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...
Galaxy Server administration - Ansible
http://galaxyproject.github.io/training-material/topics/admin/tutorials/ansible/tutorial.html
http://tess.elixir-uk.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
erasche
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
Data Manipulation - Collections: Rule Based Uploader
http://galaxyproject.github.io/training-material/topics/galaxy-data-manipulation/tutorials/upload-rules/tutorial.html
http://tess.elixir-uk.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
jmchilton
erasche
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...
Contributing to the Galaxy Training Material - Creating a new tutorial - Slides
http://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-slides/slides.html
http://tess.elixir-uk.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
erasche
bebatut
shiltemann
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...
Development in Galaxy - Galaxy Webhooks
http://galaxyproject.github.io/training-material/topics/dev/tutorials/webhooks/tutorial.html
http://tess.elixir-uk.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
blankclemens
martenson
bgruening
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...
Development in Galaxy - Galaxy Interactive Environments
http://galaxyproject.github.io/training-material/topics/dev/tutorials/interactive-environments/slides.html
http://tess.elixir-uk.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
shiltemann
bgruening
erasche
Galaxy Server administration - Advanced customisation of a Galaxy instance
Resources related to configuration and maintenance of Galaxy servers
Galaxy Server administration - Advanced customisation of a Galaxy instance
http://galaxyproject.github.io/training-material/topics/admin/tutorials/advanced-galaxy-customisation/slides.html
http://tess.elixir-uk.org/materials/galaxy-server-administration-advanced-customisation-of-a-galaxy-instance
Resources related to configuration and maintenance of Galaxy servers
bgruening
erasche
martenson
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...
Introduction to Galaxy Analyses - Galaxy 101
http://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-101/tutorial.html
http://tess.elixir-uk.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
shiltemann
nsoranzo
blankclemens
nekrut
bgruening
pajanne
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...
Introduction to Galaxy Analyses - From peaks to genes
http://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html
http://tess.elixir-uk.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
pajanne
blankclemens
bebatut
bgruening
nsoranzo
dyusuf
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...
Transcriptomics - Reference-based RNA-Seq data analysis
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
http://tess.elixir-uk.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
bebatut
malloryfreeberg
moheydarian
erxleben
pavanvidem
blankclemens
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...
Proteomics - Metaproteomics tutorial
http://galaxyproject.github.io/training-material/topics/proteomics/tutorials/metaproteomics/tutorial.html
http://tess.elixir-uk.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.
timothygriffin
pratikdjagtap
jj-umn
blankclemens
