Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=80&ordering=keywords
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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/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?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": 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": 46, "name": "BioBlend API", "description": "BioBlend module, a python library to use Galaxy API\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/bioblend_api.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy", "Python", "API" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/189/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/414/?format=api", "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": 37, "name": "Connecting Galaxy to a compute cluster", "description": "Problems\nRunning jobs on the Galaxy server negatively impacts Galaxy UI performance\nEven adding one other host helps\nCan restart Galaxy without interrupting jobs\nSolution:\nConnecter Galaxy to a computing cluster\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/05-compute-cluster/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy", "Cluster" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?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" ] }, { "id": 96, "name": "Training on Galaxy : Metagenomics", "description": "Find Rapidly OTU with Galaxy Solution\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://genoweb.toulouse.inra.fr/~formation/15_FROGS/April2016/FROGS_april_2016_Formation.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics", "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/215/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/716/?format=api" ] }, { "id": 130, "name": "Taxonomic Profiling and Visualization of Metagenomic Data", "description": "This tutorial covers the questions:\r\n- Which species (or genera, families, …) are present in my sample?\r\n- What are the different approaches and tools to get the community profile of my sample?\r\n- How can we visualize and compare community profiles?\r\n\r\nAt 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", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html", "fileName": "taxonomic-profiling", "topics": [ "http://edamontology.org/topic_3697", "http://edamontology.org/topic_3174", "http://edamontology.org/topic_0637" ], "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": 35, "name": "Defining and importing genomes, Data Managers into Galaxy", "description": "Intro to built in datasets\nBuilt in data hierarchy\nSome problems\nData Managers\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/07-genomes-datamanagers/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/662/?format=api" ] }, { "id": 34, "name": "Users, Groups, and Quotas in Galaxy", "description": "How to handle Users, Groups, and Quotas in Galaxy\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/08-quota-users-groups/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/662/?format=api" ] }, { "id": 132, "name": "Metatranscriptomics analysis using microbiome RNA-seq data", "description": "This tutorial covers the questions:\r\n- How to analyze metatranscriptomics data?\r\n- What information can be extracted of metatranscriptomics data?\r\n- How to assign taxa and function to the identified sequences?\r\n\r\nAt the end of the tutorial, learners would be able to:\r\n- Choose the best approach to analyze metatranscriptomics data\r\n- Understand the functional microbiome characterization using metatranscriptomic results\r\n- Understand where metatranscriptomics fits in ‘multi-omic’ analysis of microbiomes\r\n- Visualise a community structure", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics/tutorial.html", "fileName": "metatranscriptomics", "topics": [ "http://edamontology.org/topic_1775", "http://edamontology.org/topic_3941" ], "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": 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": 36, "name": "Galaxy Administration", "description": "How to use the administation panel of Galaxy\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day4/admin/06-admin/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/662/?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": 58, "name": "Isoform discovery and quanti cation from RNA-Seq data", "description": "Not available\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/R04_EBA2016_RNAseq_Isoforms.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/605/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/159/?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" ] } ] }