Tripal User's Meeting 2017/05/05

Meeting Date: 
Friday, May 5, 2017
Attendees: 

Stephen Ficklin, Victor Unda, Katheryn Buble (WSU)

Lacey-anne Sanderson (USASK)

Nic Herndon (UConn)

Yi Zheng (BTI)

Abdullah Almsaeed (UTK)

Ming Chen (UTK)

Meg Staton (UTK)

Bradford Condon (UTK)

Emily Grau (UConn)

Monica Poelchau (USDA/NAL)

Sean Buehler (UConn)

Ethy Cannon (ISU)

 
Agenda: 

Announcements:

 

Reminders:

 

  • Consider adding your modules into the Tripal GitHub organization.  

  • Remember to update the status of your modules on the Tripal.info site.  

  • We now have "Powered by Tripal logos" if you'd like to add one to your site:  http://tripal.info/logos

  • If you have a new site or major updates to your existing site let us now and we can publish those on the Tripal news feed and twitter accounts.

  • Send us your logo if you have shared a module with the community and would like it showcased on the Tripal.info site

Agenda:

 

  • Training

    • April Online Training:  bulk loader.

    • May Online Training

      • On Friday 5/26

      • Tripal v3 Development.  Converting template to entity fields.

    • Tripal Summer School?  

      • Interest in an all-day online hackathon (webcam encouraged) this summer?

      • Need to differentiate between "adoption" training and developers who want to collaborate on.  Documentation updating.  Have defined goals

  • Tripal v2.1

    • Any issues questions, problem?

  • Tripal v3

    • Support:

      • Example module already under development:  

        • https://github.com/tripal/tripal_example

        • Tripal legacy example module was like "drinking from a firehose".  This example module is broken out into common tasks.

        • Currently provides examples for creating custom fields.

        • Do you have an example you'd like to see provided as an example?  Please add an issue to the queue.

      • Updated API Documentation will be online

      • Tripal v3 User's Guide will be updated at the time of release, including developer's handbook.

    • Any questions about Tripal v3?  Upgrading, etc?  Conversion of custom modules?

  • Mailing list consolidation

    • Will remove gmod-tripal-announce and gmod-tripal-devel but keep gmod-tripal.

    • Major announcements will be made on the @TripalProject Twitter account and Tripal website for those who don't want to be on the mailing list.

  • Report on GO loading problem

    • Tripal v2.1 still has the GO loading problem

      • Problem in GO is a combination:

        • Of "has_part" and "part_of"

        • When updating an ontology old relationships can cause a cycle as well.  Action Item (Stephen)  Check on solution provided by Ethy for this.

      • Ontology loads fully, but cannot be added to the cvtermpath table.

    • We are working on a fix to detect cycles and avoid them.  We hope to have this fixed for Tripal v3 release.

  • Nic (Tree Genes):

  • Installation Profiles (Lacey, USASK)

    • Packages Drupal/Tripal/Extension modules needed into a bundle.

    • Simplifies Tripal installation.

    • Profiles:

      • Genomics (extensions and content types specific)

      • Breeding

      • Stock Collection (with eCommerce modules built in)

      • Headless Tripal with Loaders with privacy.

    • Current discussion on the issue queue:  https://github.com/tripal/tripal/issues/95

    • We would greatly appreciate any input on content types and/or functionality you would like to see included!

  • Wish List / Hate List

    • Gene/mRNA Pages: too chado-esque. Not as helpful to users as they could be.

      • Ethy: PeanutBase & LegumeInfo have an extension module to customize these pages. Example. Includes JBrowse image, mRNA, and protein sequences.

      • Monica: I5K has custom gene pages with a more EnSEMBL-like. Example i5k page: https://i5k.nal.usda.gov/OFAS001265

      • Transcript listing: Shows all the transcripts for a given gene including all the functional information & annotation for each transcript

        • Candidate Tripal3 Field that admin could add to their Gene pages

      • JBrowse Field to show a region of a JBrowse instance on any page.

        • This will be included in the JBrowse integration module when it has a Tripal3 release

        • And configuration to allow you to highlight a specific gene for example

        • (would be used in both LegumeInfo & I5K)

      • Sequence Field: Shows the sequence for the Gene, any transcripts and proteins (would be used in both LegumeInfo & I5K)

    • For suggestions see: https://github.com/tripal/tripal/issues/100

  • What can core developers to better help adoption/training/etc….

    •