Galaxy Training

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

Galaxy Training https://tess.elixir-europe.org/content_providers/galaxy-training GitHub repository and its website companion containing a collection of training materials for teaching next generation sequencing data analysis uing Galaxy. /system/content_providers/images/000/000/078/original/GTNLogo1000.png?1501677361
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Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are benefits and drawbacks of different quantitation methods? - How to choose which quantitation method bests suits my need? Objectives of the tutorial: - Choose your quantitation method.

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

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

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

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

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

Training material for proteomics workflows in Galaxy Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

Proteomics - Secretome Prediction https://tess.elixir-europe.org/materials/proteomics-secretome-prediction Training material for proteomics workflows in Galaxy Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

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...

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

Train the trainers

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

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

Analysis of sequences - 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

Training material for all kinds of transcriptomics analysis.

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

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

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

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...

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.

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 - Introduction 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.

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 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.

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...

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.

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

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

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

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

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

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

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

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

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

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

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 - Introduction 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, ...

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

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.

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...

Galaxy Introduction - 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

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

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

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What are Galaxy Interactive Environments (GIEs)? - How to enable GIEs in Galaxy? - How to develop your own...

Development in Galaxy - Galaxy Interactive Environments https://tess.elixir-europe.org/materials/development-in-galaxy-galaxy-interactive-environments Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What are Galaxy Interactive Environments (GIEs)? - How to enable GIEs in Galaxy? - How to develop your own GIE? Objectives of the tutorial: - Implement a Hello-World Galaxy Interactive Environment

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - How can I make a custom plugin for Charts? Objectives of the tutorial: - Learn how to add custom...

Development in Galaxy - Visualizations: charts plugins https://tess.elixir-europe.org/materials/development-in-galaxy-visualizations-charts-plugins Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - How can I make a custom plugin for Charts? Objectives of the tutorial: - Learn how to add custom javascript plugins to the Galaxy Charts framework

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What are Galaxy Webhooks? - How to create them? Objectives of the tutorial: - Discover what Galaxy...

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

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

Analysis of sequences - 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

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...

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

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 - 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.

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...

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.
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scraper created Galaxy Training at 2017-08-02 12:36:03 UTC.