Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=120&ordering=-keywords
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"Transcriptomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/159/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/605/?format=api" ] }, { "id": 61, "name": "Differential gene expression analysis : Practical part", "description": "RNA-seq: Differential gene expression analysis practical session\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/R01b_EBA2016_TP_RNA-seq.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-22", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/371/?format=api" ] }, { "id": 53, "name": "RNA - Seq de novo", "description": "\n \n\nPractical session on transciptome de novo assembly\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/A01b_Galaxy_RNASeq_denovo_ITMO2016_TP_v2red.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/134/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/388/?format=api" ] }, { "id": 51, "name": "Eukaryotic small RNA", "description": "\n \n\nSmall RNAseq data analysis for miRNA identification\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/sRNA-Seq.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/642/?format=api" ] }, { "id": 60, "name": "Differential analysis of RNA-Seq data", "description": "Design, describe, explore and model\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/R02-R03_slidesRoscoff_stats_HVaret.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/371/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/626/?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": 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": 131, "name": "16S Microbial Analysis with mothur", "description": "This tutorial covers the questions:\r\n- What is the effect of normal variation in the gut microbiome on host health?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy\r\n- Using a mock community to assess the error rate of your sequencing experiment\r\n- Visualize sample diversity using Krona and Phinch", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html", "fileName": "mothur-miseq-sop-short", "topics": [ "http://edamontology.org/topic_3697", "http://edamontology.org/topic_0637" ], "keywords": [ "Galaxy", "Metabarcoding" ], "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": 120, "name": "Initiation to Galaxy", "description": "DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/GALAXY-TP-INITIATION-Roscoff-Septembre2015.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "DNA Analysis", "Variant calling", "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [] }, { "id": 49, "name": "Development in Galaxy", "description": "Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://github.com/galaxyproject/training-material/tree/master/Dev-Corner", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/77/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ] }, { "id": 48, "name": "Tool development and integration into Galaxy", "description": "Questions:\nWhat is a tool for Galaxy?\nHow to build a tool/wrapper with the good practices?\nHow to deal with the tool environment?\n \nObjectives:\nDiscover what is a wrapper and its structure\nUse the Planemo utilities to develop a good wrapper\nDeal with the dependencies\nWrite functional tests\nMake a tool ready for publishing in a ToolShed\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/tool_integration.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-16", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/663/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ] }, { "id": 47, "name": "ToolShed upload and tool-iuc PR", "description": "Questions\nWhat is a Tool Shed?\nHow to install tools and workflows from a Tool Shed into a Galaxy instance?\nWhat are the Tool Shed repository types?\nHow to publish with Planemo?\nObjectives\nDiscover what is a Tool Shed\nBe able to install tools and workflows from a Tool Shed into a Galaxy instance\nBe able to publish tools with Planemo\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day2/toolshed/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-17", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ] }, { "id": 129, "name": "Bacterial Genome Annotation", "description": "This tutorial covers the questions:\r\n- Which genes are on a draft bacterial genome?\r\n- Which other genomic components can be found on a draft bacterial genome?\r\n\r\nAt 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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html", "fileName": "bacterial-genome-annotation", "topics": [ "http://edamontology.org/topic_3301", "http://edamontology.org/topic_0219" ], "keywords": [ "Bacterial isolate", "Annotation", "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": 45, "name": "Galaxy Visualisation - Slides", "description": "Questions\n\n\n\tHow can visualization plugins benefit science?\n\n\n\nObjectives\n\n\n\tImplement a first Galaxy visualization\n\tUnderstand the client side vs. server side principle\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/visualizations.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/690/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/691/?format=api" ] }, { "id": 44, "name": "Galaxy Visualisation - Tutorial", "description": "Visualizations may be very helpful in understanding data better. There is a whole range of visualizations, from rather simple scatter and barplots up to projections of high dimensional data or even entire genomes. Many of these visualizations often require a lot of tweaking and changes in settings like zooming in and assigning colors, etc. Therefore, visualizations are ideally interactive, and changing settings is often an initial step in exploring data. For this reason it may be inconvenient to make use of static galaxy tools because it lacks these interactive features. For these situations Galaxy offers the option to create visualizations plugins, file format specific javascripts that integrate with the history menu, without making redundant copies of data.\nIn this tutorial we shall go through how this system works and create a simple visualization plugin. The tool will create a visualization of the number of aligned reads per chromosome of a BAM file, and we will discuss possible optimizations and advantages and disadvantages of the proposed implementation.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/tutorials/visualizations", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/690/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/691/?format=api" ] }, { "id": 43, "name": "Galaxy Interactive Tour", "description": "Questions\nWhat is a Galaxy Interactive Tour?\nHow to create a Galaxy Interactive Tour?\nObjectives\nDiscover what is a Galaxy Interactive Tour\nBe able to create a Galaxy Interactive Tour\nBe able to add a Galaxy Interactive Tour in a Galaxy instance\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/interactive_tour.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api" ] }, { "id": 42, "name": "Galaxy Installation", "description": "How to install a local instance of Galaxy\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/00-installation/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/563/?format=api" ] }, { "id": 41, "name": "Galaxy Configuration Hierarchy", "description": "How to configure your local instance of Galaxy\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/01-configuration-hierarchy/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/563/?format=api" ] }, { "id": 40, "name": "Galactic Database", "description": "How to choose a database for Galaxy and configure it\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/02-database/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/563/?format=api" ] }, { "id": 39, "name": "Galaxy Handlers", "description": "Galaxy is a web application that uses handlers to perform actions.\nThere are two main types of actions that are carried out by handlers:\nRespond to user requests; These actions are carried out by web handlers\nManage the execution of tools; These actions are performed by job handlers.\nBy default, Galaxy is configured to run a single handler that handles both user queries and jobs.\nDepending on the number of users accessing your Galaxy instance or the number of jobs you need to manage you may need to start web handlers or additional job handlers.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/03-handlers/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/563/?format=api" ] } ] }