr/index.php/events/cluster-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":[],"keywords":["Linux","Cluster"],"prerequisites":["Linux - Basic Knowledge"],"openTo":"Everyone","accessConditions":"","maxParticipants":10,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[],"organisedByTeams":[{"id":22,"name":"Genotoul-bioinfo","url":"https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=json"}],"logo_url":null,"updated_at":"2023-05-17T10:14:33.722250Z","type":"Training course","start_date":"2022-10-11","end_date":"2022-10-11","venue":"","city":"Castanet Tolosan","country":"France","geographical_range":"","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2022-03-08","registration_closing":"2022-10-04","registration_status":"closed","courseMode":"Online"},{"id":462,"name":"Principes FAIR dans un projet de bioinformatique - Session 2022","shortName":"FAIR bioinfo - session 2022","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=9&username=guest","is_draft":false,"costs":["Priced"],"topics":["http://edamontology.org/topic_0769"],"keywords":["Computing Environments","NGS Sequencing Data Analysis","Workflow development"],"prerequisites":[],"openTo":"Everyone","accessConditions":"","maxParticipants":15,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/116/?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":[],"logo_url":"https://www.france-bioinformatique.fr/wp-content/uploads/logo-ifb-couleur.svg","updated_at":"2022-06-02T11:50:50.627601Z","type":"Training course","start_date":"2022-06-13","end_date":"2022-06-15","venue":"","city":"Paris","country":"France","geographical_range":"National","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":"2022-01-26","registration_closing":"2022-04-15","registration_status":"closed","courseMode":"Onsite"},{"id":458,"name":"Initiation à Git / Git Initiation - 2021 Session 2","shortName":"Git Initiation - 2021 S2","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":["https://catalogue.france-bioinformatique.fr/api/userprofile/299/?format=json"],"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":"2022-10-07T08:23:00.426374Z","type":"Training course","start_date":"2022-01-21","end_date":null,"venue":"","city":"Roscoff","country":"France","geographical_range":"National","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"past","registration_opening":null,"registration_closing":"2021-12-15","registration_status":"closed","courseMode":"Onsite"},{"id":599,"name":"Introduction au profilage taxonomique et visualisation de communautés microbiennes à partir de données métagénomiques avec Galaxy","shortName":"","description":"L’objectif de cette formation est de se familiariser avec les étapes et les outils d’analyse de données de métagénomiques pour caractériser et visualiser des communautés microbiennes. 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No specific bioinformatics skill is required: detailed instruction on the algorithm developed in each annotation methods can be found in specific training courses on «Genomic sequences analysis». Here we focus on the general idea behind each method and, above all, the way you can interpret the corresponding results and combine them with other evidences in order to change or correct the current automatic functional annotation of a given gene, if necessary.\r\n\r\nThis course will also describe how to perform effective searches and analysis of procaryotic data using the graphical functionalities of the MaGe’s interfaces. Because of the numerous pre-computation available in our system (results of “common” annotation tools, synteny with all complete bacterial genomes, metabolic pathway reconstruction, fusion/fission events, genomic islands, …), many practical exercises allow attendees to get familiar with the use the MaGe graphical interfaces in order to efficiently explore these sets of results.","homepage":"https://labgem.genoscope.cns.fr/professional-trainings/microscope-professional-trainings/training-annotation-analysis-of-prokaryotic-genomes-using-the-microscope-platform/","is_draft":false,"costs":["Priced"],"topics":["http://edamontology.org/topic_0085","http://edamontology.org/topic_3301","http://edamontology.org/topic_0797"],"keywords":[],"prerequisites":["Licence"],"openTo":"Everyone","accessConditions":"External training sessions can also be scheduled on demand, in France or abroad. See : https://labgem.genoscope.cns.fr/professional-trainings/microscope-professional-trainings/external-microscope-professional-training-sessions/","maxParticipants":12,"contacts":["https://catalogue.france-bioinformatique.fr/api/userprofile/90/?format=json"],"elixirPlatforms":[],"communities":[],"sponsoredBy":[{"id":15,"name":"Laboratory of Bioinformatics Analyses for Genomics and Metabolism","url":"https://catalogue.france-bioinformatique.fr/api/eventsponsor/Laboratory%20of%20Bioinformatics%20Analyses%20for%20Genomics%20and%20Metabolism/?format=json"}],"organisedByOrganisations":[{"id":67,"name":"University Paris-Saclay","url":"https://catalogue.france-bioinformatique.fr/api/organisation/University%20Paris-Saclay/?format=json"}],"organisedByTeams":[{"id":9,"name":"MicroScope","url":"https://catalogue.france-bioinformatique.fr/api/team/MicroScope/?format=json"}],"logo_url":"https://labgem.genoscope.cns.fr/wp-content/uploads/2019/06/MicroScope_logo-300x210.png","updated_at":"2026-03-26T14:14:19.457285Z","type":"Training course","start_date":"2026-12-07","end_date":"2026-12-11","venue":"","city":"Evry","country":"France","geographical_range":"","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"future","registration_opening":"2026-03-26","registration_closing":"2026-11-09","registration_status":"open","courseMode":"Onsite"}]}