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September 2018 Meeting of the Genomics Curriculum Advisors

There were two meetings held:

  • Monday, September 24, 2018 at 15:00:00 UTC
  • Tuesday, September 25, 2018 at 19:00:00 UTC

Attending (meeting one):

  • Erin Becker
  • Naupaka Zimmerman
  • Bob Freeman (Harvard)
  • Jason Williams (CSHL)
  • Anita Schürch
  • François Michonneau

Attending (meeting two):

  • Erin Becker
  • Sarah Stevens
  • Bob Freeman (Harvard)
  • Tracy Teal (Carpentries)
  • Jason Williams
  • Sue McClatchy (The Jackson Laboratory)
  • Ben Busby (NCBI)

Detailed Agenda:


  1. Identifying goal for final configuration of curriculum.
  • Multiple options provided (see detailed agenda)
  • No support for the idea of one workshop of 2 day shell and another with two days R.
  • People like the idea of some shell and some R, with project org/management on the first day and essential.
  • Could end up being more than 2 days of content as it comes together, so will need to be mindful of what to include and what to cut.
  • A few ideas on ordering of content, but would be the same content. Could pilot ordering a couple ways. Will want to have a core ordering recommendation.
  • One idea is that there is a core curriculum one day shell, one day R, then a possible third day that is a capstone or has some flexibility, but would be up to the instructors to put that together.
  • Question about how things in the ‘third day’ or carpentrieslab could be integrated into core. Some of this is mapped out in the draft curriculum development guidelines.
lesson lifecycle Would look at use and engagement of the content. The Genomics Advisory Committee could make these decisions too.

Action Item: The committee will vote on this asynchronously.

  1. Process / schedule for major changes in lessons. Length of “freeze” period.
  • Consensus: minimum 2 year cycle (8 of 8 votes)
  • Idea is focus is on content, not exact tools, so don’t need to update frequently
  • Can be refinements, to keep it relevant, but not big changes
  • Support for having an infrastructure group that looks at the infrastructure, separate from lesson development itself. Making sure dependencies, file systems, and how we serve it is up to date. Jason and Naupaka would be on that.
  • With the decision to not make major changes, will want to communicate that on the lessons, so people know what kinds of changes we’re looking for and people can contribute effectively
  • For the ‘third day’ content, could be different ideas and people developing. Could integrate well with carpentrieslab, and having third day materials there
  • Naupaka, Jason, (François): volunteer to help with infrastructure of lessons and tools. Consider Singularity ( This group (and others may join) will be responsible for maintaining the AWS instance and other technical infrastructure for this workshop.

Action Items:
- Put together Maintainer Infrastructure group for this workshop.
- Communicate about freeze period to contributors.

  1. Any major changes to implement in the next 6-month period?
  • Consensus to move forward with new proposed dataset and tools, provided support from community members who proposed and/or Maintainers for Shell/Wrangling lessons.

Action Items:
- Follow up with shell working group about getting stable version of VCF file and scripts.
- Schedule meeting for the Genomics R Maintainers to make timeline for the new lesson release.

  1. Items not on Agenda that have been raised to the CAC
  • Individual CAC members will follow up with Maintainers about these issues in the appropriate GitHub repos.

Other Action Items: - Coordinate between R Maintainers and Bob about proofreading and check cognitive load for R lessons.

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