Handles creating, reading and updating training events.

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            "name": "Introduction à l'analyse de données de métabarcoding 16S avec Galaxy",
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                    "id": 131,
                    "name": "16S Microbial Analysis with mothur",
                    "url": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/16S%20Microbial%20Analysis%20with%20mothur/?format=api"
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            "id": 371,
            "name": "Introduction à l'analyse de données métatranscriptomiques avec Galaxy",
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            "description": "L’objectif de cette formation est de se familiariser avec les étapes et les outils d’analyse de données métatranscriptomiques dans le but de comprendre les fonctions d’une communauté microbienne. Nous proposons au personnel non-bioinformaticien de les accompagner dans la prise en main de ces étapes  en utilisant la plateforme de bio-analyse Galaxy. \r\n\r\nAprès une introduction à la métatranscriptomique, une session pratique sur la plateforme Galaxy couvrira comment :\r\n- assigner des taxons à des données de métatranscriptomiques,\r\n- extraire des informations fonctionnelles au sein de données de métatranscriptomiques,\r\n- combiner informations taxonomiques et fonctionnelles pour faciliter la compréhension des fonctions d’une communauté microbienne",
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                "http://edamontology.org/topic_0085",
                "http://edamontology.org/topic_3941",
                "http://edamontology.org/topic_1775"
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            "id": 368,
            "name": "Introduction à l'annotation de génomes bactériens avec Galaxy",
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            "description": "L’objectif est cette formation de se familiariser avec les étapes et les outils pour annoter des génomes bactériens. Nous proposons au personnel non-bioinformaticien de les accompagner dans la prise en main de l’annotation de génomes bactériens en utilisant la plateforme de bio-analyse Galaxy. \r\n\r\nAprès une introduction à l’annotation de génomes bactériens, une session pratique sur la plateforme Galaxy couvrira comment :\r\n- faire tourner une série d’outils pour annoter un génome bactérien avec différents éléments génomiques,\r\n- évaluer l’annotation\r\n- visualiser un génome bactérien et ses annotations",
            "homepage": "",
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            ],
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                "http://edamontology.org/topic_3301",
                "http://edamontology.org/topic_0219",
                "http://edamontology.org/topic_0097"
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                "Bacterial isolate",
                "Galaxy",
                "Structural and functional annotation of genomes"
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                    "name": "Bacterial Genome Annotation",
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            ],
            "learningOutcomes": "At the end of the tutorial, learners would be able to:\r\n- Run a series of tools to annotate a draft bacterial genome for different types of genomic components\r\n- Evaluate the annotation\r\n- Process the outputs to format them for visualization needs\r\n- Visualize a draft bacterial genome and its annotations",
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        {
            "id": 367,
            "name": "Introduction à l'analyse de données de séquençage avec contrôle qualité et alignement sur un génome de référence avec Galaxy",
            "shortName": "",
            "description": "L’objectif de cette formation est de se familiariser avec les premières étapes communes à toutes les analyses de données de séquençage : le contrôle qualité des données et l’alignement sur un génome de référence. Nous proposons au personnel non-bioinformaticien de les accompagner dans la prise en main des ces étapes d’analyses en utilisant la plateforme de bio-analyse Galaxy. \r\n\r\nAprès une introduction aux données de séquençage, une session pratique sur la plateforme Galaxy couvrira comment :\r\n- évaluer la qualité de données de séquençage,\r\n- améliorer la qualité de données de séquençage\r\n- aligner des données sur un génome de référence",
            "homepage": "",
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                "http://edamontology.org/topic_0102"
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                "Quality Control",
                "Galaxy",
                "Mapping"
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            "openTo": "Internal personnel",
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            "updated_at": "2024-02-08T11:22:59.733596Z",
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                "Professional (continued)"
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                "Biologists"
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                    "id": 128,
                    "name": "Mapping with Galaxy",
                    "url": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/Mapping%20with%20Galaxy/?format=api"
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                {
                    "id": 127,
                    "name": "Quality Control with Galaxy",
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            ],
            "learningOutcomes": "At the end of the tutorial, learners would be able to:\r\n- Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC\r\n- Assess long reads FASTQ quality using Nanoplot and PycoQC\r\n- Perform quality correction with Cutadapt (short reads)\r\n-  Summarise quality metrics MultiQC\r\n- Process single-end and paired-end data\r\n- Define what mapping is\r\n- Perform mapping of reads on a reference genome\r\n- Evaluate the mapping output",
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                "https://catalogue.france-bioinformatique.fr/api/event/593/?format=api"
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        },
        {
            "id": 369,
            "name": "Introduction au profilage taxonomique et visualisation de communautés microbiennes à partir de données métagénomiques avec Galaxy",
            "shortName": "",
            "description": "L’objectif de cette formation est de se familiariser avec les étapes et les outils d’analyse de données de métagénomiques pour caractériser et visualiser des communautés microbiennes. Nous proposons au personnel non-bioinformaticien de les accompagner dans la prise en main de ces étapes en utilisant la plateforme de bio-analyse Galaxy. \r\n\r\nAprès une introduction à la métagénomique, une session pratique sur la plateforme Galaxy couvrira comment :\r\n- assigner des taxons à des données de métagénomiques,\r\n- visualiser une communauté microbienne à partir d’assignations taxonomiques",
            "homepage": "",
            "is_draft": false,
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            "topics": [
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                "http://edamontology.org/topic_3174",
                "http://edamontology.org/topic_0637"
            ],
            "keywords": [
                "Galaxy"
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                "Galaxy - Basic usage"
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                "Professional (continued)"
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            "difficultyLevel": "Novice",
            "trainingMaterials": [
                {
                    "id": 130,
                    "name": "Taxonomic Profiling and Visualization of Metagenomic Data",
                    "url": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/Taxonomic%20Profiling%20and%20Visualization%20of%20Metagenomic%20Data/?format=api"
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            "learningOutcomes": "At the end of the tutorial, learners would be able to:\r\n- Explain what taxonomic assignment is\r\n- Explain how taxonomic assignment works\r\n- Apply Kraken and MetaPhlAn to assign taxonomic labels\r\n- Apply Krona and Pavian to visualize results of assignment and understand the output\r\n- Identify taxonomic classification tool that fits best depending on their data",
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        },
        {
            "id": 372,
            "name": "Introduction à l'analyse d’images avec Galaxy",
            "shortName": "",
            "description": "L’objectif de cette formation est de se familiariser avec les premières étapes à l’analyse d’images. Nous proposons au personnel non-bioinformaticien de les accompagner dans la prise en main des ces étapes d’analyses en utilisant la plateforme de bio-analyse Galaxy. \r\n\r\nAprès une introduction à l’analyse d’images, une session pratique sur la plateforme Galaxy couvrira comment :\r\n- extraire des métadonnées d’une image,\r\n- convertir, filtrer et segmenter une image",
            "homepage": "",
            "is_draft": false,
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            ],
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                "http://edamontology.org/topic_3383",
                "http://edamontology.org/topic_3382"
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                "Galaxy"
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                },
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            "updated_at": "2024-02-08T11:25:36.663764Z",
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                "Professional (continued)"
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            "difficultyLevel": "Novice",
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            "learningOutcomes": "At the end of the tutorial, learners would be able to:\r\n- How to handle images in Galaxy.\r\n- How to perform basic image processing in Galaxy",
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            "homepage": "",
            "is_draft": false,
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            ],
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                "http://edamontology.org/topic_3382"
            ],
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            ],
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            "openTo": "Internal personnel",
            "accessConditions": "Formation ouverte au personnel de l’UCA & Associés\r\nAvoir un ordinateur portable et un accès wifi eduroam\r\nAvoir un compte sur la plateforme Galaxy (Faire une demande le cas échéant sur hub.mesocentre.uca.fr)\r\nÊtre familier avec Galaxy",
            "maxParticipants": null,
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                },
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                    "name": "Université Clermont Auvergne",
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            "logo_url": "https://mesocentre.uca.fr/medias/photo/logoaubi-2019minus_1553844844490-jpg?ID_FICHE=41175",
            "updated_at": "2024-02-08T11:28:41.024508Z",
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            ],
            "difficultyLevel": "Novice",
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                    "id": 134,
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            ],
            "learningOutcomes": "At the end, learners would be able to:\r\n- How to download images from a public image repository.\r\n- How to segment cell nuclei using CellProfiler in Galaxy.\r\n- How to segment cell nucleoli using CellProfiler in Galaxy.\r\n- How to extract features for images, nuclei and nucleoli.",
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            "homepage": "https://pf-bird.univ-nantes.fr/training/",
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            "homepage": "https://pf-bird.univ-nantes.fr/training/cluster/",
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            "homepage": "https://pf-bird.univ-nantes.fr/training/rnaseq/",
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            "logo_url": null,
            "updated_at": "2024-02-08T16:07:26.347245Z",
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            "id": 275,
            "name": "Single-Cell : Transcriptomics, Spatial and Long reads",
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            "homepage": "",
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                "Autre (Diplôme universitaire, école d'ingénieur ...)"
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            "updated_at": "2024-03-20T09:31:42.144175Z",
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            "audienceRoles": [
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                "Bioinformaticians"
            ],
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        },
        {
            "id": 365,
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            "shortName": "BOGC",
            "description": "Ce module vise à fournir une expérience d’analyse de données de génomique.\r\nLes technologies Next Generation Sequencing (NGS) ont conduit à une production massive de\r\ndonnées « Omiques » pour les plantes cultivées majeures, ce qui demande de nouvelles\r\napproches d’analyses haut débit. La connaissance de ces approches et des outils qui en\r\ndécoulent pour analyser la séquence et la structure des génomes, les annoter et caractériser\r\nleur diversité et leurs profils d’expression permet d’aborder des questions de recherche\r\nbiologique avancée sur la diversité et l’adaptation des plantes. Les espèces prises en\r\nconsidération sont des espèces phares des instituts de recherche agronomique de Montpellier\r\net font partie des cultures les plus importantes pour l’agriculture mondiale. Des plateformes\r\nd’outils bioinformatiques récents reposant sur des centres de calcul et de stockage haute\r\ncapacité, sont en place pour analyser des jeux de données originales permettant de mieux\r\ncomprendre comment les génomes de plantes évoluent et s’expriment. L’ensemble de ces\r\nconnaissances Findable, Accessible, Interoperable, Reusable car intégré dans des systèmes\r\nd’information peut soutenir l'identification de gènes responsables de caractères adaptatifs ou\r\nde production. La mobilisation de jeunes chercheurs sur ces sujets est primordiale tant la\r\ndemande est importante.\r\nLe module est structuré sous la forme de cours et de travaux tutorés avec la rencontre de\r\ngénéticiens et de bioinformaticiens permettant d’appréhender les formes variées des progrès\r\nen bioanalyse génomique. Il permet d’acquérir les lignes directrices pour l’accès, l'utilisation\r\net l'analyse de différents types de données omique (e.g. (épi)génomique, transcriptomique,\r\nprotéique, métabolique) en vue d’accélérer les recherches en génomique fonctionnelle et\r\nbiotechnologie des plantes.\r\nL’évaluation sera faite sur la base de la participation et de la qualité du projet proposé par\r\nl’étudiant en fin de module, individuellement ou en binôme, suivant les consignes détaillées en\r\ndébut de module",
            "homepage": "https://bioagro.edu.umontpellier.fr/files/2021/04/HAA906V_Bigomics.pdf",
            "is_draft": false,
            "costs": [
                "Free to academics"
            ],
            "topics": [
                "http://edamontology.org/topic_0797",
                "http://edamontology.org/topic_3810",
                "http://edamontology.org/topic_3056",
                "http://edamontology.org/topic_0780"
            ],
            "keywords": [
                "Phylogeny",
                "Biodiversity",
                "NGS Data Analysis"
            ],
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                "Basic knowledge of R"
            ],
            "openTo": "Everyone",
            "accessConditions": "Inscription via un formulaire Moodle",
            "maxParticipants": 50,
            "contacts": [
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                    "id": 82,
                    "name": "INRAE",
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                },
                {
                    "id": 85,
                    "name": "IRD",
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                    "name": "South Green",
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            ],
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            "id": 376,
            "name": "Train-the-Trainer",
            "shortName": "TtT",
            "description": "The programme objective is to give instructors tools and tips for providing an enriching learning experience to trainees, irrespective of topic, and to include best-practice guidance on course and training material development.",
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                "https://catalogue.france-bioinformatique.fr/api/userprofile/639/?format=api"
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                    "id": 6,
                    "name": "Elixir-FR",
                    "url": "https://catalogue.france-bioinformatique.fr/api/organisation/Elixir-FR/?format=api"
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                    "id": 63,
                    "name": "TAGC",
                    "url": "https://catalogue.france-bioinformatique.fr/api/organisation/TAGC/?format=api"
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            "difficultyLevel": "Novice",
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        {
            "id": 377,
            "name": "RNASEQ ALIGNMENT, QUANTIFICATION AND TRANSCRIPT DISCOVERY WITH STATISTICS",
            "shortName": "RNASeq bioinfo / biostat",
            "description": "The Toulouse Genotoul bioinformatics platform, in collaboration with the Genotoul Biostatistics platform, and the MIAT unit, organize a 3,5 days long training course for bio-informaticians and biologists aiming at learning sequence analysis. It focuses on (protein coding) gene expression analysis using reads produced by ‘RNA-Seq’. This training session is designed to introduce sequences from ‘NGS’ (Next Generation Sequencing), particularly Illumina platforms (HiSeq). You will discover the standards file formats, learn about the usual biases of this type of data and run different kinds of analyses, such as spliced alignment on a reference genome, novel gene and transcript discovery, expression quantification of coding genes and transcripts. Finally you will be able to extract the differentially expressed genes.",
            "homepage": "https://bioinfo.genotoul.fr/index.php/events/rnaseq-alignment-transcripts-assemblies-statistics/",
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                "http://edamontology.org/topic_3308",
                "http://edamontology.org/topic_0203"
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                "Langage R de base",
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                "Cluster"
            ],
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            "id": 378,
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            "description": "The Toulouse Genotoul bioinformatics platform, organizes a 2 days long training course for non computer scientist and biologists aiming at learning the foundation of Python programming. In this training you will learn the basics of programming (variables, functions, control structures such as “if” condition, “for” loop”), writing simple programs which read files, and write results to others. The training course does not require any knowledge in programming, but basic Linux/bash commands are required (cd, ls).\r\n\r\nThis training focuses on practice. It consists of modules with a large variety of exercises described hereunder (PROVISIONAL SCHEDULE):\r\n\r\nUsing a Jupyter notebook (Day 1).\r\nUsing variables (Day 1).\r\nBasic operations and functions (Day 1).\r\nReading a file, writing to a file (Day 1).\r\nCharacter string manipulation (Day 1).\r\nLists and dictionaries (Day 2).\r\nThe if and for controls (Day 2).\r\nBases of algorithms (Day 2).",
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            "id": 381,
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            "homepage": "https://bioinfo.genotoul.fr/index.php/events/how-to-run-a-nf-core-nextflow-workflow-on-genotoul-2/",
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            ],
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        },
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            "id": 298,
            "name": "LINUX",
            "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.",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/linux-2-2/",
            "is_draft": false,
            "costs": [
                "Non-academic: 550€ + 20% taxes (TVA)",
                "Academic but non-INRAE: 170 € + 20% taxes (TVA)",
                "For INRAE's staff: 150 € no VAT charged;"
            ],
            "topics": [
                "http://edamontology.org/topic_3316"
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            "updated_at": "2024-06-05T08:59:07.762580Z",
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            "hoursPresentations": 3,
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            "id": 332,
            "name": "SHORT-READ ALIGNMENT AND SMALL SIZE VARIANTS CALLING",
            "shortName": "",
            "description": "This training session, organized jointly with the Sigenae platform, is designed to introduce NGS data, in particular Illumina Solexa technologies with command line. You will discover the new sequence formats, the assembly formats and the known biases of these technologies. You will use mapping on reference genome software, polymorphisms detection with the GATK pipeline and alignment visualization software.\r\n\r\nThis training is focused on the practice. It consists of modules with a large variety of exercises:\r\n\r\nDay 1 (09:00 am to 12:30 am): Fastq format / Sequence quality. Read mapping.\r\nDay 1 (14:00 pm to 17:00 pm): SAM format. Visualisation.\r\nDay 2 (09:00 am to 17:00 am): Variant calling. VCF format. Variant annotation (SNPeff / SNPsift).\r\n \r\nThe session will take place in the room ‘salle de formation’ at INRAE center of Toulouse-Auzeville.\r\n\r\nPrerequisites: ability to use a Unix environment (see Unix training) and Cluster (see Cluster training).\r\n \r\nTool box: FastQC, BWA, Samtools, Picard tools, GATK, SnpSift / SnpEff, IGV.",
            "homepage": "https://bioinfo.genotoul.fr/index.php/events/alignment-and-small-size-variants-calling/",
            "is_draft": false,
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                "Academic but non-INRAE: 170 € + 20% taxes (TVA)",
                "For INRAE's staff: 150 € no VAT charged;"
            ],
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                "http://edamontology.org/topic_0102",
                "http://edamontology.org/topic_2885"
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            "id": 382,
            "name": "Introduction à l'analyse de données transcriptomiques avec Galaxy",
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            ],
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            "difficultyLevel": "Novice",
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                }
            ],
            "learningOutcomes": "At the end of the tutorial, learners would be able to:\r\n- Check a sequence quality report generated by FastQC for RNA-Seq data\r\n- Explain the principle and specificity of mapping of RNA-Seq data to an eukaryotic reference genome\r\n- Select and run a state of the art mapping tool for RNA-Seq data\r\n- Evaluate the quality of mapping results\r\n- Describe the process to estimate the library strandness\r\n- Estimate the number of reads per genes\r\n- Explain the count normalization to perform before sample comparison\r\n- Construct and run a differential gene expression analysis\r\n- Analyze the DESeq2 output to identify, annotate and visualize differentially expressed genes\r\n- Perform a gene ontology enrichment analysis\r\n- Perform and visualize an enrichment analysis for KEGG pathways",
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