Training List
Handles creating, reading and updating training events.
GET /api/training/?format=api&offset=40&ordering=-accessConditions
{ "count": 378, "next": "https://catalogue.france-bioinformatique.fr/api/training/?format=api&limit=20&offset=60&ordering=-accessConditions", "previous": "https://catalogue.france-bioinformatique.fr/api/training/?format=api&limit=20&offset=20&ordering=-accessConditions", "results": [ { "id": 394, "name": "Principes FAIR & Git Initiation", "shortName": "FAIR & GIT - Initiation", "description": "Objectifs\r\n- Principes FAIR :\r\n Connaître les principes FAIR\r\n Être capable de prendre en compte les principes FAIR dans l'ensemble des étapes d'un projet impliquant la \r\n collecte et/ou l'analyse de données\r\n- Initiation à Git :\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\n\r\nProgramme : \r\n- Principes FAIR\r\n Présentation des principes FAIR\r\n Exemples de bonnes pratiques dans la gestion des données : description, organisation du stockage, \r\n traitements et analyses, mise en accès\r\n- Initiation à Git\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\n push, pull) ; en ligne de commande ou en utilisant une interface graphique (GitHub et GitLab)", "homepage": "https://abims.sb-roscoff.fr/module/fair_git", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [], "prerequisites": [ "none" ], "openTo": "Everyone", "accessConditions": "Pre-registration required.", "maxParticipants": 18, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/821/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [ { "id": 65, "name": "SBR - Roscoff Marine Station", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/SBR%20-%20Roscoff%20Marine%20Station/?format=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": "2025-02-21T08:31:00.096988Z", "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "All" ], "difficultyLevel": "Novice", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": 4, "hoursHandsOn": 4, "hoursTotal": 8, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/710/?format=api" ] }, { "id": 103, "name": "Biostatistique avec R", "shortName": "", "description": "Apprendre à se servir du logiciel R dans le contexte de l’analyse de données biologiques tout en consolidant ses connaissances de base en biostatistique\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Programming Languages & Computer Sciences", "R Language" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Personnel IHU-A-ICM, gratuit\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": 104, "name": "Initiation à la programmation en R", "shortName": "", "description": "Se familiariser avec R dans le but d’utiliser ce logiciel pour faire des modèles linéaires\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Programming Languages & Computer Sciences", "R Language" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Personnel IHU-A-ICM, gratuit\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": 115, "name": "Analyse de données RNAseq sous Galaxy", "shortName": "", "description": "L’analyse des données biologiques nécessite de plus en plus l’utilisation de ressources et d’environnements informatiques difficiles à maîtriser pour le biologiste.\nCette formation présente et décompose l’utilisation de l’environnement Galaxy.\nEn se basant sur une plateforme web, comme c’est la cas avec Mobyle, cet environnement propose une nouvelle approche pour rendre l’analyse biologique plus aisée pour les non- informaticiens.\nObjectifs \nPrise en main de l’environnement Galaxy et des différentes fonctionnalités proposées.\nOrganisation pédagogique \nLa formation est exclusivement orientée pratique! Il s’agir d’utiliser des données de RNAseq fournies par l’UMR 0598 Agrocampus-Ouest / INRA pour utiliser les outils classiques d’analyse de données RNAseq (Tophat, flagstat, Cufflinks, Cuffcompare, Cuffdiff, ou htseq-count, Deseq…)\nPublic visé\nChercheurs et ingénieurs, biologistes souhaitant s’initier à l’analyse de données RNAseq.\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [ "NGS Data Analysis", "Analysis of RNAseq data", "Galaxy" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Pas de pré-requis.\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": 114, "name": "Initiation à la plateforme web GALAXY : L’analyse de données biologiques pour tous !", "shortName": "", "description": "Présentation\nL’analyse des données biologiques nécessite de plus en plus l’utilisation de ressources et d’environnements informatiques difficiles à maîtriser pour le biologiste.\nCette formation présente et décompose l’utilisation de l’environnement Galaxy.\nEn se basant sur une plateforme web, comme c’est la cas avec Mobyle, cet environnement propose une nouvelle approche pour rendre l’analyse biologique plus aisée pour les non- informaticiens.\nObjectifs \nPrise en main de l’environnement Galaxy et des différentes fonctionnalités proposées.\nOrganisation pédagogique \nLa formation comprendra un exposé théorique avec démonstrations pratiques complété par une rapide application sur la manipulation de données de régions génomiques.\nPublic visé\nChercheurs et ingénieurs, biologistes et bio-informaticiens possédant des compétences en développement bio-informatique souhaitant intégrer des outils dans le portail web Galaxy.\nPré-requis\nAucun.\n", "homepage": "", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Galaxy" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "Pas de pré-requis.\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": 275, "name": "Single-Cell : Transcriptomics, Spatial and Long reads", "shortName": "SincellTE", "description": "This workshop focuses on the large-scale study of heterogeneity across individual cells from a genomic, transcriptomic and epigenomic point of view. 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.", "homepage": "", "is_draft": false, "costs": [ "Priced" ], "topics": [], "keywords": [], "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": 4, "name": "IFB - ELIXIR-FR", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/IFB%20-%20ELIXIR-FR/?format=api" } ], "organisedByTeams": [], "logo_url": "https://ressources.france-bioinformatique.fr/sites/default/files/sincellTE_logo_0_2.png", "updated_at": "2024-03-20T09:31:42.144175Z", "audienceTypes": [], "audienceRoles": [ "Researchers", "Life scientists", "Biologists", "Bioinformaticians" ], "difficultyLevel": "Intermediate", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/199/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/405/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/422/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/177/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/606/?format=api" ] }, { "id": 304, "name": "Initiation à Galaxy", "shortName": "Bilille Galaxy Init", "description": "Bilille organise régulièrement des formations d'initiation à l'outil Galaxy d'une journée, destinée aux biologistes et médecins désirant découvrir le traitement bioinformatique de données via une interface conviviale.\r\n\r\nGalaxy est très répandu pour l’analyse de données omiques, telles que données de séquençage ou données de puces à ADN. \r\nC'est l'environnement qui est utilisé lors du cycle de formation “Analyse de données de séquençage à haut-débit”.", "homepage": "https://bilille.univ-lille.fr/training/training-offer", "is_draft": false, "costs": [ "Free" ], "topics": [], "keywords": [ "Galaxy" ], "prerequisites": [], "openTo": "Everyone", "accessConditions": "Ouvert en priorité aux participants du cycle Analyse NGS organisé par Bilille.", "maxParticipants": null, "contacts": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/763/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/487/?format=api" ], "elixirPlatforms": [], "communities": [], "sponsoredBy": [], "organisedByOrganisations": [], "organisedByTeams": [ { "id": 3, "name": "Bilille", "url": "https://catalogue.france-bioinformatique.fr/api/team/Bilille/?format=api" } ], "logo_url": "https://bilille.univ-lille.fr/fileadmin/_processed_/9/2/csm_logo_bilille_complet_65be9bda8b.png", "updated_at": "2024-12-09T17:41:37.266949Z", "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "trainingMaterials": [], "learningOutcomes": "", "hoursPresentations": null, "hoursHandsOn": null, "hoursTotal": null, "personalised": null, "event_set": [ "https://catalogue.france-bioinformatique.fr/api/event/741/?format=api", "https://catalogue.france-bioinformatique.fr/api/event/676/?format=api" ] }, { "id": 134, "name": "Initiation à l'analyse de données avec R", "shortName": "", "description": "Le cours s’adresse à des personnes qui veulent apprendre ou ré-apprendre à utiliser les statistiques à bon escient pour leurs propres projets. L’objectif est de présenter et expliquer les principales notions de statistiques utiles pour décrire un jeu de données, en explorer les propriétés afin d’en tirer des conclusions robustes, utiliser à bon escient les méthodes les plus courantes (tests d’hypothèse, ACP, …) et savoir lire, interpréter (et éventuellement aborder d’un œil critique) les résultats présentés dans les publications. Nous utiliserons le moins possible le formalisme mathématique mais insisterons sur les propriétés des méthodes, leurs pré-requis, l’interprétation des résultats. Nous aborderons les notions d’analyse exploratoire, ACP, clustering, estimation, échantillonnage, régression, tests d’hypothèse, planification d’expérience\nCe cours est une initiation à l’analyse de données. Il est préférable d’avoir une connaissance minimale de R. Dans le cas contraire, un tutoriel d’initiation est disponible sur la page web du cours et les notions de base de R seront rappelées pendant la pratique. Pour les personnes n’ayant jamais utilisé R, il peut être utile d’avoir des connaissances de base en programmation, quel que soit le langage.\nLes cours seront donnés en Français et alterneront théorie et pratique avec RStudio. Il est demandé à chaque participant de venir avec un ordinateur portable chargé sur lequel il aura préalablement installé les éléments nécessaires (R, Rstudio et les fichiers de données sur lesquels nous travaillerons). La liste complète des fichiers et logiciels nécessaires sera disponible sur la page web du cours une dizaine de jours avant le début de la session.\nderniere session: Mar 2016\n \n", "homepage": "https://c3bi.pasteur.fr", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Biostatistics", "Programming Languages & Computer Sciences", "Statistical Tests", "R Language", "Descriptive statistics" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "ouvert à tous, sur inscription.\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/534/?format=api" ] }, { "id": 146, "name": "Introduction à la Phylogénie Moléculaire : CONCEPTS, METHODES ET OUTILS", "shortName": "", "description": "Le C3BI (Institut Pasteur) propose des cours pour acquérir les notions théoriques de phylogénie et maitriser les outils et logiciels.\nLes cours d’”Introduction à la phylogénie moléculaire” sont ouverts à tous (inscription obligatoire pour les cours et travaux pratiques dans la limite des places disponibles).\nIl est possible de ne s’inscrire que pour la partie théorique. Ces cours sont dispensés en langue française.\nLundi 14 Novembre (9h30-12h30): Présentation des principales banques de données et BLAST\nMardi 15 Novembre (9h30-11h00): Alignements Multiples\nMercredi 16 Novembre (9h30-11h00): Introduction à la Phylogénie\nJeudi 17 Novembre (9h30-11h00): Modèles d’évolution\nVendredi 18 Novembre (9h30-11h00): Approches par Maximum de Parcimonie\nLundi 21 Novembre (9h30-11h00): Méthodes de Distance\nMardi 22 Novembre (9h30-11h00): Méthodes de Vraisemblance\nMercredi 23 Novembre (13h30-15h00): Reconstruction Phylogénétique & Approches Bayésiennes\nJeudi 24 Novembre (9h30-11h00): Inférence des Forces Sélectives\nVendredi 25 Novembre (9h30-11h00): Choix des Méthodes et Interprétation\nprogramme complet \ninscription par mail à formation@pasteur.fr (avec le sujet “Phylogénie Moléculaire”) + formulaire \n", "homepage": "https://c3bi.pasteur.fr/training-introduction-a-la-phylogenie-moleculaire-concep…", "is_draft": false, "costs": [], "topics": [], "keywords": [ "Phylogeny" ], "prerequisites": [], "openTo": "Internal personnel", "accessConditions": "ouvert à tous (chercheur,ingénieur, étudiant) mais inscription obligatoire par mail à formation@pasteur.fr (avec le sujet “Phylogénie Moléculaire”) + formulaire \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/275/?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": [] }, { "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": 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": 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": 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": 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": 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": 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": 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": 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" ] } ] }
