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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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...

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

Train the trainers

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

Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are benefits and drawbacks of different quantitation methods? - How to choose which quantitation method bests suits my need? Objectives of the tutorial: - Choose your quantitation method.

Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method https://tess.elixir-europe.org/materials/proteomics-label-free-versus-labelled-how-to-choose-your-quantitation-method Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are benefits and drawbacks of different quantitation methods? - How to choose which quantitation method bests suits my need? Objectives of the tutorial: - Choose your quantitation method.

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data? - How can I perform taxonomy analysis and visualize metaproteomics data? - How can I perform...

Proteomics - Metaproteomics tutorial https://tess.elixir-europe.org/materials/proteomics-metaproteomics-tutorial Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data? - How can I perform taxonomy analysis and visualize metaproteomics data? - How can I perform functional analysis on this metaproteomics data? Objectives of the tutorial: - A taxonomy and functional analysis of metaproteomic mass spectrometry data.

Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are MS1 features? - How to quantify based on MS1 features? - How to map MS1 features to MS2 identifications? - How to evaluate and optimize the results? Objectives of the tutorial: - MS1 feature...

Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL) https://tess.elixir-europe.org/materials/proteomics-peptide-and-protein-quantification-via-stable-isotope-labelling-sil Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are MS1 features? - How to quantify based on MS1 features? - How to map MS1 features to MS2 identifications? - How to evaluate and optimize the results? Objectives of the tutorial: - MS1 feature quantitation and mapping of quantitations to peptide and protein IDs.

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that - How to...

Galaxy Server administration - Galaxy Database schema https://tess.elixir-europe.org/materials/galaxy-server-administration-galaxy-database-schema Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that - How to extract usage information, which can not be gathered using the given report tools - How to move from MySQL to PostgreSQL - Is there ever a need to manually change the contents of a table Objectives of the tutorial: - Learn some of the design concepts of the Galaxy database - Extract information from the Galaxy database - Get to know SchemaSpy

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 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.

Galaxy Introduction - Collections 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.

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Galaxy Server administration - Galaxy from an administrator point of view https://tess.elixir-europe.org/materials/galaxy-server-administration-introduction Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

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 an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Development in Galaxy - Galaxy from a developer point of view https://tess.elixir-europe.org/materials/development-in-galaxy-introduction Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Metagenomics - Introduction to metagenomics https://tess.elixir-europe.org/materials/metagenomics-introduction Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

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.

Introduction to Galaxy - Introduction to Galaxy https://tess.elixir-europe.org/materials/galaxy-introduction-introduction 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.

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task 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...

Galaxy Server administration - User, Group and Quota managment https://tess.elixir-europe.org/materials/galaxy-server-administration-user-group-and-quota-managment Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task 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.

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.

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

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 are Galaxy Interactive Environments (GIEs)? - How to enable GIEs in Galaxy? - How to develop your own...

Development in Galaxy - Galaxy Interactive Environments https://tess.elixir-europe.org/materials/development-in-galaxy-galaxy-interactive-environments 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 are Galaxy Interactive Environments (GIEs)? - How to enable GIEs in Galaxy? - How to develop your own GIE? Objectives of the tutorial: - Implement a Hello-World Galaxy Interactive Environment

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 can I make a custom plugin for Charts? Objectives of the tutorial: - Learn how to add custom...

Development in Galaxy - Visualizations: charts plugins https://tess.elixir-europe.org/materials/development-in-galaxy-visualizations-charts-plugins 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 can I make a custom plugin for Charts? Objectives of the tutorial: - Learn how to add custom javascript plugins to the Galaxy Charts framework

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 are Galaxy Webhooks? - How to create them? Objectives of the tutorial: - Discover what Galaxy...

Development in Galaxy - Galaxy Webhooks https://tess.elixir-europe.org/materials/development-in-galaxy-galaxy-webhooks 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 are Galaxy Webhooks? - How to create them? Objectives of the tutorial: - Discover what Galaxy Webhooks are - Be able to create Webhooks - Be able to add a Galaxy Webhook in a Galaxy instance

Analyses of sequences Questions of the tutorial: - What two things are crucial for a correct mapping? - What is BAM? Objectives of the tutorial: - You will learn what mapping is - A genome browser is shown that helps you to understand your data

Sequence analysis - Mapping https://tess.elixir-europe.org/materials/analysis-of-sequences-mapping Analyses of sequences Questions of the tutorial: - What two things are crucial for a correct mapping? - What is BAM? Objectives of the tutorial: - You will learn what mapping is - A genome browser is shown that helps you to understand your data

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

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How to perform analysis of RNAseq data when reference genome is available? Objectives of the tutorial: - Learns basic concepts of RNAseq analysis

Transcriptomics - Reference-based RNAseq data analysis (long) https://tess.elixir-europe.org/materials/transcriptomics-reference-based-rnaseq-data-analysis-long Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How to perform analysis of RNAseq data when reference genome is available? Objectives of the tutorial: - Learns basic concepts of RNAseq analysis

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 and process...

Introduction to Galaxy - NGS data logistics https://tess.elixir-europe.org/materials/introduction-to-galaxy-ngs-data-logistics 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 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 does frequency of mitochondrial polymorphisms change from mother to child? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in bacteria,...

Variant Analysis - Calling variants in non-diploid systems https://tess.elixir-europe.org/materials/variant-analysis-calling-variants-in-non-diploid-systems Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How does frequency of mitochondrial polymorphisms change from mother to child? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to find variable sites in diploid genomes? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in human genome.

Variant Analysis - Calling variants in diploid systems https://tess.elixir-europe.org/materials/variant-analysis-calling-variants-in-diploid-systems Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to find variable sites in diploid genomes? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in human genome.

Exome sequencing means that all protein-coding genes in a genome are sequenced 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

Variant Analysis - Calling very rare variants https://tess.elixir-europe.org/materials/variant-analysis-calling-very-rare-variants Exome sequencing means that all protein-coding genes in a genome are sequenced 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

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...

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 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...

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.
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