Handles creating, reading and updating training events.

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            "name": "Linux For Jedi",
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            "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.",
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            "name": "Guide de survie à Perl pour la bioinformatique",
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            "description": "This course provides an introduction to programming using Perl and at the end of the training, participants could write simple Perl programs to handle biological data and to undertstand more complex Perl programs written by others.\n\t\t\t \n \n \n \n",
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            "name": "Survival Guide for Perl applied to Bioinformatics",
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            "description": " \n\n\t\t\tThis course provides an introduction to programming using Perl and at the end of the training, participants could write simple Perl programs to handle biological data and to undertstand more complex Perl programs written by others.\n\t\t\t\nPrerequisites\nBasic knowledge of Linux (Linux for dummies required)\n\nProgram\nPerl data structures (scalar,arrays, hashes)\nStructure control ( loops)\nBasic functions, and operators.\nWriting and running your own program\nPassing options and files to his own script.\nRegular expressions\n\n\nLearning objectives\nWriting simple Perl programs to analyze data files\nUnderstanding Perl programs written by others\nUsing Perl basic syntax and modules in their own script\nRun programs from their script, parsing and extracting data from data files\n\n\nInstructors\n\n\nChristine Tranchant  - christine.tranchant@ird.fr\nFrançois Sabot - francois.sabot@ird.fr\nNdomassi tando - ndomassi.tando@ird.fr\n\n",
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            "name": "Introduction to python",
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            "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",
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            "name": "Installing and Managing a High-Performance Computing (HPC) Cluster ",
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            "description": "This course ran for 5 days covering all the concepts necessary to  install and manage a high-performance computing (HPC) cluster. During this course,  a HPC cluster were installed at CERAAS (Thiès, Sénégal)  by the participants, IT managers from western africa (IRD, ISRA, CERAAS).\n",
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            "name": "Introduction to galaxy: looking for variants in prokaryotes",
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            "description": "This course will focus on the technical aspects of using a galaxy server. Accessible without any prerequisite in computer science, it will allow you to master the different fundamental tools of galaxy and will open the doors of bioinformatics analysis for your different projects.\r\nDifferent questions will be addressed through an example of variants analysis in a prokaryotic organism. At the end of this course, on any accessible galaxy instance, you will be able to:\r\n- upload your data\r\n- map them on a reference genome\r\n- find the variants (SNPs) and analyze the results\r\n- generate, manipulate and share your workflows, data and histories\r\n- find the right tools for other analyses and use them in your own project.\r\n\r\nUnless all participants speak French, the course will be taught in English.",
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            "name": "NGS data analysis on the command line",
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            "description": "This hands-on course will teach bioinformatic approaches for analyzing Illumina sequencing data. Our goal is to introduce the command line skills you need to make the most of your NGS data. \r\nDuring this 4-day training we will first introduce the Linux environment, shell commands and basic R scripting.  And then we will focus on two NGS data analyses -- small RNA-seq and RNA-seq -- based on published datasets from the model organism Arabidopsis thaliana",
            "homepage": "https://www.ibmp.cnrs.fr/bioinformatics-trainings/",
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            "updated_at": "2024-01-22T14:51:37.215331Z",
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            "name": "Improve your command line skills by learning a few words of Perl",
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            "description": "This “Perl one-liners” training session is organized by the Sigenae platform. Perl one-liners are small and awesome Perl programs that fit in a single line of code and perform many operations such as replacing of text, spacing, deleting, calculation, manipulation in files and many more. This training will allow you to discover the power of Perl on the command line and learn how to use it to automate your file manipulations and command line generation with classical file formats such as tabulated text, fastq, sam/bam, and vcf.\r\n\r\nThis training lasts one day and is focused on practice. It consists of 3 parts with a large variety of exercises:\r\n\r\nIntroduction to Perl and its characteristics: Perl is a widely used programming language for data processing and task automation. We will introduce the main characteristics of Perl and discuss why it is particularly suited for biologists who want to manipulate files and generate command lines.\r\nPerl on the command line: we will show how to use Perl on the command line to perform common tasks, such as searching and replacing strings, merging files, and loop over lists of files.\r\nConcrete examples: we will present several concrete examples drawn from biology, such as extracting information from genomic sequence files, converting files between different formats, and generating command lines for data biology tools.\r\n \r\nThe session will take place in the room ‘salle de formation MIAT’ at INRAE center of Toulouse-Auzeville.",
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                "Non-academic: 550€ + 20% taxes (TVA)",
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            "updated_at": "2023-04-06T13:37:15.444074Z",
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            "name": "RNAseq de novo assembly",
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            "description": "This training session has been designed to give you an overview of the methods and tools used to de novo assemble transcriptomic short reads. You will learn how to pre-process your raw data (fastq files), how an assembler works and how to use it. Finally you will learn how to assess the quality of your assemblies in order to choose the best one. Organized jointly by the Sigenae and bioinfo genotoul platforms.\n",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/rnaseq-de-novo-assembly-2/",
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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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            "id": 66,
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            "description": "This training session is designed to help you to deal with small RNA sequences produced from the SGS (Second Generation Sequencing) technology particularly Illumina platforms (HiSeq). You will discover sequence file formats, learn about expression profiles of miRNA and other small non coding RNA and run different kind of analysis such as reads cleaning, alignment on a reference genome, detection and annotation of new and known miRNA, and expression quantification. Organized jointly by the Sigenae and bioinfo genotoul platforms.\n",
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            "id": 69,
            "name": "Methods for phylogenetics trees construction",
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            "description": "This training session is organized by the bios4Biol CATI and aims at training participants to construct and interpret phylogenetic trees.\nYou will discover how to choose an evolutionary model and a phylogenetic inference method (among distance, parsimony, maximum likelihood and Bayesian methods) and how to evaluate the robustness of a tree using bootstrap.\n",
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            "keywords": [
                "Phylogeny",
                "Evolution and Phylogeny",
                "Molecular evolution",
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            "openTo": "Internal personnel",
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            "name": "Sequences alignment and phylogeny ",
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            "description": "This training session is organized by the bios4Biol CATI and the genotoul bioinfo platform and aims at initiating participants to molecular phylogenetics studies.\nYou will discover how to build a sequence dataset, to align sequences, to edit and refine the resulting alignment.\n",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/sequences-alignment-phylogeny/",
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            "id": 70,
            "name": "Phylogenomy and selection pressure ",
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            "description": "This training session is organized by the bios4Biol CATI.\nMorning : phylogenomics\nThe morning course will provide insigths about sampling problems in phylogenomics studies (genes, species) and methodological aspects of phylogenomics studies with two major focus on super-matrix and super-tree methods.\nAfternoon : selection pressure\nThe afternoon course will be dedicated to the use of the PAML4 package in order to study selection pressures in a sequence alignment.\n",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/phylogenomics-and-selection-pressure…",
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            "keywords": [
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                "Evolution and Phylogeny",
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            "openTo": "Internal personnel",
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            "name": "HOW TO RUN A NF-CORE NEXTFLOW WORKFLOW ON GENOTOUL ?",
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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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            "updated_at": "2024-06-03T14:51:40.327145Z",
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            "audienceRoles": [
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            ],
            "difficultyLevel": "Novice",
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            "name": "LINUX",
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            "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)",
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            "topics": [
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            "updated_at": "2024-06-05T08:59:07.762580Z",
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            "name": "Analysis of shotgun metagenomic data",
            "shortName": "",
            "description": "This training session is organized by the Genotoul bioinfo platform. This course is dedicated to the analysis of prokaryotic shotgun metagenomic data from Illumina and Pacbio HiFi sequencing technology. \r\n\r\nAfter an overview of metagenomics and the biases and limitations of analyses, we will look at the main steps involved in analysing metagenomic data and launch independent tools on the genobioinfo cluster.\r\nLearners will then test a workflow to automate processing on a test dataset (metagWGS ).\r\nOn the third day, learners will choose which analysis strategy to start with according to their experimental design and launch the first stage of metagWGS on their own data.\r\nBy the end of the course, trainees will be familiar with the scope, advantages and limitations of shotgun sequencing data analysis and will have started the analysis on their own data.\r\n\r\ncalendar\r\n \r\n\r\nThis training is focused on practice. It consists of several modules with a large variety of exercises:\r\n\r\nFirst Day\r\nStart at 09:00 am\r\nTour de table\r\nIntroduction to metagenomics, Illumina and Pacbio data, analysis stages, analysis limits, etc.\r\nPresentation of some key tools for each stage\r\nPractical work on the main stages launched independently\r\nEnd at 17:00 pm\r\nSecond Day\r\nStart at 09:00 am\r\nIntroduction to the advantages and disadvantages of workflows and containers\r\nLaunch of the data cleansing stage\r\nLaunch of the rest of the workflow and analysis of the multiQC report\r\nEnd at 17:00 pm\r\nThird Day – BYOD\r\nStart at 09:00 am\r\nDefine the analysis strategy and launch the start of the analysis of your own data.\r\nEnd at 17:00 pm maximum",
            "homepage": "https://bioinfo.genotoul.fr/index.php/events/analysis-of-shotgun-metagenomic-data/",
            "is_draft": false,
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                "Non-academic for non-academic: 1650€ + 20% taxes (TVA)",
                "Academic non-INRAE for academic but non-INRAE: 510 € + 20% taxes (TVA)",
                "INRAE for INRAE's staff: 450 € no VAT charged"
            ],
            "topics": [
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            "prerequisites": [
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                "Cluster"
            ],
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                    "id": 82,
                    "name": "INRAE",
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                    "id": 88,
                    "name": "BioinfOmics",
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            "logo_url": "http://bioinfo.genotoul.fr/wp-content/uploads/bioinfo_logo-rvb-petit.png",
            "updated_at": "2024-12-06T20:57:37.754921Z",
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            "id": 75,
            "name": "Galaxy: metagenomic: sequence analysis of amplicons from MiSeq and 454 sequencing with FROGS with Galaxy first step and statistics",
            "shortName": "",
            "description": "This training session, organized by Bioinfo Genotoul, Sigenae, NED (GenPhySE) and TWB, is designed to help you to deal with NGS data of 16S, 18S ... DNA produced with MiSeq from Illumina and Roche 454 technologies in the Galaxy workbench.\nYou will discover how to use our Galaxy instance, clean reads, clusterize them, do the taxonomic affiliation and perform statistics to interpret your results.\nPrerequisites: knowledge of R or in another programming language\n",
            "homepage": "http://bioinfo.genotoul.fr/index.php",
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            "id": 144,
            "name": "FROGS formation : tools for bioinformatics and statistics analyses with amplicon metagenomics data",
            "shortName": "",
            "description": "This training session, organized by Bioinfo Genotoul, Sigenae, NED (GenPhySE) and TWB, is designed to help you to deal with NGS data of 16S, 18S ... DNA produced with MiSeq from Illumina and Roche 454 technologies in the Galaxy workbench.\nYou will discover how to use our Galaxy instance, clean reads, clusterize them, do the taxonomic affiliation and perform statistics to interpret your results.\nPrerequisites: knowledge of R or in another programming language\n",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/metagenomic-amplicons-and-stats-with…",
            "is_draft": false,
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            "openTo": "Internal personnel",
            "accessConditions": "Subscribe by the web page : http://bioinfo.genotoul.fr/index.php/training-2/galaxy-training/.\nPrices : 165 euros per day for academic people, 550 per day otherwise.\n",
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        {
            "id": 64,
            "name": "Read alignment and SNP calling",
            "shortName": "",
            "description": "This training session, organized jointly with the Sigenae platform, is designed to help you deal with NGS data, in particular Roche 454 and Illumina Solexa technologies. You will discover the new sequence formats, the new assembly formats and the known biases of these technologies. You will use mapping on reference genome software, polymorphisms detection (with the GATK pipeline), polymorphisms annotation and alignment visualization software. Organized jointly by the Sigenae and bioinfo genotoul platforms.\n",
            "homepage": "http://bioinfo.genotoul.fr/index.php/events/alignment-and-small-size-variants-ca…",
            "is_draft": false,
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            ],
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            "keywords": [
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                "Variant analysis",
                "Genomics (DNA-seq)"
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