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Galaxy Training Network

Galaxy Training: Resources

There are many resources available that are helpful for teaching Galaxy. This page attempts to summarize them in one location. This page links to workshop materials for different topics.  That material can be in this wiki, inside Galaxy instances, or anywhere on the web.

Following the GTN workshop at the GCC 2016 meeting, we are in the process of setting up a a github repository for community training resources. Don't worry about format. At this stage, we are just collecting as much material as possible for the GTN. At a later stage, we will try to make all chapter looking similar and will move the repository under the Galaxy project umbrella.

Training Resources

Resource Types Domains Owners Formats Date
Biotrac Next Generation Sequencing Course Syllabus Syllabus Genomics, RNA-Seq, Assembly, Annotation, Variation, Quality Control, ChIP-Seq Ben Busby, Sijung Yun Documents 2014/07
CHB Harvard ChIP-Seq Workshop Tutorial, Datasets ChIP-Seq Shannan Ho Sui, Oliver Hofmann, Radhika Khetani, Winston Hide, Center for Health Bioinformatics at the Harvard School of Public Health Web Pages 2014/11
CHB Harvard Running your own Galaxy instance (in the cloud) Tutorial Cloud Shannan Ho Sui, Oliver Hofmann, Radhika Khetani, Winston Hide, Center for Health Bioinformatics at the Harvard School of Public Health Web Page 2014/11
CHB Harvard Exome-Seq Workshop Tutorial, Datasets Exome-Seq Shannan Ho Sui, Oliver Hofmann, Radhika Khetani, Winston Hide, Center for Health Bioinformatics at the Harvard School of Public Health Web Pages 2013/01
CHB Harvard Introduction to Galaxy Tutorial Genomics Shannan Ho Sui, Oliver Hofmann, Radhika Khetani, Winston Hide, Center for Health Bioinformatics at the Harvard School of Public Health Web Pages 2014/11
CHB Harvard RNA-Seq Workshop Tutorial, Datasets RNA-Seq Shannan Ho Sui, Oliver Hofmann, Radhika Khetani, Winston Hide, Center for Health Bioinformatics at the Harvard School of Public Health Web Pages 2014/11
ChIP-Seq avec Galaxy Tutorial ChIP-Seq Jean-Charles Cadoret, Université Paris Diderot. Video 2014/02
Détection de variants structuraux Tutorial Structural variant detection Bruno Zeitouni, Institut Curie Video 2014/02
Analyse de données ExomeSeq avec Galaxy Tutorial ExomeSeq Elodie Girard and Romain Daveau, Institut Curie Video 2014/03
Galaxy Freiburg Hands-On Training Tutorial, Dataset RNA-Seq, ChIP-Seq, Genome Annotation, MethylC-Seq, Exom-Seq Contributors Document, Github repo, Slides 2016/04
GVL RNA-seq Differential Gene Expression Introductory tutorial Tutorial RNA-Seq Genomics Virtual Lab by University of Queensland, Victorian Life Sciences Computation Initiative, Queensland Facility for Advanced Bioinformatics, and Garvan Institute Web Pages 2014/08
GVL RNA-seq Differential Gene Expression Advanced Tutorial Tutorial RNA-Seq Genomics Virtual Lab by University of Queensland, Victorian Life Sciences Computation Initiative, Queensland Facility for Advanced Bioinformatics, and Garvan Institute Web Pages 2013/06
GVL Variant Detection Advanced Tutorial Tutorial Variation Genomics Virtual Lab by University of Queensland, Victorian Life Sciences Computation Initiative, Queensland Facility for Advanced Bioinformatics, and Garvan Institute Web Pages 2013/06
GVL Variant Detection Introductory Tutorial Tutorial Variation Genomics Virtual Lab by University of Queensland, Victorian Life Sciences Computation Initiative, Queensland Facility for Advanced Bioinformatics, and Garvan Institute Web Pages 2012/12
GVL de Novo Genome Assembly (Small Genome) Tutorial Assembly Genomics Virtual Lab by University of Queensland, Victorian Life Sciences Computation Initiative, Queensland Facility for Advanced Bioinformatics, and Garvan Institute Web Pages 2012/12
Galaxy 101 Tutorial Basic Genomics Anton Nekrutenko and the Galaxy Project Galaxy Page 2010/12
Galaxy Events Archive Slides, Posters Everything Galaxy Community Everything 2014/10
Introduction to Galaxy Project Slides, in Arabic Slides Galaxy Project Abdelazeem Abdelhameed <abdelazeem_abdelhameed2015505@yahoo.com> Slides 2016/10
Galaxy NGS 101 Tutorial RNA-Seq, Variation, Quality Control Galaxy Project Web Pages, Screencasts 2015/06
Galaxy Project Workshop CloudMan on AWS Share CloudMan on AWS share RNA-Seq, ChIP-Seq, Introduction Galaxy Project a CloudMan on AWS share string 2014/12
Genomic Data Science with Galaxy on Coursera Tutorial RNA-Seq, ChIP-Seq, Installation, Workflows, Quality Control James Taylor Web Tutorial, Screencasts 2015/07
Microbial analysis with Orione Tutorial Microbial Resequencing, RNA-Seq, Assembly, Metagenomics Orione Team and 鈴木 治夫 (Haruo Suzuki) Web Page 2016/09
Differential Expression with Tuxedo Instructions RNA-Seq Cynthia Gibas Web Page 2015/04
UC Davis Bioinformatics Core Galaxy AMI AMI Genomics UC Davis Bioinformatics Core Amazon Machine Image 2014/06
UC Davis Using Galaxy for Analysis of High Throughput Sequence Data Workshop Presentations, Tutorials, Exercises, Datasets, AMI Genomics: QC, Alignment, Variants, Assembly, RNA-Seq UC Davis Bioinformatics Core Entire workshop package 2014/06
UC Davis RNA-Seq and ChIP-Seq Analysis with Galaxy Workshop Tutorial, Datasets, AMI Quality Control, RNA-Seq, ChIP-Seq UC Davis Bioinformatics Core Entire workshop package 2014/12
UC Riverside NGS Tutorial Tutorial, Datasets Variant Calling, RNA-Seq, Intro Neerja Katiyar, Tyler Backman, Rebecca Sun, and Thomas Girke, UC Riverside Slides, Web pages, Documents 2013/12

Add a Training Resource

Have you created or know of a resource that is useful for teaching with Galaxy? Then please share it! This will help others and also help get the word out about your resource.

Use the Wiki

To add a training resource to this directory, create a wiki page describing the resource. Here are the directions:

  1. Login to the wiki. If you don't have an account, you'll need to create one.

  2. Pick a good descriptive, CamelCase name for your deployment.  This will become part of the URL for the page describing your deployment.  Avoid embedded spaces as they make lousy URLs.

  3. Type the CamelCase name in box below and hit the "Create" button.

  4. A template for the new page will appear.  Replace the template text with details about the resource.
  5. Save, review, and edit the page until you are happy with it.
  6. Return to this page, and review how the resource appears in this listing.

Use a Google Form

If the wiki option seems a little daunting, you can also describe this resource in a Google Form. Once the form has been submitted, the information will be reviewed and an training resource page will be created within a week or two. You will be notified via email when the page is created.

   Describe the resource using the Google Form