Training List
Handles creating, reading and updating training events.
GET /api/training/?format=api&offset=320&ordering=accessConditions
{ "count": 391, "next": "https://catalogue.france-bioinformatique.fr/api/training/?format=api&limit=20&offset=340&ordering=accessConditions", "previous": "https://catalogue.france-bioinformatique.fr/api/training/?format=api&limit=20&offset=300&ordering=accessConditions", "results": [ { "id": 138, "name": "Rôles multiples de l’ARN", "shortName": "", "description": "Ce cours théorique et pratique de deux semaines est orienté sur les méthodes pour étudier la synthèse, maturation et la dégradation d’une large variété de molécules d’ARN dans les cellules eucaryotes - voir plus\n", "homepage": "https://www.pasteur.fr/fr/enseignement/programmes-doctoraux-et-cours/cours-paste…", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Analysis of RNAseq data", "Transcriptomics (RNA-seq)", "NGS Sequencing Data Analysis" ], "prerequisites": [ "Master" ], "openTo": "Internal personnel", "accessConditions": "Les candidats doivent avoir de bonnes connaissances en génétique, biologie moléculaire et biochimie du niveau de la fin de première année de Master, ainsi qu’un niveau minimum (B1) en français ET en anglais. Les candidatures sont sélectionnées et évaluées par le Comité du cours.\n", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [], "logo_url": "", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/268/?format=api" ] }, { "id": 123, "name": "Master Bio-informatique", "shortName": "", "description": "Forme au traitement et à l'analyse des données « à haut débit » (génomique, transcriptomique, protéomique, métabolomique). Cette formation inclus l’acquisition des connaissances fondamentales et des compétences opérationnelles liées à l’interprétation de ce type de données, à travers des enseignements de biologie, bioinformatique, informatique et statistiques appliquées à la Biologie. Elle se caractérise par une formation orientée vers le développement de web services et l’usage de ressources de calcul distribuées.\n \n", "homepage": "", "is_draft": false, "costs": [ "Priced" ], "topics": [], "keywords": [], "prerequisites": [ "Master" ], "openTo": "Internal personnel", "accessConditions": "Licence de biologie / lic. Pro sur dossier\n", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [], "logo_url": "", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [] }, { "id": 81, "name": "Master Sciences & Numérique pour la Santé", "shortName": "", "description": "La spécialité BCD a pour objectif de former les étudiants issus des Sciences du vivant (agronomie, biologie moléculaire, cellulaire, physiologie animale et végétale, biochimie), des sciences médicales, de l'informatique ou des mathématiques aux besoins spécifiques de la bioinformatique, des systèmes d'informations, de l'extraction de connaissances et de la modélisation du vivant tout en renforçant les compétences de leur profil initial.\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [], "prerequisites": [ "Master" ], "openTo": "Internal personnel", "accessConditions": "M1 : licence math, info, physique, EEA, biologie, STAPS + équiv. L3 de la formation pharma/médecine (ou tout équiv. 180 ECTS acquis) - M2 : master 1 ou équiv. (formation continue, VAE, ...)\n", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [], "logo_url": "", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [] }, { "id": 344, "name": "Analyses Single Cell RNA-seq (ScRNA-seq) avec R", "shortName": "", "description": "Cette formation introduira notamment la librairie Seurat permettant la manipulation et l'analyse de données Single Cell RNA-seq ainsi que la visualisation des résultats d'analyse\r\n\r\n- Rappels des concepts du séquençage Single Cell RNA-seq\r\n- Importation des données Single Cell dans R\r\n- Intégration de données Single Cell multiples\r\n- Quality Check et pré-traitement des données\r\n- Normalisation de données\r\n- Identification de marqueurs\r\n- Clustering et assignation cellulaire\r\n- Analyse différentielle des groupes cellulaires\r\n- Savoir intégrer les données de spatialisation\r\n- Savoir intégrer les données de trajectoire\r\n- Savoir intégrer les données de communication cellulaire\r\n- Savoir intégrer les données d'épigénétique (ATAC-seq)", "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", "maxParticipants": 12, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/154/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [ { "id": 6, "name": "CNRS formation entreprise", "url": "https://catalogue.france-bioinformatique.fr/api/eventsponsor/CNRS%20formation%20entreprise/?format=api" } ], "organisedByOrganisations": [ { "id": 1, "name": "CNRS formation entreprises", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/CNRS%20formation%20entreprises/?format=api" } ], "organisedByTeams": [ { "id": 6, "name": "CBiB", "url": "https://catalogue.france-bioinformatique.fr/api/team/CBiB/?format=api" } ], "logo_url": "https://services.cbib.u-bordeaux.fr/utils/logo_cbib.png", "updated_at": "2023-08-31T09:19:56.754683Z", "audienceTypes": [ "Graduate", "Professional (initial)" ], "audienceRoles": [ "Biologists", "Bioinformaticians" ], "difficultyLevel": "Intermediate", "trainingMaterials": [], "learningOutcomes": "- Savoir expertiser et manipuler des données issues d'expériences Single Cell RNA-seq\r\n- Savoir mener une analyse différentielle à de multiples niveaux\r\n- Savoir intégrer des données complémentaires pour l'analyse Single Cell RNA-seq (spatial, trajectoire, cell communication, cell identification...)", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/650/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/653/?format=api" ] }, { "id": 139, "name": "Programmation et scripting ", "shortName": "", "description": " Ce cours s'adresse à toute personne de l'institut Pasteur ou appartenant au réseau international (RIIP) souhaitant acquérir des bases de la programmation et du scripting utiles à la bioinformatique et ayant du mal à trouver du temps pour se former tout le long de l'année. \nInitiation unix 3 jours\nProgrammation Python 6 jours\nUtilisation d'un cluster de calcul 1 jour\nBiopython 2 jours\n \n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Programming Languages & Computer Sciences", "Autres langages" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Membre de l'institut Pasteur ou au réseau international de l'Institut Pasteur (RIIP)\n", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [], "logo_url": "", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [] }, { "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 development" ], "prerequisites": [], "openTo": "Everyone", "accessConditions": "NA", "maxParticipants": 20, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/810/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/762/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/116/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [ { "id": 3, "name": "IFB", "url": "https://catalogue.france-bioinformatique.fr/api/eventsponsor/IFB/?format=api" } ], "organisedByOrganisations": [ { "id": 43, "name": "IFB-core", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/IFB-core/?format=api" } ], "organisedByTeams": [ { "id": 29, "name": "IFB Core", "url": "https://catalogue.france-bioinformatique.fr/api/team/IFB%20Core/?format=api" } ], "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=api", "https://catalogue.france-bioinformatique.fr/api/event/803/?format=api" ] }, { "id": 1, "name": "Formation de base", "shortName": "", "description": "None EN\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "None EN\n", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [], "logo_url": "", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/202/?format=api" ] }, { "id": 393, "name": "Pandas : gérer, analyser, visualiser vos données efficacement", "shortName": "", "description": "Les objectifs de cette formation sont :\r\n- Importer, exporter, gérer, analyser des données tabulaires\r\n- Calculer des données dérivées\r\n- Combiner et interroger des données complexes\r\n- Calculer des statistiques descriptives des données\r\n- Visualiser et synthétiser les données sous formes graphiques", "homepage": "https://cnrsformation.cnrs.fr/python-et-module-pandas-pour-gerer-et-analyser-donnees?mc=Pandas", "is_draft": false, "costs": [ "Priced" ], "topics": [ "http://edamontology.org/topic_0091" ], "keywords": [ "Python Language" ], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Everyone", "accessConditions": "- Notions de base en informatique : fichiers, répertoire, organisation des données\r\n- Connaissance de base de la programmation en Python (activité régulière d'écriture de scripts en Python)\r\n- Maitrise d'un environnement de développement ou éditeur de programmes/scripts", "maxParticipants": 12, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/528/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [ { "id": 6, "name": "CNRS formation entreprise", "url": "https://catalogue.france-bioinformatique.fr/api/eventsponsor/CNRS%20formation%20entreprise/?format=api" } ], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 7, "name": "ATGC", "url": "https://catalogue.france-bioinformatique.fr/api/team/ATGC/?format=api" } ], "logo_url": "http://www.atgc-montpellier.fr/pictures/ATGClogo.svg", "updated_at": "2025-02-11T08:32:41.454179Z", "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "Jour 1\r\nMatin :\r\n- Initiation Pandas, structures de données Series et DataFrame, chargement de données à partir de fichiers de données tabulaires\r\nAprès-midi :\r\n- Requêtes et outils de sélection\r\n\r\nJour 2\r\nMatin :\r\n- Fusion, concaténation, jointure de tables, regroupement de sous-ensembles\r\nAprès-midi :\r\n- Indexation simple et multiple, réindexation, export et sauvegarde\r\n\r\nJour 3\r\nMatin :\r\n- Visualisation et réalisation de graphiques\r\nAprès-midi :\r\n- Analyse de données des participants", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": 21, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/702/?format=api" ] }, { "id": 38, "name": "Workshop, introduction to JalView editor", "shortName": "", "description": "in collaboration with the developers of Jalview\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Autre" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Open access after registration\n", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [], "logo_url": "", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [] }, { "id": 312, "name": "Introduction to python", "shortName": "", "description": "This course provides an introduction to programming using python. At the end of the training, participants should be able to write simple python programs to handle biological data and to understand more complex programs written by others.\r\nNote : This course in currently available only in french", "homepage": "https://southgreenplatform.github.io/trainings//python/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": 15, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 10, "hoursHandsOn": 18, "hoursTotal": null, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/470/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/556/?format=api" ] }, { "id": 257, "name": "Metabarcoding analyses (using FROGS in Galaxy and Phyloseq)", "shortName": "", "description": "This course offers an introduction to metabarcoding analyses at two different levels/steps: bioinformatics with FROGS pipeline in the Galaxy environment, biostatistics with PhyloSeq R package. This includes preprocessing, clustering and OTU picking, taxonomic assignation, estimation of diversity, visualization of statistics results.\r\nPrerequisites\r\nGalaxy, R knowledge\r\n\r\nProgram\r\nIntroduction to metagenomics and metabarcoding\r\nPre-processing, Clustering, taxonomic affiliation (FROGS)\r\nHandling and visualizing OTU table using PhyloSeq R package (PhyloSeq)\r\n\r\n\r\nLearning objectives\r\nManipulate tools available for metabarcoding analysis\r\nStudy sample diversity by using NGS and post-NGS analysis tools\r\nVisualize diversity metrics in metabarcoding approach\r\n\r\n\r\nInstructors\r\nJulie Orjuela - julie.orjuela@ird.fr\r\nFlorentin Constancias - florentin.constancias@cirad.fr\r\nAlexis Dereeper - alexis.dereeper@ird.fr", "homepage": "https://southgreenplatform.github.io/trainings//metabarcoding/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2023-01-24T10:25:28.170059Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/566/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/389/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/535/?format=api" ] }, { "id": 349, "name": "Reproducible Research", "shortName": "", "description": "The following topics and tools are covered in the course:\r\n\r\n Data management\r\n Project organisation\r\n Git\r\n Conda\r\n Snakemake\r\n Nextflow\r\n R Markdown\r\n Jupyter\r\n Docker\r\n Singularity\r\n\r\nAt the end of the course, students should be able to:\r\n\r\n Use good practices for data analysis and management\r\n Clearly organise their bioinformatic projects\r\n Use the version control system Git to track and collaborate on code\r\n Use the package and environment manager Conda\r\n Use and develop workflows with Snakemake and Nextflow\r\n Use R Markdown and Jupyter Notebooks to document and generate automated reports for their analyses\r\n Use Docker and Singularity to distribute containerized computational environments", "homepage": "https://southgreenplatform.github.io/training_reproducible_research/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": 20, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2023-12-04T15:16:00.921744Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "trainingMaterials": [], "learningOutcomes": "At the end of the course, students should be able to:\r\n\r\n Use good practices for data analysis and management\r\n Clearly organise their bioinformatic projects\r\n Use the version control system Git to track and collaborate on code\r\n Use the package and environment manager Conda\r\n Use and develop workflows with Snakemake and Nextflow\r\n Use R Markdown and Jupyter Notebooks to document and generate automated reports for their analyses\r\n Use Docker and Singularity to distribute containerized computational environments", "hoursPresentations": 8, "hoursHandsOn": 13, "hoursTotal": 21, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/567/?format=api" ] }, { "id": 256, "name": "RNASeq analyses (using Galaxy and TOGGLe)", "shortName": "", "description": "This course offers an introduction to RNASeq analyses using two different workflow management systems: Galaxy and TOGGLe. This includes reference-based mapping, estimates of transcript levels, differential expression (DE) analyses, visualization of statistics results.\r\nPrerequisites\r\nWorkflow management system (Galaxy, TOGGLe)\r\n\r\nProgram\r\nMapping of RNASeq against a transcriptome reference with kallisto (Galaxy)\r\nMapping of RNASeq against an annotated genome reference with TopHat (TOGGLe)\r\nDifferential expression analysis using EdgeR and DESeq2\r\nPlots, clustering, co-expression network: degust, WGCNA\r\n\r\n\r\nLearning objectives\r\nManipulate packages/tools available for searching DE genes\r\nThink about different normalisation methods\r\nDetect differentially expressed genes\r\nCompare results between two approaches\r\n\r\n\r\nInstructors\r\nAlexis Dereeper - alexis.dereeper@ird.fr\r\nSebastien Cunnac - sebastien.cunnac@ird.fr\r\nSebastien Ravel - sebastien.ravel@cirad.fr\r\nChristine Tranchant - christine.tranchant@ird.fr", "homepage": "https://southgreenplatform.github.io/trainings//rnaseq/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2023-01-24T10:26:00.180547Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/388/?format=api" ] }, { "id": 294, "name": "Linux for Dummies", "shortName": "", "description": "This course offers an introduction to work with Linux. We will describe the Linux environment, the first linux commands so participants can start to utilize command-line tools and feel comfortable using bioinformatics softwares through a linux terminal", "homepage": "https://southgreenplatform.github.io/trainings//linux/", "is_draft": false, "costs": [], "topics": [], "keywords": [], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": 15, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2023-12-04T15:05:31.847400Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 3, "hoursHandsOn": 4, "hoursTotal": 7, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/468/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/555/?format=api" ] }, { "id": 313, "name": "RNA-Seq analysis", "shortName": "", "description": "Introduction to RNA-Seq analysis", "homepage": "https://southgreenplatform.github.io/trainings//rnaseq/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": 15, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2023-12-04T15:04:39.023455Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 6, "hoursHandsOn": 8, "hoursTotal": 14, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/473/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/471/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/563/?format=api" ] }, { "id": 347, "name": "Introduction to Microbial Comparative Genomics", "shortName": "", "description": "This course offers an introduction to microbial genomics analysis.\r\nIt includes 5 issues: assembly, genome annotation, circos visualization, pan-genome construction, pan-GWAS.", "homepage": "https://southgreenplatform.github.io/trainings//bacterialGenomics/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [ "genomics", "Structural genomics", "Genome analysis" ], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": 20, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/174/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/771/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/772/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/773/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2023-12-04T14:54:55.468140Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 5, "hoursHandsOn": 5, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/558/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/561/?format=api" ] }, { "id": 322, "name": "Introduction to Structural variant detection analyses", "shortName": "", "description": "Program\r\n\r\n* Handling mapping tools suitable for ILLUMINA and ONT data (bwa, minimap2)\r\n* SNP detection from mapping of short reads against a reference genome: SNP calling, filters and SNP annotation. Examples of possible studies based on SNP arrays\r\n* Detecting Structural Variations (SV) in short and long reads (breakdancer, sniffle)\r\n* SV detection from genome assembly and comparison (minimap2, nucmer, assemblytics, siry)", "homepage": "https://southgreenplatform.github.io/trainings//sv/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [ "Linux and knowledge of NGS formats" ], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2023-01-24T10:41:28.470404Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 14, "hoursHandsOn": 14, "hoursTotal": 28, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/564/?format=api" ] }, { "id": 250, "name": "Linux For Jedi", "shortName": "", "description": "This course offers to develop and enhance advanced Linux shell command line and scripting skills for the processing and analysis of NGS data. We will work on a HPC server and use linux powerful commands to allow to analyze big amount of biological data.", "homepage": "https://southgreenplatform.github.io/trainings/linuxJedi/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Internal personnel", "accessConditions": "Open to South Green close collaborators", "maxParticipants": 15, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 4, "hoursHandsOn": 10, "hoursTotal": 14, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/469/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/382/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/560/?format=api" ] }, { "id": 348, "name": "Advanced HPC Trainings", "shortName": "", "description": "This course continues the explanation on how to work on HPC Southgreen clusters. It is intended for experienced users, with the goals of improving LC user productivity and minimizing the obstacles. New notions and tools are presented such as job arrays, basic softwares installation,module environment and singularity. All these notions will be developped.", "homepage": "https://southgreenplatform.github.io/trainings//Advanced_HPC/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [ "HPC", "SLURM" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Oprn to South Green close collaborators", "maxParticipants": 20, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/589/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 85, "name": "IRD", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/IRD/?format=api" } ], "organisedByTeams": [ { "id": 24, "name": "South Green", "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api" } ], "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png", "updated_at": "2023-12-04T14:46:58.108350Z", "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "All" ], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/557/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/565/?format=api" ] }, { "id": 40, "name": "Formation ABiMS", "shortName": "", "description": "L'offre de formation repose sur des modules de formation d'initiation aux environnements (Linux, Cluster, etc.), d'utilisation des outils (Galaxy, etc.) et langages (PERL, R, etc.), et de compréhension des méthodes (RNA-seq, Analyses statistiques, etc.). ABiMS est également en mesure de proposer des formations à façon pour des communautés (e.g. Métabolomique) ou des projets (École thématique).\nUniversitaires.\n \nGalaxy pour l'analyse de données métabolomique (1 jour)\nCluster (1 jour)\nLinux Initiation (1 jour)\nLinux avancé (1 jour)\nLinux scripting (1 jour)\nGalaxy initiation (1 jour)\nGalaxy RNAseq de novo/avec référence & cleaning (2 jours)\nGalaxy : initiation à la phylogénie (2 jours)\nR initiation (1 jour)\nR avancé (1 jour)\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Autre" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Ouvert à tous avec facturation\n", "maxParticipants": null, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [], "logo_url": "", "updated_at": "2022-06-02T11:50:50.812642Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [] } ] }
