Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=120&ordering=difficultyLevel
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Create your own Gene-regulation appliance\nCreation of an instance\nInstalling programs and dependencies\nGet the gene-regulation repository\nRun makefile to install the dependencies\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/rioualen/gene-regulation/blob/master/doc/gene-regulation_tutorials/gene-regulation_with_IFB_cloud.Rmd", "fileName": "missing.txt", "topics": [], "keywords": [ "Gene regulation", "Cloud Computing" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-05-31", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/660/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api" ] }, { "id": 124, "name": "Snakemake tutorial: Gene regulation", "description": "Workflow 1: Rules and targets\nWorkflow 2: Introducing wildcards\nWorkflow 3: Keywords\nWorkflow 4: Combining rules\nWorkflow 5: Configuration file\nWorkflow 6: Separated files\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://gene-regulation.readthedocs.io/en/latest/snakemake.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Gene regulation", "Snakemake" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-13", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/660/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api" ] }, { "id": 126, "name": "Galaxy 101 for everyone", "description": "This practical aims at familiarizing you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows and sharing your work. Not everyone has the same background and that’s ok!", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html", "fileName": "galaxy-intro-101-everyone", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 147, "name": "Data-brokering script", "description": "This project generates metadata in JSON-LD format for plant and animal biological samples and submits them to the European Nucleotide Archive (ENA)'s BioSamples database. The metadata is extracted from an Excel file and validated against the Plant MIAPPE checklist for plant samples and against the BioSamples minimal checklist for animal samples. Samples are then either submitted as new entries or updated if they already exist in the database.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://forgemia.inra.fr/urgi-is/data-brokering", "fileName": "submit_data_biosamples_X.py", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [ { "id": 26, "name": "URGI", "url": "https://catalogue.france-bioinformatique.fr/api/team/URGI/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/441/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/813/?format=api" ] }, { "id": 146, "name": "Processing_large_files_with_sed_awk_2024", "description": "This “Sed and AWK to modify large text files” training session is organized by the Genotoul bioinfo platform.\r\n\r\nThe Linux sed command is a powerful and very fast text editor without an interface. Sed can select, substitute, add, delete, and modify text in files and streams. Sed relies heavily on regular expressions for pattern matching and text selection. We’ll manipulate regexes and the sed command to modify and filter several type of file often used in bioinformatics.\r\n\r\nAWK enables to easily process columns in large text files but is also a quite powerfull programming language. This training session aims at introducing you AWK principles. You will learn about variables, operators and functions useful to manipulate very large files. \r\n\r\nFor example you can use AWK to generate your unix command lines to be launched on the cluster. AWK enables to process millions of lines in text files. The course includes short feature presentations between long hands-on sessions in which you will be able to understand the global ideas as well as details.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://web-genobioinfo.toulouse.inrae.fr/~klopp/SedAwk2024/Processing_large_files_with_sed_awk_2024.pdf", "fileName": "Processing_large_files_with_sed_awk_2024.pdf", "topics": [], "keywords": [], "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "Biologists", "Bioinformaticians" ], "difficultyLevel": "Intermediate", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": "2024-03-01", "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 151, "name": "Metagenomic training", "description": "Slides and link to practical session parts", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://bioinfo.genotoul.fr/wp-content/uploads/Formation2025.pdf", "fileName": "Formation2025.pdf", "topics": [ "http://edamontology.org/topic_3174" ], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 148, "name": "One line perl", "description": "Improve your command line skills by learning a few words of Perl (08/12/2025)\r\nThe GenoToul bioinformatics platform and Sigenae organize a series of training courses to familiarize yourself with the various resources it provides. These resources are currently: the hardware infrastructure, biological data banks and widely used bioinformatics softwares. 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\ncalendar\r\n \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.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://web-genobioinfo.toulouse.inrae.fr/~ccabau/Perl_One-liner.pdf", "fileName": "Perl_One-liner.pdf", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 135, "name": "training RNASEQ Bioinfo part", "description": "Cette formation a pour but de vous aider à traiter les séquences courtes issues des plates-formes de séquençage Illumina. Vous y découvrirez les formats de séquences et d’alignement les biais connus et mettrez en œuvre des logiciels d'alignement épissé sur génome de référence, la recherche de nouveaux gènes, de nouveaux transcrits et la quantification de l'expression de ces gènes et transcrits.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genotoul-bioinfo.pages.mia.inra.fr/training-rnaseq", "fileName": "training-rnaseq", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 141, "name": "training material sed and awk training", "description": "training material sed and awk training (genotoul bioinfo facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genoweb.toulouse.inra.fr/~klopp/SedAwk2024/Processing_large_files_with_sed_awk_2024.pdf", "fileName": "Processing_large_files_with_sed_awk_2024.pdf", "topics": [ "http://edamontology.org/topic_3316" ], "keywords": [ "Programming Languages & Computer Sciences" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "Creative Commons Attribution 4.0 International License", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 136, "name": "training RNASeq biostat part", "description": "This course is part of the INRAE training session about “bioinformatics and biostatistics analysis of RNA-seq data” and of the Biostatistics platform “Initiation à LA statistique, niveau 4”. \r\nThe material provided on the present webpage is related to the biostatistics part and covers the following topics:\r\n\r\nR and RStudio\r\ndesign of experiments\r\nvariability\r\ncount data normalization\r\ndifferential analysis\r\nThe material has originally been prepared by Ignacio Gonzales, Annick Moisan and myself. The class has already been taught by these persons but also by Gaëlle Lefort and Jérôme Mariette.\r\n\r\nPre-requisites: A background in R programming is necessary for this class. Before the class, please download the course material and install R, RStudio and the packages as described below. To produce high quality figures, I will use ggplot2 for plots but will not enter into details about the ggplot2 syntax. If you are not familiar with it, you can just use these command lines or switch to base plots instead.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://www.nathalievialaneix.eu/teaching/rnaseq.html", "fileName": "rnaseq.html", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Intermediate", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 134, "name": "Nucleoli segmentation and feature extraction using CellProfiler", "description": "This tutorial covers the following questions:\r\n- How do I run an image analysis pipeline on public data using CellProfiler?\r\n- How do I analyse the DNA channel of fluorescence siRNA screens?\r\n- How do I download public image data into my history?\r\n- How do I segment and label cell nuclei?\r\n- How do I segment nucleoli (as the absence of DNA)?\r\n- How do I combine nuclei and nucleoli into one segmentation mask?\r\n- How do I extract the background of an image?\r\n- How do I relate the nucleoli to their parent nucleus?\r\n- How do I measure the image and object features?\r\n- How do I measure the image quality?\r\n\r\nAt the end of the tutorial, 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.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/tutorial.html", "fileName": "tutorial-CP", "topics": [ "http://edamontology.org/topic_3383", "http://edamontology.org/topic_3382" ], "keywords": [ "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 133, "name": "Introduction to image analysis using Galaxy", "description": "This tutorial covers the questions:\r\n- How do I use Galaxy with imaging data?\r\n- How do I convert images using Galaxy?\r\n- How do I display images in Galaxy?\r\n- How do I filter images in Galaxy?\r\n- How do I segment simple images in Galaxy?\r\n\r\nAt 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.", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html", "fileName": "imaging-introduction", "topics": [ "http://edamontology.org/topic_3383", "http://edamontology.org/topic_3382" ], "keywords": [ "Galaxy" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 142, "name": "Introduction to python", "description": "Training slides (theory and exercises)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training-python-for-biology-genotoul-bioinfo-a77c191514cdd1dc1b.pages.mia.inra.fr/#/title-slide", "fileName": "training-python-for-biology", "topics": [ "http://edamontology.org/topic_3316" ], "keywords": [ "Python Language" ], "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "Life scientists" ], "difficultyLevel": "Novice", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "Creative Commons Attribution 4.0 International License", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 143, "name": "workflows nf-core", "description": "Tutorial to launch and configure nf-core workflows on genotoul bioinfo cluster", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genotoul-bioinfo.pages.mia.inra.fr/use-nextflow-nfcore-course/", "fileName": "use-nextflow-nfcore-course", "topics": [ "http://edamontology.org/topic_0769" ], "keywords": [ "Nextflow" ], "audienceTypes": [ "Professional (continued)" ], "audienceRoles": [ "Life scientists" ], "difficultyLevel": "Novice", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 137, "name": "Linux slides", "description": "Slides for linux session (genotoul bioinfo facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://bioinfo.genotoul.fr/wp-content/uploads/Formation_LINUX_GenoToul_2024.pdf", "fileName": "Formation_LINUX_GenoToul_2024.pdf", "topics": [], "keywords": [ "Operating systems" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 138, "name": "Linux TP", "description": "TP for linux training (genotoul bioinfo facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genotoul-bioinfo.pages.mia.inra.fr/linux-cluster/", "fileName": "linux-cluster", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 139, "name": "Cluster Slides", "description": "Slides for Cluster training (bioinfo genotoul facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://bioinfo.genotoul.fr/wp-content/uploads/Formation_cluster_SLURM_2024.pdf", "fileName": "Formation_cluster_SLURM_2024.pdf", "topics": [], "keywords": [ "Cluster" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 140, "name": "TP Cluster", "description": "TP for cluster training (bioinfo genotoul facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://genotoul-bioinfo.pages.mia.inra.fr/linux-cluster/", "fileName": "linux-cluster", "topics": [], "keywords": [ "Cluster" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 144, "name": "Reference-based RNA-Seq data analysis with Galaxy", "description": "This tutorial covers the questions:\r\n- What are the steps to process RNA-Seq data?\r\n- How to identify differentially expressed genes across multiple experimental conditions?\r\n- What are the biological functions impacted by the differential expression of genes?\r\n\r\nAt 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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html", "fileName": "rna-seq", "topics": [ "http://edamontology.org/topic_0102", "http://edamontology.org/topic_1775", "http://edamontology.org/topic_0203", "http://edamontology.org/topic_3308", "http://edamontology.org/topic_3170" ], "keywords": [ "Galaxy", "RNA-seq" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] }, { "id": 145, "name": "Introduction to Transcriptomics", "description": "This slidedecks presents the concepts behind transcriptomics", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/introduction/slides.html", "fileName": "transcriptomics-introduction", "topics": [ "http://edamontology.org/topic_0203", "http://edamontology.org/topic_3308", "http://edamontology.org/topic_3170" ], "keywords": [ "RNA-seq", "Transcriptomics (RNA-seq)" ], "audienceTypes": [ "Undergraduate", "Graduate", "Professional (initial)", "Professional (continued)" ], "audienceRoles": [ "Researchers", "Life scientists", "Biologists" ], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC-BY-4.0", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api" ] } ] }