Training List
Handles creating, reading and updating training events.
GET /api/training/?format=api&offset=320&ordering=-prerequisites
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"https://www.imgt.org/IMGTeducation/webinar.php", "is_draft": false, "costs": [], "topics": [ "http://edamontology.org/topic_2814", "http://edamontology.org/topic_3930", "http://edamontology.org/topic_3948" ], "keywords": [ "Protein structures", "Immunogenetics", "Monoclonal antibody" ], "prerequisites": [ "none" ], "openTo": "Everyone", "accessConditions": "free inscription", "maxParticipants": null, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/339/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 46, "name": "IMGT", "url": "https://catalogue.france-bioinformatique.fr/api/team/IMGT/?format=api" } ], "logo_url": null, "updated_at": "2024-12-04T10:46:29.357307Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": 1, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/654/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/656/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/657/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/672/?format=api" ] }, { "id": 295, "name": "Introduction to the use of a computing cluster", "shortName": "", "description": "Knowledge of the concepts and best practices for using the computing resources of the mesocenter cluster Clermont Auvergne in a bioinformatics context.\r\nBecome familiar with the work environment of the computing cluster, become autonomous in the use of its resources and learn to use a scheduler. \r\nPresentation of the resources accessible on the cluster (computing nodes, storage spaces, tools).\r\nConcept of jobs, queues and parallel computing.\r\nJob management (submission, follow-up, deletion).", "homepage": "https://mesocentre.uca.fr/", "is_draft": false, "costs": [ "Free to academics" ], "topics": [ "http://edamontology.org/topic_0091", "http://edamontology.org/topic_0605" ], "keywords": [], "prerequisites": [ "Linux and knowledge of NGS formats" ], "openTo": "Internal personnel", "accessConditions": "Have an account on the Mesocentre UCA computing cluster (make a request if necessary on the site https://hub.mesocentre.uca.fr)\r\nAlternation of theoretical courses and practical work.\r\nCOME WITH A LAPTOP with an operational Eduroam connection.\r\nThe training is in French.", "maxParticipants": 10, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 45, "name": "UMR 454 MEDIS INRA-Université Clermont Auvergne", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/UMR%20454%20MEDIS%20INRA-Universit%C3%A9%20Clermont%20Auvergne/?format=api" } ], "organisedByTeams": [ { "id": 31, "name": "AuBi", "url": "https://catalogue.france-bioinformatique.fr/api/team/AuBi/?format=api" } ], "logo_url": null, "updated_at": "2023-01-24T10:21:58.347905Z", "audienceTypes": [ "Graduate" ], "audienceRoles": [ "Researchers", "Computer scientists" ], "difficultyLevel": "Novice", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 3, "hoursHandsOn": 4, "hoursTotal": 8, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/487/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/616/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/461/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/708/?format=api" ] }, { "id": 320, "name": "Ecole Thématique de Bioinformatique Intégrative / Integrative Bioinformatics Training School", "shortName": "ETBII", "description": "Dans l’objectif de développer et fédérer des compétences en bioinformatique intégrative au sein de la communauté, l’IFB propose une nouvelle école thématique ayant un double objectif :\r\n- une montée en compétences théoriques et pratiques des bioinformaticiens,\r\n- la constitution de matériel pédagogique partagé sur ce sujet.\r\n\r\nCette école rassemble une équipe pédagogique de 10 personnes et pourra accueillir 30 participants pour sa première édition.\r\nL’ensemble de la formation reposera sur l’utilisation des ressources de calcul et de la plateforme pédagogique de l’Institut Français de Bioinformatique.\r\n\r\nObjectifs pédagogiques \r\n\r\nLa formation a pour but :\r\n- d’introduire les concepts de bases et les différents types d’approches utilisées en bioinformatique intégrative,\r\n- de proposer un approfondissement et une mise en pratique d’une de ces approches sur un/des jeux de données intégrant différents types de données omiques. Cette mise en oeuvre permettra de balayer l’ensemble des points d’attention d’une analyse intégrative, de la préparation des données jusqu’à l’interprétation des résultats,\r\n- de créer, améliorer et partager les ressources pédagogiques (supports de formation, jeux de données, tutoriels) sur le thème de la bioinformatique intégrative.\r\n\r\nA la fin de cette formation les participants :\r\n- auront acquis un socle de connaissances générales en bioinformatique intégrative, \r\n- auront mis en oeuvre une analyse intégrative depuis la préparation des données jusqu’à l’analyse critique de résultats sur un/des jeux de données proposés lors de la formation,\r\n- auront contribué à constituer du matériel pédagogique partagé sur le sujet.\r\n\r\nPré-requis\r\n- Connaissances de base en Unix/shell, R et/ou Python \r\n- Autonomie dans la gestion de son poste de travail (installation de librairies et maîtrise des environnements de packaging type conda)", "homepage": "https://www.france-bioinformatique.fr/formation/etbii/", "is_draft": false, "costs": [ "770 TTC pour les académiques et 1540 TTC pour les privés" ], "topics": [ "http://edamontology.org/topic_0091", "http://edamontology.org/topic_3391", "http://edamontology.org/topic_3366" ], "keywords": [ "Methodology", "Biostatistics", "Biological network inference and analysis", "Dimension reduction", "Semantic web", "Integration of heterogeneous data", "Data Integration", "Tool integration" ], "prerequisites": [ "Linux and knowledge of NGS formats", "Basic knowledge of R" ], "openTo": "Everyone", "accessConditions": "Cette formation est ouverte à toute la communauté mais cette première édition s’adresse en priorité à des bioinformaticien·ne·s des plateformes membres et équipes associées IFB souhaitant contribuer à la constitution de matériel pédagogique pour se préparer au montage de futures formations sur ce thème.", "maxParticipants": 30, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/762/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [ { "id": 1, "name": "CNRS - IFB", "url": "https://catalogue.france-bioinformatique.fr/api/eventsponsor/CNRS%20-%20IFB/?format=api" } ], "organisedByOrganisations": [ { "id": 4, "name": "IFB", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/IFB/?format=api" } ], "organisedByTeams": [ { "id": 29, "name": "IFB Core", "url": "https://catalogue.france-bioinformatique.fr/api/team/IFB%20Core/?format=api" } ], "logo_url": "https://drive.google.com/file/d/1a_fuOgqOU812GRJLApGMofJ87WTlxDI0/view?usp=sharing", "updated_at": "2024-12-03T15:46:48.157120Z", "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "Life scientists", "Computer scientists", "Bioinformaticians" ], "difficultyLevel": "Novice", "trainingMaterials": [], "learningOutcomes": "A la fin de cette formation les participants :\r\n- auront acquis un socle de connaissances générales en bioinformatique intégrative, \r\n- auront mis en oeuvre une analyse intégrative depuis la préparation des données jusqu’à l’analyse critique de résultats sur un/des jeux de données proposés lors de la formation,\r\n- auront contribué à constituer du matériel pédagogique partagé sur le sujet.", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/489/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/505/?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": 287, "name": "Introduction to Oxford Nanopore Technology data analyses", "shortName": "Introduction to ONT data analyses", "description": "This course offers an introduction to ONT data analysis. It includes 5 issues: basecalling, reads quality control, assemblies and polishing/correction, contig quality and structural variants detection.", "homepage": "https://southgreenplatform.github.io/trainings//ont/", "is_draft": false, "costs": [ "Free" ], "topics": [ "http://edamontology.org/topic_3673", "http://edamontology.org/topic_0196", "http://edamontology.org/topic_3168" ], "keywords": [], "prerequisites": [ "Linux and knowledge of NGS formats" ], "openTo": "Everyone", "accessConditions": "", "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": "2023-01-24T10:21:58.467251Z", "audienceTypes": [ "Professional (initial)" ], "audienceRoles": [ "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "trainingMaterials": [ { "id": 1, "name": "SG-ONT-slides", "url": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/SG-ONT-slides/?format=api" } ], "learningOutcomes": "* Understanding limits and advantages of ONT technology\r\n* Manipulating ONT data on a virtual machine on jupyter environment\r\n* Handling mapping, assembly, polishing tools and be able to analyse your own data\r\n* Detecting structural variations using long reads", "hoursPresentations": 6, "hoursHandsOn": 6, "hoursTotal": 12, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/441/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/450/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/562/?format=api" ] }, { "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": 350, "name": "Formation Principes FAIR dans un projet de bioinformatique", "shortName": "FAIR-Bioinfo-Strasbourg", "description": "Cette formation sur 3 jours est destinée à des bioinformaticiens et biostatisticiens souhaitant acquérir des compétences théoriques et pratiques sur les principes \"FAIR\" (Facile à trouver, Accessible, Interopérable, Réutilisable) appliqués à un projet d'analyse et/ou de développement.", "homepage": "", "is_draft": false, "costs": [ "Free to academics" ], "topics": [], "keywords": [ "Programming Languages & Computer Sciences", "FAIR", "Snakemake", "Docker" ], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Everyone", "accessConditions": "Academics", "maxParticipants": 14, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/563/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/124/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 79, "name": "UPR2357", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/UPR2357/?format=api" }, { "id": 83, "name": "IGBMC", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/IGBMC/?format=api" } ], "organisedByTeams": [ { "id": 14, "name": "BiGEst", "url": "https://catalogue.france-bioinformatique.fr/api/team/BiGEst/?format=api" } ], "logo_url": null, "updated_at": "2023-12-20T15:44:00.254606Z", "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "Bioinformaticians" ], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "A l'issue de cette formation, les participants pourront mettre en oeuvre les principes de la science reproductible : encapsuler un environnement de travail (Docker, Singularity), concevoir et exécuter des workflows (Snakemake), gérer des versions de code (Git), passer à l’échelle sur un cluster de calcul (Slurm), gérer des environnements logiciels (Conda) et assurer la traçabilité de leur analyse à l’aide de Notebooks (Jupyter).", "hoursPresentations": 10, "hoursHandsOn": 11, "hoursTotal": 21, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/568/?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": 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": 378, "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=29", "is_draft": false, "costs": [], "topics": [ "http://edamontology.org/topic_0091", "http://edamontology.org/topic_0769" ], "keywords": [ "FAIR", "Reproducibility", "Nextflow", "Snakemake" ], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Everyone", "accessConditions": "", "maxParticipants": 20, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/116/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/326/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/804/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 4, "name": "IFB", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/IFB/?format=api" } ], "organisedByTeams": [ { "id": 38, "name": "PB-IBENS", "url": "https://catalogue.france-bioinformatique.fr/api/team/PB-IBENS/?format=api" } ], "logo_url": "https://moodle.france-bioinformatique.fr/pluginfile.php/1/core_admin/logocompact/300x300/1654772049/IFB-HAUT-COULEUR-PETIT.png", "updated_at": "2024-03-26T16:42:31.487108Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/664/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/613/?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": 363, "name": "Introduction au text-mining avec AlvisNLP", "shortName": "Introduction to text-mining with AlvisNLP", "description": "Objectifs pédagogiques\r\nCette formation est dédiée à l’analyse de données textuelles (text-mining). L’objectif est l’acquisition des principales techniques pour la Reconnaissance d’Entités Nommées (REN) à partir de textes. Les entités nommées étudiées dans cette formation sont des objets ou concepts d’intérêts mentionnés dans les articles scientifiques ou les champs en texte libre (taxons, gènes, protéines, marques, etc.).\r\n\r\nLes participants vont acquérir les compétences pratiques nécessaires pour effectuer de façon autonome une première approche pour une application de text-mining. Le format est celui de Travaux Pratiques utilisant AlvisNLP, un outil pour la création de pipelines en text-mining développé par l’équipe Bibliome de l’unité MaIAGE. La formation s’adresse à des chercheurs et ingénieurs en (bio)-informatique ou en maths-info-stats appliquées\r\n\r\nProgramme\r\n* Présentation du text-mining et de la Reconnaissance des Entités Nommées (REN)\r\n* Travaux Pratiques sur des techniques de REN en utilisant AlvisNLP\r\n* Projection de lexiques\r\n* Application de patrons\r\n* Apprentissage automatique", "homepage": "https://documents.migale.inrae.fr/trainings.html", "is_draft": false, "costs": [ "Priced" ], "topics": [ "http://edamontology.org/topic_0605", "http://edamontology.org/topic_3474" ], "keywords": [ "Text mining" ], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Everyone", "accessConditions": "", "maxParticipants": 10, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/769/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 82, "name": "INRAE", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/INRAE/?format=api" }, { "id": 88, "name": "BioinfOmics", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/BioinfOmics/?format=api" } ], "organisedByTeams": [ { "id": 10, "name": "MIGALE", "url": "https://catalogue.france-bioinformatique.fr/api/team/MIGALE/?format=api" } ], "logo_url": "https://migale.inrae.fr/sites/default/files/migale-orange_0.png", "updated_at": "2024-01-18T14:56:19.822106Z", "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "Life scientists", "Biologists", "Bioinformaticians" ], "difficultyLevel": "Novice", "trainingMaterials": [], "learningOutcomes": "Cette formation est dédiée à l’analyse de données textuelles (text-mining). L’objectif est l’acquisition des principales techniques pour la Reconnaissance d’Entités Nommées (REN) à partir de textes. Les entités nommées étudiées dans cette formation sont des objets ou concepts d’intérêts mentionnés dans les articles scientifiques ou les champs en texte libre (taxons, gènes, protéines, marques, etc.).\r\n\r\nLes participants vont acquérir les compétences pratiques nécessaires pour effectuer de façon autonome une première approche pour une application de text-mining. Le format est celui de Travaux Pratiques utilisant AlvisNLP, un outil pour la création de pipelines en text-mining développé par l’équipe Bibliome de l’unité MaIAGE. La formation s’adresse à des chercheurs et ingénieurs en (bio)-informatique ou en maths-info-stats appliquées", "hoursPresentations": 5, "hoursHandsOn": 7, "hoursTotal": 12, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/588/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/680/?format=api" ] }, { "id": 374, "name": "Environments and best practices for using the BiRD cluster", "shortName": "Best practices BiRD cluster", "description": "Objectives\r\n- Understand and implement the principles of reproducible science in analysis and development projects\r\n- Acquire basic commands necessary for optimal use of the cluster\r\n\r\nPedagogical Content\r\n- Introduction to reproducibility\r\n- Best practices on code history and sharing: Git\r\n- Conda environment\r\n- Presentation of the computing cluster\r\n- Introduction to workflows using Snakemake", "homepage": "https://pf-bird.univ-nantes.fr/training/cluster/", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Everyone", "accessConditions": "Have an account on the BiRD cluster.", "maxParticipants": 20, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/596/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 16, "name": "BiRD", "url": "https://catalogue.france-bioinformatique.fr/api/team/BiRD/?format=api" } ], "logo_url": null, "updated_at": "2024-02-08T15:56:16.390499Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 7, "hoursHandsOn": null, "hoursTotal": 7, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/602/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/641/?format=api" ] }, { "id": 286, "name": "Utilisation du cluster - SLURM / Cluster usage - SLURM", "shortName": "Cluster SLURM", "description": "Objectifs\r\n- Disposer des concepts et de bonnes pratiques d’utilisation des ressources de calcul.\r\n- Être capable d’utiliser les ressources de calcul de la plateforme en toute autonomie.\r\nProgramme\r\n- Introduction : les équipements (calcul et stockage), espaces de travail, les outils et les données.\r\n- Calcul parallèle : concepts, ressources\r\n- Soumission de jobs (srun, sbatch)\r\n- Monitorer, vérifier, controler les jobs (squeue, scontrol, scancel, sacct).\r\n- Base de l’optimisation d’un job\r\n- Solutions de parallélisation des jobs : (--array)", "homepage": "https://abims.sb-roscoff.fr/module/cluster_slurm", "is_draft": false, "costs": [ "Free" ], "topics": [ "http://edamontology.org/topic_3316" ], "keywords": [], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Everyone", "accessConditions": "Preregistration required using: https://abims.sb-roscoff.fr/ateliers/preinscription", "maxParticipants": 18, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 65, "name": "SBR", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/SBR/?format=api" } ], "organisedByTeams": [ { "id": 4, "name": "ABiMS", "url": "https://catalogue.france-bioinformatique.fr/api/team/ABiMS/?format=api" } ], "logo_url": "https://abims.sb-roscoff.fr/sites/default/files/abims.png", "updated_at": "2025-02-21T08:43:49.795981Z", "audienceTypes": [ "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "All" ], "difficultyLevel": "Intermediate", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/625/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/714/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/498/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/440/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/522/?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": 285, "name": "Linux Avancé / Advanced Linux", "shortName": "Advanced Linux", "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/module/linux_advanced", "is_draft": false, "costs": [ "Free" ], "topics": [ "http://edamontology.org/topic_3316" ], "keywords": [], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Everyone", "accessConditions": "Preregistration required using: https://abims.sb-roscoff.fr/ateliers/preinscription", "maxParticipants": 18, "contacts": [], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 65, "name": "SBR", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/SBR/?format=api" } ], "organisedByTeams": [ { "id": 4, "name": "ABiMS", "url": "https://catalogue.france-bioinformatique.fr/api/team/ABiMS/?format=api" } ], "logo_url": "https://abims.sb-roscoff.fr/sites/default/files/abims.png", "updated_at": "2025-02-21T08:42:13.294211Z", "audienceTypes": [ "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [], "difficultyLevel": "Intermediate", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 3, "hoursHandsOn": 4, "hoursTotal": 7, "personalised": false, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/497/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/435/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/521/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/713/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/624/?format=api" ] }, { "id": 335, "name": "FAIR_bioinfo_@_AuBi", "shortName": "FAIR_bioinfo", "description": "Introduction aux bonnes pratiques en bio-informatique afin de pérenniser son travail de recherche.\r\n\r\nCette formation permet de découvrir les bonnes pratiques dans le cadre d’un travail nécessitant des approches programmatiques (statistiques, programmation d’outils, analyses de données biologiques). Elle s’inscrit aussi dans l’aspect science-ouverte afin de rendre plus facilement disponible et pérenne le travail bio-informatique. Après une introduction aux pratiques FAIR axées notamment sur les notions de reproductibilité et de répétabilité du code, plusieurs approches seront abordées: les bonnes pratiques de partage et gestion des versions des outils utilisés ; la gestion des environnements de travail (conda, docker, singularity) ; découverte du gestionnaire de workflow Snakemake : et enfin la documentation du code avec Rmarkdown et Jupyter.", "homepage": "https://mesocentre.uca.fr/actualites/pratiques-fair-en-bioinformatique-pour-des-analyses-reproductibles", "is_draft": false, "costs": [ "Free to academics" ], "topics": [ "http://edamontology.org/topic_0091", "http://edamontology.org/topic_0769", "http://edamontology.org/topic_3307", "http://edamontology.org/topic_3068" ], "keywords": [ "Methodology", "Programming Languages & Computer Sciences", "Cloud", "Linux", "Snakemake", "Docker", "R" ], "prerequisites": [ "Linux - Basic Knowledge" ], "openTo": "Everyone", "accessConditions": "Having an account on Mesocentre Clermont Auvergne Infrastructure", "maxParticipants": 15, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/261/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 87, "name": "AuBi", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/AuBi/?format=api" }, { "id": 94, "name": "Université Clermont Auvergne", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/Universit%C3%A9%20Clermont%20Auvergne/?format=api" } ], "organisedByTeams": [ { "id": 31, "name": "AuBi", "url": "https://catalogue.france-bioinformatique.fr/api/team/AuBi/?format=api" } ], "logo_url": "https://mesocentre.uca.fr/medias/photo/logoaubi-2019minus_1553844844490-jpg?ID_FICHE=41175", "updated_at": "2023-06-14T10:18:52.160465Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 10, "hoursHandsOn": 20, "hoursTotal": 30, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/537/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/709/?format=api" ] }, { "id": 140, "name": "Bioinformatique et Analyses Mutationnelles", "shortName": "", "description": "Module de formation à la bioinformatique appliquée à l'analyse des données génétiques dans le cadre des maladies génétiques humaines. Cet enseignement fait partie du Master 2 de Pathologie Humaine dispensé à la faculté de Médecine de la Timone à Marseille.\n \n", "homepage": "http://formations.univ-amu.fr/ME5APH-ENAPHCU41.html", "is_draft": false, "costs": [], "topics": [], "keywords": [ "NGS Data Analysis", "Bioinformatics & Biomedical", "Sequence analysis", "NGS Sequencing Data Analysis" ], "prerequisites": [ "Master (M2 uniquement)" ], "openTo": "Internal personnel", "accessConditions": "Inscription au Master 2 de Pathologie Humaine\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/269/?format=api" ] }, { "id": 61, "name": "NGS data analysis", "shortName": "", "description": " Master 2 Bioinformatics research students, University of Bordeaux.\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [ "NGS Data Analysis" ], "prerequisites": [ "Master (M2 uniquement)" ], "openTo": "Internal personnel", "accessConditions": "", "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": [] } ] }
