Tripal Developer's Meeting 2016-05-03

Meeting Date
Attendees

Stephen Ficklin, WSU

Meg Staton, Ming Chen, Nate Henry, UTK

Nathan Weeks, USDA-ARS

Samyadeep Basu , BITS Pilani, India (Google Summer of Code ‘16)

Valentin Guignon, Bioversity International (CGIAR)

Deepak Unni, University of Missouri (Apollo developer team)

Andrew Farmer (NCGR)

Ethy Cannon (Iowa State University)

Sudhansu Dash (NCGR)

Dorrie Main, Chun-Huai Cheng, Taein Lee, Katheryn Buble (Washington State University)
Steven Cannon (ARS - Iowa)

This is our bi-monthly open agenda meeting.  There is no formal agenda (aside from a few announcements) in order to allow attendees to bring up topics of interest to them.

 

  • Status of Tripal v3

    • Still on working towards a July 1st alpha2 or beta release

    • Web Services demo in May.

  • Status of Tripal v2.1 release

    • Lacey and Stephen will meet and announce a specific date for release.  Perhaps June 1st.

    • Support for Chado v1.3

    • Lots of bug fixes

    • Multi-Chado support (maybe)

    • NCBI Taxonomy loader.

  • Usage of Tripal:  https://www.drupal.org/project/usage/tripal

  • Report on Phylotree Module discussion

    • Try to integrate the d3 tree display.

  • Google School of Code 2016

  • Reminders:

    • Help with mailing list responses.

    • Please consider adding your Tripal extension modules to our Tripal organization on GitHub

    • Remember to add/update your module status on tripal.info

  • Training Topics for next month’s meeting?

    • Drupal coding standards.

    • Writing generic code for sharing.

    • Creating custom hooks.

    • How to use the d3 module.

    • Flag module

    • June 7th.

    • Web Services Tripal v3 (perhaps help with Blast UI)

    • Site-wide searching.

  • “Open Mic” Topics:

    • QTL module (Ethy): PeanutBase, LegumeInfo, Mainlab databases keep using what they each have and when Tripal v3 is released they groups will try to consolidate

    • Network module (Stephen):  Samyadeep is with the GSoC ‘16 and is working on this for the summer.  

    • Multi-chado (Valentin):  a few issues left to work out.  There is some prefixing of the ‘public’ schema in Tripal code we don’t need + some hooks are missing for (multi-)chado schema installation.

      • Try to get support into Tv2.1 release

      • Ensure Tv3 continue to support multi-chado instance.

    • Ontology search module (Ethy) for finding children, siblings, and/or parents for trait searching (i.e. QTLs). Use ontologies to expand searches.

    • Expression module (Meg Staton):  should be finished and can be shown in the next developer’s meeting, working on documentation.

    • Elastic Search module (Meg Staton):  working on hardwoods site, can demo at next meeting if anyone interested.

    • Chado Export for Apollo (Deepak): can export to an empty Chado database (with ontologies pre-loaded), working on a dump to an existing Chado database or an incremental updates.

      • Work with Apollo and Tv3 for RESTful updates to Chado.

Meeting Type
Users