2018 PAG Hackathon

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The GMOD hackathon will take place January 10-11, 2018 (a few days before PAG, but not on January 12 so as not to overlap with the Tripal user meeting). It will take place at the Town and Country Hotel in the Brittany room. The Brittany room is in the eastern edge of the property in the north/south center, off of the Regency Courtyard). We expect that topics will include JBrowse (server-side stuff and plugins), Galaxy connectivity and plugins, and Tripal plugins (this hackathon overlaps the Tripal hackathon and user meeting that runs January 11-12).

Registration is $50 which covers part of the fee for the room (where the rest is made up from the kind JBrowse folks) and lunch on the first day. Please use the Eventbrite page to register and pay.

Suggested Topics

  1. Improving the Python library for interacting with the Apollo API
    1. Done! PRs: 1, 2
  2. Fix dot-object notation to work with Apollo
  3. Adding an “Instructor” role to facilitate the usage of Apollo in an educational setting [1]
    1. A list of what permissions the instructor role would have would be very useful. Siloed by organism?
  4. Incorporating additional metadata to an organism in Apollo to facilitate integration with Galaxy Histories
  5. CRAM support for JBrowse and CRAI indexes and extend to Apollo.
    1. Might not be hard, but we don't know
  6. Customize BAM tracks in Apollo: original from last hackathon
  7. Updating table descriptions to generalize mage to include next-gen sequencing experiments and other possible analyses instead of microarray only
    1. Make issue in Chado add a link for 1.4 outline. See related bug report
    2. Done! Pull request
  8. Adding a cvalue_id field to the biomaterialprop table, as is done for the natural diversity module. This allows the property values to also utilize a cvterm.
    1. Make an issue in Chado. See the related bug report
    2. Done! Pull request
  9. Adding track-level permissions to JBrowse tracks in Apollo and JBrowse directly. (need to flesh out some policies. Generally, this feature is available with JBServer.)
  10. Plugin in JBrowse that goes to the next isoform (similar to the behavior in Apollo's manual annotation area).
  11. Customize BAM tracks. Per Chris Elsik: better filtering (spliced reads on top, sort by score or other attributes, filter unspiced reads)
  12. Simplify JBrowse minification
  13. Get an EST glyph similar to what GBrowse has. Done! Commits: LinkedEST.js Supporting files
  14. Add type_id to analysis table Done! Pull request
  15. Add linker tables to make working with biomaterials easier Done! Pull request
  16. Get more organized for 1.4 Chado release Done! List of issues to address for 1.4



  • Stephen Ficklin
  • Connor Wytko
  • Margaret Staton
  • Taein Lee
  • Ming Chen
  • Anh-Dao Nguyen
  • Deepak Unni
  • Richard Hayes
  • JoAnn Takabayashi
  • Bradford Condon
  • Yating Liu
  • Nathan Dunn
  • Gerard Lazo
  • Emily Grau
  • Eric Yao
  • Scott Cain