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
Showing 120 materials out of 120. View all results.
Sequence analysis - 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

Resource type: Tutorial

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
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.

Resource type: Tutorial

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.
Galaxy Server administration - Docker and Galaxy

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - Why Docker? What is it? - How to use Docker? - How to integrate Galaxy in Docker to facilitate its deployment? Objectives of the tutorial: - Docker basics - Galaxy Docker image (usage) - Galaxy...

Resource type: Slides

Galaxy Server administration - Docker and Galaxy https://tess.elixir-europe.org/materials/galaxy-server-administration-docker-and-galaxy Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - Why Docker? What is it? - How to use Docker? - How to integrate Galaxy in Docker to facilitate its deployment? Objectives of the tutorial: - Docker basics - Galaxy Docker image (usage) - Galaxy Docker (internals) - Galaxy flavours
Metagenomics - Analyses of metagenomics data - The global picture

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms Questions of the tutorial: - How to analyze metagenomics data? - What information can be extracted of metagenomics data? - What is the difference between amplicon and shotgun data? - What are the difference...

Resource type: Tutorial

Metagenomics - Analyses of metagenomics data - The global picture https://tess.elixir-europe.org/materials/metagenomics-analyses-of-metagenomics-data-the-global-picture Metagenomics is a discipline that enables the genomic study of uncultured microorganisms Questions of the tutorial: - How to analyze metagenomics data? - What information can be extracted of metagenomics data? - What is the difference between amplicon and shotgun data? - What are the difference in the analyses of amplicon and shotgun data? Objectives of the tutorial: - Choosing the best approach to analyze metagenomics data - Selection of tools to analyze amplicon data or shotgun data - Visualisation of a community structure
Statistics - Interval-Wise Testing for omics data

Statistical Analyses for omics data Questions of the tutorial: - How to visualize high-resolution omics data in different groups of genomic regions? - How to evaluate differences in high-resolution omics data between groups of genomic regions? - How to detect locations and scales at which the...

Resource type: Tutorial

Statistics - Interval-Wise Testing for omics data https://tess.elixir-europe.org/materials/statistics-interval-wise-testing-for-omics-data Statistical Analyses for omics data Questions of the tutorial: - How to visualize high-resolution omics data in different groups of genomic regions? - How to evaluate differences in high-resolution omics data between groups of genomic regions? - How to detect locations and scales at which the significant effects unfold? Objectives of the tutorial: - Pre-process high-resolution omics data - Create pointwise boxplots corresponding to different groups of genomic regions - Perform the Interval-Wise Testing between two groups of genomic regions - Visualize and inspect test results - Detect relevant locations and scales
Transcriptomics - Reference-based RNA-Seq data analysis

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What are the effects of Pasilla (PS) gene depletion on splicing events? - How to analyze RNA sequencing data using a reference genome? Objectives of the tutorial: - Analysis of RNA sequencing data using...

Resource type: Tutorial

Transcriptomics - Reference-based RNA-Seq data analysis https://tess.elixir-europe.org/materials/transcriptomics-reference-based-rna-seq-data-analysis Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What are the effects of Pasilla (PS) gene depletion on splicing events? - How to analyze RNA sequencing data using a reference genome? Objectives of the tutorial: - Analysis of RNA sequencing data using a reference genome - Analysis of differentially expressed genes - Identification of functional enrichment among differentially expressed genes
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...

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
Proteomics - Peptide and Protein ID using OpenMS tools

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Peptide and Protein ID using OpenMS tools https://tess.elixir-europe.org/materials/proteomics-peptide-and-protein-id-using-openms-tools Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.
Galaxy Server administration - Galaxy from an administrator point of view

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
Sequence analysis - RAD-Seq de-novo data analysis

Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data without a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data without a reference genome - SNP calling from RAD sequencing data - Calculate...

Resource type: Tutorial

Sequence analysis - RAD-Seq de-novo data analysis https://tess.elixir-europe.org/materials/analysis-of-sequences-rad-seq-de-novo-data-analysis Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data without a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data without a reference genome - SNP calling from RAD sequencing data - Calculate population genomics statistics from RAD sequencing data
Introduction to Galaxy Analyses - Galaxy 101

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 coding exon has the...

Resource type: Tutorial

Introduction to Galaxy Analyses - Galaxy 101 https://tess.elixir-europe.org/materials/galaxy-introduction-galaxy-101 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 coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
Train the trainers - Introduction to training 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
Assembly - Unicycler Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Unicycler Assembly https://tess.elixir-europe.org/materials/assembly-unicycler-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - I have short reads and long reads. How do I assemble a genome? Objectives of the tutorial: - Perform Quality Control on your reads - Perform a Small genome Assembly with Unicycler - Evaluate the Quality of the Assembly with Quast - Annotate the assembly with Prokka
Transcriptomics - Introduction to Transcriptomics

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 - 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

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
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...

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
Introduction to Galaxy Analyses - Introduction to Genomics and 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: - Do genes on opposite strands...

Resource type: Tutorial

Introduction to Galaxy Analyses - Introduction to Genomics and Galaxy https://tess.elixir-europe.org/materials/introduction-to-galaxy-introduction-to-genomics-and-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: - Do genes on opposite strands ever overlap? If so, how often? Objectives of the tutorial: - Learn some of the basic concepts of genomics and bioinformatics - Familiarize yourself with the basics of Galaxy
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 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.
Introduction to Galaxy - Using dataset collection

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 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 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: - - -
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...

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
Contributing to the Galaxy Training Material - Good practices to run a workshop

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: Slides

Contributing to the Galaxy Training Material - Good practices to run a workshop https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-good-practices-to-run-a-workshop 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: - 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 Server administration - Advanced customisation of a Galaxy instance

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
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...

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
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.

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.
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...

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
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

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 - 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

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
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...

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
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...

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
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...

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.
Data Manipulation - Data: Getting data into 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
Data Manipulation - Collections: Multisample Analysis

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
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...

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
Introduction to Galaxy - Using dataset collection

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...

Introduction to Galaxy - Using dataset collection https://tess.elixir-europe.org/materials/introduction-to-galaxy-using-dataset-collection 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
Introduction to Galaxy - Rule Based Uploader

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 use the rule based...

Resource type: Tutorial

Introduction to Galaxy - Rule Based Uploader https://tess.elixir-europe.org/materials/introduction-to-galaxy-rule-based-uploader 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 use the rule based uploader to create complex collections Objectives of the tutorial: - Learn about the Rule Based Uploader
Tutorials using public Galaxy at usegalaxy.org - Calling variants in diploid systems

This tutorials cover a variety of analyses that can be performed at usegalaxy.org 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.

Tutorials using public Galaxy at usegalaxy.org - Calling variants in diploid systems https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-calling-variants-in-diploid-systems This tutorials cover a variety of analyses that can be performed at usegalaxy.org 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.
Metagenomics - Introduction to metagenomics

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
Introduction to Galaxy Analyses - Introduction to 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.

Introduction to Galaxy Analyses - 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.
ChIP-Seq data analysis - Introduction to ChIP-Seq data analysis

ChIP-sequencing is a method used to analyze protein interactions with DNA.

ChIP-Seq data analysis - Introduction to ChIP-Seq data analysis https://tess.elixir-europe.org/materials/chip-seq-data-analysis-introduction ChIP-sequencing is a method used to analyze protein interactions with DNA.
Tutorials using public Galaxy at usegalaxy.org - Calling variants in non-diploid systems

This tutorials cover a variety of analyses that can be performed at usegalaxy.org 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,...

Tutorials using public Galaxy at usegalaxy.org - Calling variants in non-diploid systems https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-calling-variants-in-non-diploid-systems This tutorials cover a variety of analyses that can be performed at usegalaxy.org 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.
Contributing to the Galaxy Training Material - Contributing with GitHub via command-line

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 command-line https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-contributing-with-github-via-command-line 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? - What is the GitHub flow? Objectives of the tutorial: - Fork a repository on GitHub - Clone a remote repository locally - Create a branch - Commit changes - Push changes to a remote repository - Create a pull request - Update a pull request
Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How is raw CLIP-Seq data processed and analysed? - How do I find binding motifs and targets for a protein (e.g., RBFOX2)? Objectives of the tutorial: - Remove Adapters, Barcodes and Unique Molecular...

Resource type: Tutorial

Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection https://tess.elixir-europe.org/materials/transcriptomics-clip-seq-data-analysis-from-pre-processing-to-motif-detection Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How is raw CLIP-Seq data processed and analysed? - How do I find binding motifs and targets for a protein (e.g., RBFOX2)? Objectives of the tutorial: - Remove Adapters, Barcodes and Unique Molecular Identifiers (UMIs) from the reads - Align trimmed reads with STAR - De-duplicate the read library - Inspect the read mapping and de-duplication quality - Perform peak calling with PEAKachu - Analyse the peaks and find potential binding motifs and targets - Check the quality of the peak calling
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...

Resource type: Slides

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
Train the trainers - Creating a new tutorial - Building a Docker flavor for a tutorial

Train the trainers Questions of the tutorial: - How can we define the technical infrastructure for a tutorial? - How to define the tools needed for a tutorial? - How to add the needed data directly in an instance? - How to add the workflows related to a tutorial? - How can we check the...

Train the trainers - Creating a new tutorial - Building a Docker flavor for a tutorial https://tess.elixir-europe.org/materials/train-the-trainers-creating-a-new-tutorial-building-a-docker-flavor-for-a-tutorial Train the trainers Questions of the tutorial: - How can we define the technical infrastructure for a tutorial? - How to define the tools needed for a tutorial? - How to add the needed data directly in an instance? - How to add the workflows related to a tutorial? - How can we check the technical infrastructure is working? Objectives of the tutorial: - Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial - Testing the Galaxy Docker flavor of a tutorial
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...

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
Data Manipulation - Collections: Rule Based Uploader

A collection of microtutorials explaining data manipulation within Galaxy Questions of the tutorial: - How to use the rule based uploader to create complex collections Objectives of the tutorial: - Learn about the Rule Based Uploader

Resource type: Tutorial

Data Manipulation - Collections: Rule Based Uploader https://tess.elixir-europe.org/materials/data-manipulation-collections-rule-based-uploader A collection of microtutorials explaining data manipulation within Galaxy Questions of the tutorial: - How to use the rule based uploader to create complex collections Objectives of the tutorial: - Learn about the Rule Based Uploader
Introduction to Galaxy - Extracting Workflows from Histories

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: - What is a workflow? - How can I...

Resource type: Tutorial

Introduction to Galaxy - Extracting Workflows from Histories https://tess.elixir-europe.org/materials/introduction-to-galaxy-extracting-workflows-from-histories 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: - 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
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...

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
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...

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
Variant Analysis - Calling very rare variants

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - What frequency of variants is so low that it is obscured by sequencing error rate? - What are the different types of consensus sequences produced from duplex sequencing? Objectives of...

Resource type: Tutorial

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 frequency of variants is so low that it is obscured by sequencing error rate? - What are the different types of consensus sequences produced from duplex sequencing? Objectives of the tutorial: - Processing raw duplex sequencing data into consensus sequences - Find rare variants without relying on diploid assumptions
Development in Galaxy - Galaxy from a developer point of view

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, ...
Tutorials using public Galaxy at usegalaxy.org - Reference-based RNAseq

This tutorials cover a variety of analyses that can be performed at usegalaxy.org 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

Tutorials using public Galaxy at usegalaxy.org - Reference-based RNAseq https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-reference-based-rnaseq This tutorials cover a variety of analyses that can be performed at usegalaxy.org 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
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...

Resource type: Tutorial

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
Train the trainers - Creating a new tutorial - Writing content in Markdown

Train the trainers Questions of the tutorial: - How to integrate a new tutorial? - How to write a tutorial with hands-on? Objectives of the tutorial: - Creating a tutorial from scratch - Creating hands-on

Train the trainers - Creating a new tutorial - Writing content in Markdown https://tess.elixir-europe.org/materials/train-the-trainers-creating-a-new-tutorial-writing-content-in-markdown Train the trainers Questions of the tutorial: - How to integrate a new tutorial? - How to write a tutorial with hands-on? Objectives of the tutorial: - Creating a tutorial from scratch - Creating hands-on
Development in Galaxy - Contributing with GitHub

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 contribute to an open-source project with GitHub Objectives of the tutorial: - Understand what...

Development in Galaxy - Contributing with GitHub https://tess.elixir-europe.org/materials/development-in-galaxy-contributing-with-github 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 contribute to an open-source project with GitHub Objectives of the tutorial: - Understand what is a pull request
Train the trainers - Creating a new tutorial - Creating Interactive Galaxy Tours

Train the trainers Questions of the tutorial: - What is a Interactive Galaxy Tour? - How can we create an Interactive Tour? Objectives of the tutorial: - Creating a Galaxy tour from scratch - Deploying and running a tour

Train the trainers - Creating a new tutorial - Creating Interactive Galaxy Tours https://tess.elixir-europe.org/materials/train-the-trainers-creating-a-new-tutorial-creating-interactive-galaxy-tours Train the trainers Questions of the tutorial: - What is a Interactive Galaxy Tour? - How can we create an Interactive Tour? Objectives of the tutorial: - Creating a Galaxy tour from scratch - Deploying and running a tour
Tutorials using public Galaxy at usegalaxy.org - Understanding Galaxy history system

This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories

Tutorials using public Galaxy at usegalaxy.org - Understanding Galaxy history system https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-understanding-galaxy-history-system This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories
Assembly - Introduction to Genome Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Introduction to Genome Assembly https://tess.elixir-europe.org/materials/assembly-introduction-to-genome-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - How do we perform a very basic genome assembly from short read data? Objectives of the tutorial: - assemble some paired end reads using Velvet - examine the output of the assembly.
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,...

Resource type: Tutorial

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.
Contributing to the Galaxy Training Material - Overview of the Galaxy Training Material

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...

Contributing to the Galaxy Training Material - Overview of the Galaxy Training Material https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-overview-of-the-galaxy-training-material 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.
Tutorials using public Galaxy at usegalaxy.org - Using dataset collection

This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections

Tutorials using public Galaxy at usegalaxy.org - Using dataset collection https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-using-dataset-collection This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections
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...

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
Contributing to the Galaxy Training Material - Generating PDF artefacts of the website

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 - Generating PDF artefacts of the website https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-generating-pdf-artefacts-of-the-website 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 generate PDF of the different tutorials and slides? Objectives of the tutorial: - Generating PDFs
Variant Analysis - Exome sequencing data analysis

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to identify the genetic variation with the use of exome sequencing? - What is the pipeline of the process of finding genetic variation which caused the disease? Objectives of the...

Resource type: Tutorial

Variant Analysis - Exome sequencing data analysis https://tess.elixir-europe.org/materials/variant-analysis-exome-sequencing-data-analysis Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to identify the genetic variation with the use of exome sequencing? - What is the pipeline of the process of finding genetic variation which caused the disease? Objectives of the tutorial: - Identification of the genetic variation using the exome sequencing - Using FreeBayes calls for variants generating - Variant analysis and GEMINI queries
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 -...

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
Sequence analysis - RAD-Seq to construct genetic maps

Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data for a genetic map study? Objectives of the tutorial: - SNP calling from RAD sequencing data - Find and correct haplotypes - Create input files for genetic map building software

Resource type: Tutorial

Sequence analysis - RAD-Seq to construct genetic maps https://tess.elixir-europe.org/materials/analysis-of-sequences-rad-seq-to-construct-genetic-maps Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data for a genetic map study? Objectives of the tutorial: - SNP calling from RAD sequencing data - Find and correct haplotypes - Create input files for genetic map building software
Galaxy Server administration - Galaxy Database schema

Resources related to configuration and maintenance of Galaxy servers 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,...

Resource type: Tutorial

Galaxy Server administration - Galaxy Database schema https://tess.elixir-europe.org/materials/galaxy-server-administration-galaxy-database-schema Resources related to configuration and maintenance of Galaxy servers 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
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...

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.
User Interface and Features - Jupyter: Use Jupyter notebooks in Galaxy

A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - How to use a Jupyter Notebook in Galaxy Objectives of the tutorial: - Learn about the Jupyter Interactive Environment

Resource type: Tutorial

User Interface and Features - Jupyter: Use Jupyter notebooks in Galaxy https://tess.elixir-europe.org/materials/user-interface-and-features-jupyter-use-jupyter-notebooks-in-galaxy A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - How to use a Jupyter Notebook in Galaxy Objectives of the tutorial: - Learn about the Jupyter Interactive Environment
Galaxy Server administration - Ansible

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - Why Ansible? - How and when to use Ansible? - How to write a role? - How to leverage community build roles? Objectives of the tutorial: - Learn Ansible basics - Write a simple role - Install a...

Resource type: Tutorial

Galaxy Server administration - Ansible https://tess.elixir-europe.org/materials/galaxy-server-administration-ansible Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - Why Ansible? - How and when to use Ansible? - How to write a role? - How to leverage community build roles? Objectives of the tutorial: - Learn Ansible basics - Write a simple role - Install a role from Ansible Galaxy
Epigenetics - Introduction to DNA Methylation data analysis

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Epigenetics - Introduction to DNA Methylation data analysis https://tess.elixir-europe.org/materials/epigenetics-introduction DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.
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...

Resource type: Tutorial

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.
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...

Resource type: Tutorial

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.
Sequence analysis - Genome Annotation

Analyses of sequences

Sequence analysis - Genome Annotation https://tess.elixir-europe.org/materials/analysis-of-sequences-genome-annotation Analyses of sequences
Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker https://tess.elixir-europe.org/materials/proteomics-peptide-and-protein-id Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to convert LC-MS/MS raw files? - How to identify peptides? - How to identify proteins? - How to evaluate the results? Objectives of the tutorial: - Protein identification from LC-MS/MS raw files.
Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can protein N-termini be enriched for LC-MS/MS? - How to analyze the LC-MS/MS data? Objectives of the tutorial: - Run an N-TAILS data analysis.

Resource type: Tutorial

Proteomics - Detection and quantitation of N-termini (degradomics) via N-TAILS https://tess.elixir-europe.org/materials/proteomics-ntails Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can protein N-termini be enriched for LC-MS/MS? - How to analyze the LC-MS/MS data? Objectives of the tutorial: - Run an N-TAILS data analysis.
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...

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
Contributing to the Galaxy Training Material - Creating a new tutorial - Writing content in Markdown

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 - Writing content in Markdown https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-writing-content-in-markdown 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 write a tutorial with hands-on? - What are the different boxes? - How can I add a caption to an image? Objectives of the tutorial: - Create hands-on - Use the different boxes
Contributing to the Galaxy Training Material - Creating a new tutorial - Creating Interactive Galaxy Tours

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 - Creating Interactive Galaxy Tours https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-creating-interactive-galaxy-tours 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: - What is a Interactive Galaxy Tour? - How can we create an Interactive Tour? Objectives of the tutorial: - Creating a Galaxy tour from scratch - Deploying and running a tour
Galaxy Server administration - Deployment and Platform options

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - What options to deploy Galaxy do I have? - Which platforms are supported by Galaxy? - What requirements does Galaxy have? Objectives of the tutorial: - Learn about different options about Galaxy...

Resource type: Slides

Galaxy Server administration - Deployment and Platform options https://tess.elixir-europe.org/materials/galaxy-server-administration-deployment-and-platform-options Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - What options to deploy Galaxy do I have? - Which platforms are supported by Galaxy? - What requirements does Galaxy have? Objectives of the tutorial: - Learn about different options about Galaxy deployment. - Make an educated decision about your preferred deployment model.
Contributing to the Galaxy Training Material - Creating a new tutorial - Defining the technical infrastructure

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 - Defining the technical infrastructure https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-defining-the-technical-infrastructure 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 we define the technical infrastructure for a tutorial? - How to define the tools needed for a tutorial? - How to add the needed data directly in an instance? - How to add the workflows related to a tutorial? - How can we check the technical infrastructure is working? - How can we make an existing Galaxy instance able to run a tutorial? Objectives of the tutorial: - Extracting the technical description for a tutorial - Populating an existing instance with the needed tools, data and workflows for a tutorial - Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial - Testing the Galaxy Docker flavor of a tutorial
Assembly - Making sense of a newly assembled genome

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Making sense of a newly assembled genome https://tess.elixir-europe.org/materials/assembly-making-sense-of-a-newly-assembled-genome DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - I just assembled a genome. How does it compare with already sequenced genomes? - How do I find rearranged, inserted, or deleted regions? Objectives of the tutorial: - Identification of the most closely related genome to my new assembly - Perform sequence comparison to locate rearrangements - Identify genes located in deletions
Development in Galaxy - Tool Dependencies and Conda

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 connect tools to applications and libraries? - What are the advantages of declaring dependencies...

Resource type: Tutorial

Development in Galaxy - Tool Dependencies and Conda https://tess.elixir-europe.org/materials/development-in-galaxy-tool-dependencies-and-conda 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 connect tools to applications and libraries? - What are the advantages of declaring dependencies for my tool? - What are Conda and Bioconda? - What are Conda recipes and environments? - How do I find and use existing Conda recipes? - How do I develop Conda recipes for use within Galaxy tools? Objectives of the tutorial: - Learn to use existing Conda recipes to enable best practice tool dependency management in Galaxy. - Learn the basics of building Conda recipes and contributing to Bioconda. - Learn to use Planemo to assist in developing Galaxy tools from existing and new Conda recipes.
Introduction to Galaxy - Multisample 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.

Resource type: Tutorial

Introduction to Galaxy - Multisample Analysis https://tess.elixir-europe.org/materials/galaxy-introduction-multisample-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.
Sequence analysis - Genome annotation with Prokka

Analyses of sequences 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

Sequence analysis - Genome annotation with Prokka https://tess.elixir-europe.org/materials/sequence-analysis-genome-annotation-with-prokka Analyses of sequences 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
Variant Analysis - Introduction to Variant analysis

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

Variant Analysis - Introduction to Variant analysis https://tess.elixir-europe.org/materials/variant-analysis-introduction Exome sequencing means that all protein-coding genes in a genome are sequenced
Introduction to Galaxy - Getting data into 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.

Resource type: Slides

Introduction to Galaxy - Getting data into Galaxy https://tess.elixir-europe.org/materials/galaxy-introduction-getting-data-into-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.
Introduction to Galaxy Analyses - IGV 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.

Resource type: Tutorial

Introduction to Galaxy Analyses - IGV Introduction https://tess.elixir-europe.org/materials/galaxy-introduction-igv-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.
Sequence analysis - Quality Control

Analyses of sequences Questions of the tutorial: - How to control quality of NGS data? - What are the quality parameters to check for each dataset? - How to improve the quality of a sequence dataset? Objectives of the tutorial: - Manipulate FastQ files - Control quality from a FastQ file -...

Resource type: Tutorial

Sequence analysis - Quality Control https://tess.elixir-europe.org/materials/analysis-of-sequences-quality-control Analyses of sequences Questions of the tutorial: - How to control quality of NGS data? - What are the quality parameters to check for each dataset? - How to improve the quality of a sequence dataset? Objectives of the tutorial: - Manipulate FastQ files - Control quality from a FastQ file - Use FastQC tool - Understand FastQC output - Use tools for quality correction
Contributing to the Galaxy Training Material - Creating a new tutorial - Slides

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: Slides

Contributing to the Galaxy Training Material - Creating a new tutorial - Slides https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-slides 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 format slides? - How do we add presenter notes? - How to use the features of the slide show tool? - What sort of content should be included in slides? Objectives of the tutorial: - Create a new set of slides - Add presenter comments
User Interface and Features - Histories: Understanding Galaxy history system

A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories

Resource type: Tutorial

User Interface and Features - Histories: Understanding Galaxy history system https://tess.elixir-europe.org/materials/user-interface-and-features-histories-understanding-galaxy-history-system A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories
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.

Resource type: Tutorial

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.
Data Manipulation - Collections: Using dataset collection

A collection of microtutorials explaining data manipulation within Galaxy Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections

Resource type: Tutorial

Data Manipulation - Collections: Using dataset collection https://tess.elixir-europe.org/materials/data-manipulation-collections-using-dataset-collection A collection of microtutorials explaining data manipulation within Galaxy Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections
Galaxy Server administration - Upgrading Galaxy

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - What is the release cycle of Galaxy? - What do I need to do before updating my Galaxy server? - How to upgrade Galaxy to a new release? Objectives of the tutorial: - Identify the challenges...

Resource type: Slides

Galaxy Server administration - Upgrading Galaxy https://tess.elixir-europe.org/materials/galaxy-server-administration-upgrading-galaxy Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - What is the release cycle of Galaxy? - What do I need to do before updating my Galaxy server? - How to upgrade Galaxy to a new release? Objectives of the tutorial: - Identify the challenges involved in the Galaxy upgrade process. - Complete the upgrade to a new release.
Galaxy Server administration - Server Monitoring and Maintenance

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - How to monitor a Galaxy service? - What are the best practices to maintain a Galaxy server? Objectives of the tutorial: - Learn about different monitoring strategies. - Setup and start the...

Resource type: Tutorial

Galaxy Server administration - Server Monitoring and Maintenance https://tess.elixir-europe.org/materials/galaxy-server-administration-server-monitoring-and-maintenance Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - How to monitor a Galaxy service? - What are the best practices to maintain a Galaxy server? Objectives of the tutorial: - Learn about different monitoring strategies. - Setup and start the Galaxy reports app.
Assembly - De Bruijn Graph Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - De Bruijn Graph Assembly https://tess.elixir-europe.org/materials/assembly-de-bruijn-graph-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - What are the factors that affect genome assembly? - How does Genome assembly work? Objectives of the tutorial: - Perform an optimised Velvet assembly with the Velvet Optimiser - Compare this assembly with those we did in the basic tutorial - Perform an assembly using the SPAdes assembler.
Development in Galaxy - Tool Dependencies and Containers

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 the advantages of running my Galaxy tool inside of a container? - How does Galaxy find a container...

Resource type: Tutorial

Development in Galaxy - Tool Dependencies and Containers https://tess.elixir-europe.org/materials/development-in-galaxy-tool-dependencies-and-containers 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 the advantages of running my Galaxy tool inside of a container? - How does Galaxy find a container to run my tool in? - What are BioContainers and how are they related to Galaxy? Objectives of the tutorial: - Explore the differences between containerizing Galaxy and tool execution. - Discuss the advantages of containerizing tools. - Learn to build best practice tools ready to be containerized.
Sequence analysis - RAD-Seq Reference-based data analysis

Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data using a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data using a reference genome - SNP calling from RAD sequencing data - Calculate population...

Resource type: Tutorial

Sequence analysis - RAD-Seq Reference-based data analysis https://tess.elixir-europe.org/materials/analysis-of-sequences-rad-seq-reference-based-data-analysis Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data using a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data using a reference genome - SNP calling from RAD sequencing data - Calculate population genomics statistics from RAD sequencing data
Introduction to Galaxy Analyses - 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...

Resource type: Tutorial

Introduction to Galaxy Analyses - 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.
Train the trainers - Creating a new tutorial - Setting up the infrastructure

Train the trainers 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 website locally - Tracking changes to the content live in the webbrowser

Train the trainers - Creating a new tutorial - Setting up the infrastructure https://tess.elixir-europe.org/materials/train-the-trainers-creating-a-new-tutorial-setting-up-the-infrastructure Train the trainers 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 website locally - Tracking changes to the content live in the webbrowser
Development in Galaxy - Tool Shed: sharing Galaxy tools

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 Shed? - How to install tools and workflows from a Tool Shed into a Galaxy instance? - What...

Resource type: Slides

Development in Galaxy - Tool Shed: sharing Galaxy tools https://tess.elixir-europe.org/materials/development-in-galaxy-tool-shed-sharing-galaxy-tools 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 Shed? - How to install tools and workflows from a Tool Shed into a Galaxy instance? - What are the Tool Shed repository types? - How to publish with Planemo? Objectives of the tutorial: - Discover what is a Tool Shed - Be able to install tools and workflows from a Tool Shed into a Galaxy instance - Be able to publish tools with Planemo
Galaxy Server administration - Connecting Galaxy to a compute cluster

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - How to connect Galaxy to a compute cluster? - How can I configure job dependent resources, like cores, memory for my DRM? Objectives of the tutorial: - Be familiar with the basics of installing,...

Resource type: Tutorial

Galaxy Server administration - Connecting Galaxy to a compute cluster https://tess.elixir-europe.org/materials/galaxy-server-administration-connecting-galaxy-to-a-compute-cluster Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - How to connect Galaxy to a compute cluster? - How can I configure job dependent resources, like cores, memory for my DRM? Objectives of the tutorial: - Be familiar with the basics of installing, configuring, and using Slurm - Understand all components of the Galaxy job running stack - Understand how the `job_conf.xml` file controls Galaxy's jobs subsystem - Have a strong understanding of Galaxy job destinations - Know how to map tools to job destinations - Be able to use the dynamic job runner to make arbitrary destination mappings - Understand the job resource selector config and dynamic rule creation
Genome Annotation - Genome Annotation

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.

Resource type: Tutorial

Genome Annotation - Genome Annotation https://tess.elixir-europe.org/materials/genome-annotation-genome-annotation 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.
Contributing to the Galaxy Training Material - Creating a new tutorial - Defining metadata

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 - Defining metadata https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-creating-a-new-tutorial-defining-metadata 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: - 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
Variant Analysis - Mapping and molecular identification of phenotype-causing mutations

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - What is mapping-by-sequencing? - How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens? Objectives of the tutorial: - Use joint...

Resource type: Tutorial

Variant Analysis - Mapping and molecular identification of phenotype-causing mutations https://tess.elixir-europe.org/materials/variant-analysis-mapping-by-sequencing Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - What is mapping-by-sequencing? - How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens? Objectives of the tutorial: - Use joint variant calling and extraction to facilitate variant comparison across samples - Perform variant linkage analyses for phenotypically selected recombinant progeny - Filter, annotate and report lists of variants
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...

Resource type: Tutorial

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
Proteomics - Secretome Prediction

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to predict cellular protein localization based upon GO-terms? - How to combine multiple localization predictions? Objectives of the tutorial: - Predict proteins in the cellular secretome by using...

Resource type: Tutorial

Proteomics - Secretome Prediction https://tess.elixir-europe.org/materials/proteomics-secretome-prediction Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to predict cellular protein localization based upon GO-terms? - How to combine multiple localization predictions? Objectives of the tutorial: - Predict proteins in the cellular secretome by using GO-terms. - Predict proteins in the cellular secretome by using WolfPSORT. - Combine the results of both predictions.
Contributing to the Galaxy Training Material - Including a new topic

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 - Including a new topic https://tess.elixir-europe.org/materials/contributing-to-the-galaxy-training-material-including-a-new-topic 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 include a new topic? Objectives of the tutorial: - Create a new topic - Set up the metadata for a topic
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

Resource type: Tutorial

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
Introduction to Galaxy Analyses - From peaks to genes

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 use Galaxy? - How to get...

Resource type: Tutorial

Introduction to Galaxy Analyses - From peaks to genes https://tess.elixir-europe.org/materials/galaxy-introduction-from-peaks-to-genes 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 use Galaxy? - How to get from peak regions to a list of gene names? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
Development in Galaxy - Prerequisites for building software/conda packages

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 does 'installing a software' means on a Linux architecture? - Why my compilations always fail? - How...

Resource type: Slides

Development in Galaxy - Prerequisites for building software/conda packages https://tess.elixir-europe.org/materials/development-in-galaxy-prerequisites-for-building-software-conda-packages 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 does 'installing a software' means on a Linux architecture? - Why my compilations always fail? - How to solve common compiling and installation issues? Objectives of the tutorial: - Learn how to compile and install tools using standard procedures. - Learn needed tricks to write conda build.sh files.
Transcriptomics - De novo transcriptome reconstruction with RNA-Seq

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What genes are differentially expressed between G1E cells and megakaryocytes? - How can we generate a transcriptome de novo from RNA sequencing data? Objectives of the tutorial: - Analysis of RNA...

Resource type: Tutorial

Transcriptomics - De novo transcriptome reconstruction with RNA-Seq https://tess.elixir-europe.org/materials/transcriptomics-de-novo-transcriptome-reconstruction-with-rna-seq Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What genes are differentially expressed between G1E cells and megakaryocytes? - How can we generate a transcriptome de novo from RNA sequencing data? Objectives of the tutorial: - Analysis of RNA sequencing data using a reference genome - Reconstruction of transcripts without reference transcriptome (de novo) - Analysis of differentially expressed genes
Transcriptomics - Differential abundance testing of small RNAs

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What small RNAs are expressed? - What RNA features have significantly different numbers of small RNAs targeting them between two conditions? Objectives of the tutorial: - Process small RNA-seq datasets...

Resource type: Tutorial

Transcriptomics - Differential abundance testing of small RNAs https://tess.elixir-europe.org/materials/transcriptomics-differential-abundance-testing-of-small-rnas Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What small RNAs are expressed? - What RNA features have significantly different numbers of small RNAs targeting them between two conditions? Objectives of the tutorial: - Process small RNA-seq datasets to determine quality and reproducibility. - Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets. - Differentiate between subclasses of small RNAs based on their characteristics. - Identify differently abundant small RNAs and their targets.
Proteomics - Protein FASTA Database Handling

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to download protein FASTA databases of a certain organism? - How to download a contaminant database? - How to create a decoy database? - How to combine databases? Objectives of the tutorial: - Creation of a...

Resource type: Tutorial

Proteomics - Protein FASTA Database Handling https://tess.elixir-europe.org/materials/proteomics-protein-fasta-database-handling Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to download protein FASTA databases of a certain organism? - How to download a contaminant database? - How to create a decoy database? - How to combine databases? Objectives of the tutorial: - Creation of a protein FASTA database ready for use with database search algorithms.
Metagenomics - 16S Microbial Analysis with Mothur

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms Questions of the tutorial: - What is the effect of normal variation in the gut microbiome on host health? Objectives of the tutorial: - Analyze of 16S rRNA sequencing data using the Mothur toolsuite in...

Resource type: Tutorial

Metagenomics - 16S Microbial Analysis with Mothur https://tess.elixir-europe.org/materials/metagenomics-16s-microbial-analysis-with-mothur Metagenomics is a discipline that enables the genomic study of uncultured microorganisms Questions of the tutorial: - What is the effect of normal variation in the gut microbiome on host health? Objectives of the tutorial: - Analyze of 16S rRNA sequencing data using the Mothur toolsuite in Galaxy
Epigenetics - DNA Methylation data analysis

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - What is methylation and why it cannot be...

Resource type: Tutorial

Epigenetics - DNA Methylation data analysis https://tess.elixir-europe.org/materials/epigenetics-dna-methylation-data-analysis DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - What is methylation and why it cannot be recognised by a normal NGS procedure? - Can a different methylation influence the expression of a gene? How? - Which tools you can use to analyse methylation data? Objectives of the tutorial: - Learn how to analyse methylation data - Get a first intuition what are common pitfalls.
Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - Why is a Hi-C analysis useful? - What is...

Resource type: Tutorial

Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://tess.elixir-europe.org/materials/epigenetics-hi-c-analysis-of-drosophila-melanogaster-cells-using-hicexplorer DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - Why is a Hi-C analysis useful? - What is 'chromosome conformation capture'? - What are main steps in order to generate and plot a Hi-C contact matrix?
Introduction to Galaxy Analyses - 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?

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?
Development in Galaxy - Visualizations: generic 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 visualization plugins benefit science? Objectives of the tutorial: - Implement a first Galaxy...

Resource type: Tutorial

Development in Galaxy - Visualizations: generic plugins https://tess.elixir-europe.org/materials/development-in-galaxy-visualizations-generic-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 visualization plugins benefit science? Objectives of the tutorial: - Implement a first Galaxy visualization - Understand the client side vs. server side principle
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