Tripal Developer's Meeting 2016-02-02

Apollo + Chado + Tripal:  workflow for publication of curated results.

• preference for the workflows

• data staging methods?

• For i5K:

  • Possible of export to Chado directly to help alleviate QC rather than to a GFF3 file.

  • ID systems.  Want to convert gene IDs to local ID system.

  • Merging issues: merge curated gene models w/ existing data sets.

  • Apollo -> Chado.   DB authentication, require firewall port to DB server if on separate servers.

  • Apollo Services Tripal could pull from using a Apollo Tripal module.

  • Where to do QC checks on Apollo side or on import to Chado side.

• Knowpulse (Lacey)… interested in integrating Apollo + Tripal.

• Legume Info (Andrew)... interested in using tripal modules like phylotree/genome context viewes to help identify missing gene models between species and provide feedback into annotation system

• Planaria…. etc… (Sofia), has WA now.

• GenSAS uses Apollo.  Integration of GenSAS with GDR, CottonGen, etc.

Ethy:  Adoption of Phylotree (example)

• It would help to both increase the urgency to complete the module and to ensure Tripal compliance if a group would like to deploy it.

• Anyone else interested in a phylotree module?

  • i5K is interested but not yet ready.  

  • Chado loader for Newick formatted data exists.

  • Interest in using this for taxonomy, but not yet pursued.

Results of the Tripal PAG Codefest

• Meeting Notes

• Meeting Summary on Tripal.info

Site-wide searching overview

• Tripal 3 Tutorial

Chado v1.3 integration

Tripal v3

• Overview from PAG talk.

• Status

  • Currently expanding to support additional tables (Stephen)

  • Adding site-wide indexing (Lacey)

    • Tripal 3 Tutorial

  • Working on Panels display (Chun-huai)

  • Shooting for a beta release in summer of 2016

  • User’s Guide is in progress.

  • Introduction meeting?

  • We think we can make v2 sites fully backwards compatible with v3.

    • We will work to include conversion scripts from “nodes” to “entities”

  • Web services…. have a special meeting next month to talk solely on this.

  • Will include unit testing!

  • TODO:  setup a separate meeting for a Tripal v3 overview.

• Requests

  • Data Export

• Questions?

Tripal v2

• Status

  • A v2.1 release coming soon

Galaxy Integration

• Working on PHP library to interact with Galaxy API.

• Alpha module coming Fall of 2016

Round table

• Any new modules?

• Status of existing modules.

Tripal.info site

• Please add your modules

Paper:

• Extensions and site papers.

• Give credit to folks for their work.

• Motivate to finish up.

• Too big?

• Oxford Database virtual issue?

• Dorrie’s group will release several modules, will do a paper on those.  Would like to submit as a separate paper.  Something published by the summer.

• TODO:  Is there a way to link a project extension on the tripal.info site to a GitHub account.

• TODO: how many publications do we need for a virtual issue.

• LegumeInfo and PeanutBase were recently published but not ready for another publication.