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            "name": "Workshop nf-core et sarek - 8 et 9 Décembre 2022",
            "shortName": "",
            "description": "Dans le cadre du réseau métier ingénieur.e.s lillois, bilille organise un workshop de 2 jours autour de la communauté internationale et des pipelines de bioinformatique nf-core, les 8 et 9 Décembre sur le campus Cité Scientifique de l’Université de Lille, à Villeneuve d’Ascq.\r\n\r\nLe projet nf-core a été créé en 2018 afin de proposer et maintenir de manière collaborative des pipelines d’analyse de bioinformatique en Nextflow selon des standards stricts de qualité et de reproductibilité, tout en facilitant leur mise en œuvre sur la majorité des infrastructures de calcul. La communauté, très active, qui s’organise autour de cette collection de pipelines rassemble des scientifiques du monde entier, issus de parcours très divers.\r\n\r\nÀ l’occasion de cet atelier, nous accueillerons Maxime Garcia (Seqera labs, Stockholm), membre de l’équipe d’administration nf-core et développeur principal du pipeline d’analyse de variants génomique Sarek. Il présentera la communauté aux participant.e.s et les formera à l’utilisation de ces pipelines d’analyse, en alternant les présentations avec des mises en pratique. Il présentera également les outils de développement mis en place par nf-core pour permettre aux participant.e.s de contribuer aux outils existants et de proposer, si elles et ils le souhaitent, leurs propres pipelines selon les standards de la communauté.",
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            "updated_at": "2024-12-09T17:37:41.821856Z",
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            "name": "Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy - 2026",
            "shortName": "Analyse de données NGS sous Galaxy 2026",
            "description": "Objectifs pédagogiques\r\nConnaître les concepts et méthodes bioinformatiques utilisés pour l’analyse primaire de données issues de séquenceurs nouvelle génération (NGS). Savoir effectuer un alignement sur un génome de référence, un assemblage de novo d’un génome bactérien\r\n\r\nProgramme\r\nThéorie\r\n* Présentation des différents types de technologies de séquençage (lectures longues et courtes)\r\n\r\nPratique : Analyse des données de séquençage d’un génome bactérien\r\n* Contrôle qualité\r\n* Assemblage de-novo\r\n* Nettoyage des données\r\n* Assemblage\r\n* Visualisation et statistiques sur l’assemblage\r\n* Alignement de lectures sur un génome de référence et visualisation\r\nTous les TPs seront réalisés sous l’environnement d’exécution de traitements Galaxy.",
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            "updated_at": "2026-02-12T10:33:27.380562Z",
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            "name": "Introduction to Microbial Comparative Genomics 2022",
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            "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.",
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            "updated_at": "2023-12-04T15:32:33.606313Z",
            "type": "Training course",
            "start_date": "2022-06-14",
            "end_date": "2022-06-14",
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            "city": "Montpellier",
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            "name": "Analyse statistique de données RNA-Seq - Recherche des régions d’intérêt différentiellement exprimées (2024)",
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            "description": "Objectifs pédagogiques\r\n* Se sensibiliser aux concepts et méthodes statistiques pour l’analyse de données transcriptomiques de type RNA-Seq.\r\n* Comprendre le matériel et méthodes (normalisation et tests statistiques) d’un article.\r\n* Réaliser une étude transcriptomique avec R dans l’environnement RStudio.\r\n\r\nProgramme\r\n* Planification expérimentale des expériences RNA-Seq (identification des biais, répétitions, biais contrôlables).\r\n* Normalisation et analyse différentielle : recherche de “régions d’intérêt” différentiellement exprimées (modèle linéaire généralisé).\r\n*Prise en compte de la multiplicité des tests.\r\n\r\nLe cours sera illustré par différents exemples. Un jeu de données à deux facteurs sera analysé avec les packages R DESeq2 et edgeR dans l’environnement RStudio.",
            "homepage": "https://documents.migale.inrae.fr/trainings.html",
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            "updated_at": "2024-01-18T14:52:00.895148Z",
            "type": "Training course",
            "start_date": "2024-06-10",
            "end_date": "2024-06-11",
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            "name": "Annotation and analysis of prokaryotic genomes using the MicroScope platform - March 2025",
            "shortName": "MicroScope training - March 2025",
            "description": "In an effort to inform members of the research community about our annotation methods, to provide training for collaborators and other scientists who use the MicroScope platfom, and to inform scientific public on the analysis available in PkGDB (Prokaryotic Genome DataBase), we have developed a 4.5-day course in Microbial Genome Annotation and Comparative Analysis using the MaGe graphical interfaces.\r\n\r\nThis course will familiarize attendees with LABGeM’s annotation pipeline and the manual annotation software MaGe (Magnifying Genome) . No specific bioinformatics skill is required: detailed instruction on the algorithm developed in each annotation methods can be found in specific training courses on «Genomic sequences analysis». Here we focus on the general idea behind each method and, above all, the way you can interpret the corresponding results and combine them with other evidences in order to change or correct the current automatic functional annotation of a given gene, if necessary.\r\n\r\nThis course will also describe how to perform effective searches and analysis of procaryotic data using the graphical functionalities of the MaGe’s interfaces. Because of the numerous pre-computation available in our system (results of “common” annotation tools, synteny with all complete bacterial genomes, metabolic pathway reconstruction, fusion/fission events, genomic islands, …), many practical exercises allow attendees to get familiar with the use the MaGe graphical interfaces in order to efficiently explore these sets of results.",
            "homepage": "https://labgem.genoscope.cns.fr/professional-trainings/microscope-professional-trainings/training-annotation-analysis-of-prokaryotic-genomes-using-the-microscope-platform/",
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                "http://edamontology.org/topic_0085",
                "http://edamontology.org/topic_3301"
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                "Licence"
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                    "name": "University of Évry Val d'Essonne",
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            "updated_at": "2025-01-23T13:31:47.576548Z",
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            "city": "Evry",
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            "name": "New session of FAIR_bioinfo_@_AuBi",
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            "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",
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            "updated_at": "2025-02-17T13:11:26.183643Z",
            "type": "Training course",
            "start_date": "2025-05-19",
            "end_date": "2025-02-21",
            "venue": "",
            "city": "Aubière",
            "country": "France",
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        {
            "id": 632,
            "name": "LINUX - session 07/10/2024",
            "shortName": "",
            "description": "This training session is organized by the Genotoul bioinfo platform and aims at learning sequence analysis. This training session has been designed to familiarize yourself with the platform resources and its organization. You will learn to access the platform from your work station, what is an Linux environment and how to use it, how to create and manipulate files, how to transfer them from and to your personal computer.\r\n\r\nThis training is focused on practice. It consists of 3 modules with a large variety of exercises:\r\n\r\n- Connect to « genotoul » server (09:00 am to 10:30 am): Platform presentation, Linux basics, opening an user account, Putty installation, first connection.\r\n- Files and basics commands  (10:45 am to 12:00 pm): types of files and secure access, file manipulation commands, text editors and viewers, disk space management .\r\n- Transfers and file manipulation (14:00 pm to 17:00 pm): download/transfer, compress/uncompress, utility commands and data extraction, output redirections.",
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            "costs": [
                "Non-academic: 550€ + 20% taxes (TVA)",
                "Academic but non-INRAE: 170 € + 20% taxes (TVA)",
                "For INRAE's staff: 150 € no VAT charged;"
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                "http://edamontology.org/topic_3316"
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            "updated_at": "2024-06-05T09:15:55.325587Z",
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            "start_date": "2024-10-07",
            "end_date": "2024-10-07",
            "venue": "",
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            "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,
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            "updated_at": "2023-12-04T15:32:22.626277Z",
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            "description": "This training session is designed to help you deal with the platform compute cluster and data banks. You will launch your first processing batch on the cluster and will learn how to track and manage them. Organized jointly by the Sigenae and bioinfo genotoul platforms.",
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            "name": "Using sed and awk to modify large large text files - 13 March 2025",
            "shortName": "",
            "description": "Many analysis generate large result text files which have to be checked, merged, split, reduced. Several tools have been developed and are available on Unix to do this, including sed and AWK. During this course you will be trained to process large files with sed and AWK. Sed is tool enabling to select and process lines. You can easily insert, delete, modify, append lines to very large files with millions of lines. AWK will enable to perform more fine tuned file modifications based on columns. It includes also more mathematical and string functions.  The course is based mainly on exercises with small sections presenting concepts and commands.",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/modify-and-extract-information-from-large-text-files-day-2-3/",
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            "updated_at": "2024-12-06T20:47:41.482360Z",
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            "end_date": "2025-03-13",
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            "city": "castanet-tolosan",
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            "name": "Introduction au text-mining avec AlvisNLP (session 2024)",
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            ],
            "topics": [
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            "prerequisites": [
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                    "id": 88,
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            ],
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            ],
            "logo_url": "https://migale.inrae.fr/sites/default/files/migale-orange_0.png",
            "updated_at": "2024-01-18T14:58:57.757098Z",
            "type": "Training course",
            "start_date": "2024-06-12",
            "end_date": "2024-06-13",
            "venue": "https://migale.inrae.fr/how-to-come",
            "city": "Jouy-en-Josas",
            "country": "France",
            "geographical_range": "",
            "trainers": [
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                "https://catalogue.france-bioinformatique.fr/api/userprofile/744/?format=api"
            ],
            "trainingMaterials": [],
            "computingFacilities": [],
            "realisation_status": "past",
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            "registration_closing": "2024-05-29",
            "registration_status": "closed",
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        {
            "id": 563,
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            "shortName": "",
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            "is_draft": false,
            "costs": [
                "Free"
            ],
            "topics": [],
            "keywords": [],
            "prerequisites": [
                "Linux - Basic Knowledge"
            ],
            "openTo": "Internal personnel",
            "accessConditions": "Open to South Green close collaborators",
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            "updated_at": "2023-12-04T15:35:29.445559Z",
            "type": "Training course",
            "start_date": "2023-05-31",
            "end_date": "2023-06-01",
            "venue": "",
            "city": "Montpellier",
            "country": "",
            "geographical_range": "Local",
            "trainers": [
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                "https://catalogue.france-bioinformatique.fr/api/userprofile/174/?format=api",
                "https://catalogue.france-bioinformatique.fr/api/userprofile/558/?format=api",
                "https://catalogue.france-bioinformatique.fr/api/userprofile/775/?format=api",
                "https://catalogue.france-bioinformatique.fr/api/userprofile/564/?format=api"
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            "computingFacilities": [],
            "realisation_status": "past",
            "registration_opening": null,
            "registration_closing": null,
            "registration_status": "unknown",
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        },
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            "id": 535,
            "name": "Analyse de données de métabarcoding : 2025",
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            "description": "Cette formation est dédiée à l'analyse de données de type \"metabarcoding\" issues de la technologie de séquençage Illumina. Nous aborderons les différentes étapes bioinformatiques nécessaires pour transformer les données de séquençage brutes en table d'abondances. Nous présenterons également les outils et méthodologies classiquement utilisés pour décrire la diversité observée et comparer les échantillons.\r\nA l’issue des 4 jours de formation, les stagiaires connaîtront le périmètre, les avantages et limites des analyses de données de séquençage amplicons (métabarcoding).\r\nIls seront capables d’utiliser les outils de FROGS sur les jeux de données de la formation (16S et ITS).\r\nIls seront capables d’identifier les outils et méthodes adaptées au cadre de leurs analyses.\r\nS’ils ont en leur possession un jeu de données à analyser, ils sont encouragés à venir avec celui- ci.",
            "homepage": "https://migale.inrae.fr/trainings/",
            "is_draft": false,
            "costs": [],
            "topics": [],
            "keywords": [],
            "prerequisites": [],
            "openTo": "Everyone",
            "accessConditions": "",
            "maxParticipants": 10,
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            "elixirPlatforms": [],
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                    "id": 82,
                    "name": "INRAE",
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            ],
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                    "id": 10,
                    "name": "MIGALE",
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            ],
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            "type": "Training course",
            "start_date": "2025-06-23",
            "end_date": "2025-06-26",
            "venue": "Access to the INRAE center reception\r\n By car\r\n\r\n    Take the N118 from the Paris rotary Porte de Saint-Cloud > Pont de Sèvres > Follow direction Bordeaux/Nantes – take exit 6A Jouy-en-Josas/Bièvres\r\n    Take the N12 from Plaisir > Follow direction Paris exit 1 towards the D53\r\n    Take the A12 Rambouillet > Jouy – take exit 2 via the D446\r\n\r\n By the RER (train to the suburbs)\r\n\r\nRER C Line: Get off at the Jouy-en-Josas station. The research center is a 15 minute walk (you must walk towards the town hall (Mairie de Jouy).\r\n\r\n    From Chatelet-Les Halles, take the RER B line until the Massy-Palaiseau station (32 min.) then take the RER C line CIME train (14 min.)\r\n    From Versailles-Chantier RER C station take the VICK or VITY train (8 min.)\r\n    From the Bibliothèque François Mitterand RER C station, take the CIME train (1 hour)",
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            "country": "frnce",
            "geographical_range": "",
            "trainers": [
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                "https://catalogue.france-bioinformatique.fr/api/userprofile/743/?format=api",
                "https://catalogue.france-bioinformatique.fr/api/userprofile/415/?format=api"
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            "computingFacilities": [],
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            "registration_opening": "2025-01-22",
            "registration_closing": "2025-06-08",
            "registration_status": "closed",
            "courseMode": "Onsite"
        },
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            "id": 564,
            "name": "Introduction to Structural variant detection analyses 2022",
            "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": [
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                    "name": "South Green",
                    "url": "https://catalogue.france-bioinformatique.fr/api/team/South%20Green/?format=api"
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            "logo_url": "https://southgreenplatform.github.io/trainings//images/southgreenlong.png",
            "updated_at": "2023-12-04T15:32:04.974511Z",
            "type": "Training course",
            "start_date": "2022-06-21",
            "end_date": "2022-06-24",
            "venue": "",
            "city": "montpellier",
            "country": "france",
            "geographical_range": "",
            "trainers": [],
            "trainingMaterials": [],
            "computingFacilities": [],
            "realisation_status": "past",
            "registration_opening": null,
            "registration_closing": null,
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            "courseMode": "Onsite"
        },
        {
            "id": 712,
            "name": "Linux - Initiation / Linux for Beginners",
            "shortName": "Linux Initiation",
            "description": "Objectifs :\r\n- Être capable de se connecter à une machine Linux\r\n- Être capable de transférer des fichiers à partir de/vers une machine Linux\r\n- Être capable de naviguer dans le système de fichiers\r\n- Être capable d’examiner le contenu d’un fichier et de gérer l’espace disque\r\n- Être capable de gérer les droits d’accès aux répertoires et aux fichiers.\r\n- Être capable de gérer le lancement, l’interruption et l’arrêt de processus",
            "homepage": "https://abims.sb-roscoff.fr/ateliers/2025",
            "is_draft": false,
            "costs": [
                "Free"
            ],
            "topics": [
                "http://edamontology.org/topic_3316"
            ],
            "keywords": [
                "Linux",
                "Operating systems"
            ],
            "prerequisites": [],
            "openTo": "Everyone",
            "accessConditions": "Preregistration required using: https://abims.sb-roscoff.fr/ateliers/preinscription",
            "maxParticipants": 16,
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            ],
            "organisedByTeams": [
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                    "id": 4,
                    "name": "ABiMS",
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            "logo_url": "https://abims.sb-roscoff.fr/sites/default/files/abims.png",
            "updated_at": "2025-02-21T08:52:59.581686Z",
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            "end_date": "2025-05-14",
            "venue": "",
            "city": "Roscoff",
            "country": "France",
            "geographical_range": "",
            "trainers": [],
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            "computingFacilities": [],
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            "registration_opening": "2025-02-09",
            "registration_closing": "2025-04-30",
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}