Galaxy Training

GitHub repository and its website companion containing a collection of training materials for teaching next generation sequencing data analysis uing Galaxy.

Galaxy Training https://tess.elixir-europe.org/content_providers/galaxy-training GitHub repository and its website companion containing a collection of training materials for teaching next generation sequencing data analysis uing Galaxy. /system/content_providers/images/000/000/078/original/GTNLogo1000.png?1501677361
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Resources related to configuration and maintenance of Galaxy servers

Resource type: Slides

Galaxy Server administration - Advanced customisation of a Galaxy instance https://tess.elixir-europe.org/materials/galaxy-server-administration-advanced-customisation-of-a-galaxy-instance Resources related to configuration and maintenance of Galaxy servers

Resources related to configuration and maintenance of Galaxy servers

Galaxy Server administration - Galaxy from an administrator point of view https://tess.elixir-europe.org/materials/galaxy-server-administration-introduction Resources related to configuration and maintenance of Galaxy servers

ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of the Estrogen receptor? Objectives of the tutorial: - Inspect read quality with FastQC - Map reads with...

Resource type: Tutorial

ChIP-Seq data analysis - Identification of the binding sites of the Estrogen receptor https://tess.elixir-europe.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-estrogen-receptor ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of the Estrogen receptor? Objectives of the tutorial: - Inspect read quality with FastQC - Map reads with Bowtie2 - Assess the quality of an ChIP-seq experiments - Extract coverage files - Call enriched regions or peaks

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What is a tool for Galaxy? - How to build a tool/wrapper with the good practices? - How to deal with the...

Resource type: Tutorial

Development in Galaxy - Tool development and integration into Galaxy https://tess.elixir-europe.org/materials/development-in-galaxy-tool-development-and-integration-into-galaxy Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What is a tool for Galaxy? - How to build a tool/wrapper with the good practices? - How to deal with the tool environment? Objectives of the tutorial: - Discover what is a wrapper and its structure - Use the Planemo utilities to develop a good wrapper - Deal with the dependencies - Write functional tests - Make a tool ready for publishing in a ToolShed

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What is a Galaxy Interactive Tour? - How to create a Galaxy Interactive Tour? Objectives of the...

Resource type: Slides

Development in Galaxy - Galaxy Interactive Tours https://tess.elixir-europe.org/materials/development-in-galaxy-galaxy-interactive-tours Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What is a Galaxy Interactive Tour? - How to create a Galaxy Interactive Tour? Objectives of the tutorial: - Discover what is a Galaxy Interactive Tour - Be able to create a Galaxy Interactive Tour - Be able to add a Galaxy Interactive Tour in a Galaxy instance

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Running the Galaxy Training material website locally https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-running-the-galaxy-training-material-website-locally Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy. Questions of the tutorial: - How to setup the infrastructure to build training webpages? Objectives of the tutorial: - Installing packages needed for rendering the webpage - Running the GTN material website locally - Tracking changes to the content live in the webbrowser

Train the trainers

Train the trainers - Introduction to training with Galaxy https://tess.elixir-europe.org/materials/train-the-trainers-introduction Train the trainers

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Creating a new tutorial https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy. Questions of the tutorial: - How to integrate a new tutorial? - How to make a tutorial robust and reproducible? Objectives of the tutorial: - Create a tutorial from scratch - Link a tutorial to a topic - Create hands-on - Add technical support for a tutorial

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile...

Resource type: Tutorial

Genome Annotation - Genome annotation with Prokka https://tess.elixir-europe.org/materials/genome-annotation-genome-annotation-with-prokka Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements. Questions of the tutorial: - How to annotate a bacterial genome? - How to visualize annoted genomic features? Objectives of the tutorial: - Load genome into Galaxy - Annotate genome with Prokka - View annotations in JBrowse

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Set up a Galaxy for Training https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-set-up-a-galaxy-for-training Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy. Questions of the tutorial: - How do I prepare my Galaxy instance to support a training module? - How can I generate a Docker Galaxy instance for my topic? Objectives of the tutorial: - Use ephemeris to install the training requirements to a Galaxy instance - Create a docker image for a training topic

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How are RNA-Seq results stored? - Why are visualization techniques needed? - How to select our desired subjects for differential gene expression analysis? Objectives of the tutorial: - Manage RNA-Seq...

Resource type: Tutorial

Transcriptomics - Visualization of RNA-Seq results with CummeRbund https://tess.elixir-europe.org/materials/transcriptomics-visualization-of-rna-seq-results-with-cummerbund Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How are RNA-Seq results stored? - Why are visualization techniques needed? - How to select our desired subjects for differential gene expression analysis? Objectives of the tutorial: - Manage RNA-Seq results - Extract the desired subject for differential gene expression analysis - Visualize information

ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? Objectives of the tutorial: - Inspect read quality with FastQC -...

Resource type: Tutorial

ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) https://tess.elixir-europe.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-t-cell-acute-lymphocytic-leukemia-protein-1-tal1 ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? Objectives of the tutorial: - Inspect read quality with FastQC - Perform read trimming with Trimmomatic - Align trimmed reads with BWA - Assess quality and reproducibility of experiments - Identify Tal1 binding sites with MACS2 - Determine unique/common Tal1 binding sites from G1E and Megakaryocytes - Identify unique/common Tal1 peaks occupying gene promoters - Visually inspect Tal1 peaks with Trackster

Training material for all kinds of transcriptomics analysis.

Transcriptomics - Introduction to Transcriptomics https://tess.elixir-europe.org/materials/transcriptomics-introduction Training material for all kinds of transcriptomics analysis.

Train the trainers Questions of the tutorial: - What do we need to take care when running a workshop? - What are the good practices? Objectives of the tutorial: - Reflect on the things to do before, during and after a workshop

Train the trainers - Good practices to run a workshop https://tess.elixir-europe.org/materials/train-the-trainers-good-practices-to-run-a-workshop Train the trainers Questions of the tutorial: - What do we need to take care when running a workshop? - What are the good practices? Objectives of the tutorial: - Reflect on the things to do before, during and after a workshop

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - How is the Galaxy code structured? - What do the various other projects related to Galaxy do? - What...

Resource type: Slides

Development in Galaxy - Galaxy Code Architecture https://tess.elixir-europe.org/materials/development-in-galaxy-galaxy-code-architecture Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - How is the Galaxy code structured? - What do the various other projects related to Galaxy do? - What happens when I start Galaxy? Objectives of the tutorial: - Explore various aspects of the Galaxy codebase. - Understand the various top-level files and modules in Galaxy. - Understand how dependencies work in Galaxy's frontend and backend.

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What is the use of BioBlend? - How to use Galaxy through command line? Objectives of the tutorial: - Get...

Resource type: Slides

Development in Galaxy - BioBlend module, a Python library to use Galaxy API https://tess.elixir-europe.org/materials/development-in-galaxy-bioblend-module-a-python-library-to-use-galaxy-api Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What is the use of BioBlend? - How to use Galaxy through command line? Objectives of the tutorial: - Get familiar with BioBlend using IPython - Launch a Galaxy job / Visualize your actions with Galaxy - Launch a Galaxy workflow / Visualize your actions with Galaxy

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Galaxy Introduction - Visualization https://tess.elixir-europe.org/materials/galaxy-introduction-visualization Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to manipulate large numbers...

Resource type: Tutorial

Introduction to Galaxy - Using dataset collection https://tess.elixir-europe.org/materials/galaxy-introduction-collections Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which Galaxy instance should I use?

Resource type: Slides

Introduction to Galaxy Analyses - Options for using Galaxy https://tess.elixir-europe.org/materials/galaxy-introduction-options-for-using-galaxy Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which Galaxy instance should I use?

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - - Objectives of the tutorial: - - -

Galaxy Server administration - Move from dev instance to production instance https://tess.elixir-europe.org/materials/galaxy-server-administration-move-from-dev-instance-to-production-instance Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - - Objectives of the tutorial: - - -

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How do Galaxy histories...

Resource type: Tutorial

Introduction to Galaxy - Understanding Galaxy history system https://tess.elixir-europe.org/materials/introduction-to-galaxy-understanding-galaxy-history-system Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Tutorial

Contributing to the Galaxy Training Material - Contributing with GitHub via its interface https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-contributing-with-github-via-its-interface Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them accessible to researchers, it is scalable. In 2016, the Galaxy Training Network decide to set up a new infrastructure for delivering easily Galaxy related training material. The idea was to develop something open and online based on a community effort, as always in Galaxy. Questions of the tutorial: - How can I contribute to an open-source project with GitHub and its interface Objectives of the tutorial: - Edit a file via GitHub interface - Create a pull request - Update a pull request

This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - How to manipulate and process NGS data Objectives of the tutorial: - Learn about Fastq, SAM, and BAM.

Tutorials using public Galaxy at usegalaxy.org - NGS data logistics https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-ngs-data-logistics This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - How to manipulate and process NGS data Objectives of the tutorial: - Learn about Fastq, SAM, and BAM.

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How do we detect differences between a set of reads from a microorganism and a reference genome Objectives of the tutorial: - Find variants between a reference genome and a set of...

Resource type: Tutorial

Variant Analysis - Microbial Variant Calling https://tess.elixir-europe.org/materials/variant-analysis-microbial-variant-calling Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How do we detect differences between a set of reads from a microorganism and a reference genome Objectives of the tutorial: - Find variants between a reference genome and a set of reads - Visualise the SNP in context of the reads aligned to the genome - Determine the effect of those variants on genomic features - Understand if the SNP is potentially affecting the phenotype

This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - What is frequency of variants is so low that it is obscured by sequencing error rate? Objectives of the tutorial: - Learn about duplex sequencing and analysis of duplex reads

Tutorials using public Galaxy at usegalaxy.org - Calling very rare variants https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-calling-very-rare-variants This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - What is frequency of variants is so low that it is obscured by sequencing error rate? Objectives of the tutorial: - Learn about duplex sequencing and analysis of duplex reads

Train the trainers Questions of the tutorial: - What does Metadata in GTN means? - Which kind of metadata can I annotate? - For what is metadata used? Objectives of the tutorial: - Adding metadata for a tutorial - Defining learning objectives

Train the trainers - Creating a new tutorial - Defining metadata https://tess.elixir-europe.org/materials/train-the-trainers-creating-a-new-tutorial-defining-metadata Train the trainers Questions of the tutorial: - What does Metadata in GTN means? - Which kind of metadata can I annotate? - For what is metadata used? Objectives of the tutorial: - Adding metadata for a tutorial - Defining learning objectives

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - How does Galaxy manage users and groups? - How can I assign Quotas to specific users/groups? Objectives of the tutorial: - Learn the Galaxy user/group management and assign Quotas. - Understand...

Resource type: Slides

Galaxy Server administration - User, Group and Quota managment https://tess.elixir-europe.org/materials/galaxy-server-administration-user-group-and-quota-managment Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - How does Galaxy manage users and groups? - How can I assign Quotas to specific users/groups? Objectives of the tutorial: - Learn the Galaxy user/group management and assign Quotas. - Understand the Role Based Access Control (RBAC) of Galaxy.

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Slides

Data Manipulation - Data: Getting data into Galaxy https://tess.elixir-europe.org/materials/data-manipulation-data-getting-data-into-galaxy A collection of microtutorials explaining data manipulation within Galaxy

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Tutorial

Data Manipulation - Collections: Multisample Analysis https://tess.elixir-europe.org/materials/data-manipulation-collections-multisample-analysis A collection of microtutorials explaining data manipulation within Galaxy

A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - What is a workflow? - How can I create a workflow based on my analysis history? Objectives of the tutorial: - Learn how to extract a workflow from a Galaxy history - Learn how...

Resource type: Tutorial

User Interface and Features - Workflows: Extracting Workflows from Histories https://tess.elixir-europe.org/materials/user-interface-and-features-workflows-extracting-workflows-from-histories A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - What is a workflow? - How can I create a workflow based on my analysis history? Objectives of the tutorial: - Learn how to extract a workflow from a Galaxy history - Learn how to change a workflow using the workflow editor
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