Galaxy Training Network

GCC2014 BoFs!

This page describes the Galaxy Training NetworkBirds of a Feather meetup being held at GCC2014.

When: Tuesday, July 1, 5:45pm

Where: Multipurpose Room 324

Contact: [Simon Gladman](mailto:simon DOT gladman AT monash DOT edu), [Andrew Lonie](mailto:alonie AT unimelb DOT edu DOT au), Teaching hub page


The plan is to have a discussion surrounding:


Anyone interested in using Galaxy for bioinformatics and related learning and teaching. People who need to support such activities.

When and Where

  • When: Tuesday, July 1, 5:45pm
  • Where: Multipurpose Room 324


  • Simon Gladman
  • Maria Doyle
  • Ron Horst
  • Hans-Rudolf Hotz
  • Richard Everson
  • Ulf Schaefer
  • Fred Tan
  • Ravi Alla
  • Ben Busby
  • Andrew Lonie
  • Marius van den Beek
  • Christophe Antoniewski
  • Sebastian Schaaf
  • Peter Cock
  • Ira Cooke
  • Pratik Jagtap
  • Jen Hillman-Jackson
  • Anton Nekrutenko
  • Dave Clements
  • ...


  • Is the goal to teach how to use tools, or to teach understanding of concepts? What's the balance?
    • Focusing on basics. They aren't going to remember specific parameter settings a week later.


  • Published histories
  • Galaxy Pages
    • Fabulous resource, but not portable


  • Video is tough: takes time, and then ages very quickly.
  • Galaxy Project videos are very popular, even the old ones.
  • Mayve have a vido directory on Vimeo? Might be better to have the directoy on wiki. Can link anywhere.

GTN Resources Directory

Galaxy Training Network

This has been created.

Some aspirations for the resource directory:

  • List the tools and packages
  • Estimates of needed memory
  • Datasets
  • Target Audience: Beginner, intermediate, advanced
  • Describe the cool result that participants will see at the end.
  • Any licensing Issues.
  • also suggested depositing a test workflow in the ToolShed: If this workflow runs on your server, then this workshop should also work on your server

Best Practices

The list below was created during this BoF. A published list of best practices now exists, and it incorporates many of these practices.

  • Suggest starting with an hour of hand-holding where students are told exactly what to do. Then, open it up to give them an opportunity to try things themselves

  • Better to teach in concentrated bursts or spread out? Spread out is probably better, but is often not possible due to trainer or student travel constraints.

  • Two trainers start with assembly/mapping because it is easier for people to understance than starting with something like RNA-Seq.

  • Teach programmers what the biologists are trying to do. One group just did a workshop with pairs - one member from IT, one from medical.

  • Ask Tech savvy people to be teaching assistants. They may not be familiar with Galaxy or the biology, but they are familiar with computers and are already aware that it may matter, for example, if there are tabs or spaces in a file. This pairing allows biologists to pick up these general computer interaction skills.

  • Set up a mailing list / Google Group for every course. This creates a "micro-SeqAnswers" for a group of people who know each other from a course. A much less intimidating forum than public boards.

  • Having all materials be licensed under CC-BY makes things much easier.

Support for Trainers

  • Start a training mailing list.
  • Core Team is pushing training organization, both in terms of trainer support and in terms of content.

Training Servers?

Is it possible to have a persistent training server? Some ideas:

  • Disable data importing.
  • Prominently state that all user data and accounts will be deleted at specific time intervals.


  • Everybody really wants to do BLAST.
  • If anyone ever has problems getting NCBI data into Galaxy, talk to Ben.

Action Items

  • Create a galaxy-teach or galaxy-train mailing list / forum
  • Work with that list to establish what the Resource Directory (and the Trainer Directory) should look like
    • Resource Directory and Trainer Directory are up.
  • Push these best practices to the GTN Best Practices area.
    • Done
  • Include a video training directory