Tripal User's Meeting 2019/05/07

Agenda

• Tripal Releases

  • Tripal v3.2 coming out soon (May or June)

    • more frequent minor releases of Tripal 3 to follow

  • Tripal v4 (drupal 8 upgrade) is in the planning stage

    • Let us know if you have time available to help! We can all learn Drupal 8 together ;-P

  • Tripal v5 is still up for discussion as a possible decoupling of Drupal and addition of microservices

  • Drupal 8 introduction

• The new Tripal Steering Committee: Ethy Cannon [ekcannon@iastate.edu], Stephen Ficklin [stephen.ficklin@wsu.edu], Valentin Guignon [v.guignon@cgiar.org], Dorrie Main [dorrie@wsu.edu], Monica Polechau [monica.poelchau@ars.usda.gov] , Meg Staton [mestato@gmail.com], Manuel Ruiz [manuel.ruiz@cirad.fr], Jill Wegrzyn [jill.wegrzyn@uconn.edu], Lacey Sanderson [las166@mail.usask.ca]

  • Kick off meeting being scheduled

  • All should review the by-laws/governance (https://tripal.readthedocs.io/en/latest/contributing/governance.html) and send comments to steering committee members.

• Open Agenda!

  • Anything you’re working on to share with the community? New modules?

  • New Modules!

    • TSeq (Tripal Sequence Similarity Search) (Developer: Sean, TreeGenes)

      • Diamond & BLAST jobs on existing site data/user-submitted data on external application servers with Tripal Remote Job module

      • Progress - fully functional, adding more features/bugfixes

      • Next milestone: Use Tripal Galaxy rather than Tripal Remote Job

    • TCP (Tripal Contact Profile) (Developer: Rish, TreeGenes)

      • Creates user profiles, data is submitted into contact and contactprop chado tables

      • Progress: Live on Mimubase.org and DEV, to push to TG LIVE

      • Latest Milestone: integrate with any Tripal 3 site

    • TPPS (Tripal Plant Popgen Submit pipeline) (Developer: Peter, TreeGenes)

      • Submit association genetics/landscape genomics study data in a uniform way to Tripal sites

      • Progress - Live in TreeGenes site (links)

      • Upcoming Milestone: Fix portability issues and issues with interfacing with CartograTree

    • CartograTree (Developer: Nic, Rish, Ronald, TreeGenes)

      • Map-based module for analyzing/visualizing phenotypic, genotypic, and environmental study data

      • Progress - In Progress on Tripal Galaxy integration

      • Upcoming Milestones: Complete basic analysis aspects by August 2019

    • OrthoQuery (Developer: Sumaira, TreeGenes)

      • Orthologous gene family analysis (OrthoFinder), uses Tripal Galaxy API

      • Process, annotate, and visualize gene families in a phylogenetic context

      • Progress: Completion of visualization, Completion of storing Unigenes in TreeGenes, Developing the tripal-galaxy workflow for each use cases.

      • Upcoming Milestones: Updated Release Date for August 2019 include implementation of galaxy workflows in the module for all use cases and enabling the visualization to query functional annotations through the database.  

    • Modified gFACs (Gene Filtering Analysis and Conversion) (Developer: Alyssa, TreeGenes)

      • Uses Tripal Galaxy to run a custom workflow featuring gFACs where GTF/GFF files can be filtered and formatted for Jbrowse loads.

      • Filtering focuses on structural and functional aspects of gene models that are problematic following gene prediction.

      • Progress - New project for Summer 2019

      • Upcoming milestones: September 2019 - Complete module.  Currently exists as an independent application: https://gfacs.readthedocs.io/en/latest/index.html

    • EnTAP (Eukaryotic Non-model Transcriptome Annotation Pipeline)

      • Uses Tripal Galaxy to run sequence similarity, protein domain, gene ontology, and gene family assignment.  Specifically features a phylogenetic and contaminant filtering component.

      • Progress - Early Stages of Development.  Currently exists as an independent application: https://entap.readthedocs.io/en/latest/

    • HQ (https://github.com/statonlab/tripal_hq)

      • Tripal HQ provides a user-contributed content control center and administrative toolbox for your Tripal site. This means that users are able to create whatever Chado content you'd like them, but withhold inserting it into the database until someone has approved it.

    • EUtils (https://github.com/NAL-i5K/tripal_eutils)

      • This module connects to the NCBI EUtils API to load in accessions for the Assembly, BioProject, and BioSample databases. Primary, as well as linked, records are loaded into Chado.

  • Job openings in Staton lab! 2!

  • Questions? Concerns?

    • Andrew Farmer brings up their Phylotree module: is there overlay with orthoquery and room for collaboration

    • Andrew Farmer has functionality for on the fly synteny comparisons which TreeGenes may be interested in (GenomeContextViewer). Uses a Chado backend with a services layer above that. Single Page application

    • Meg brings up performance concerns with the Tripal 3 fields.

    • Should you leapfrog over Tripal 3 if you still have a Tripal 2 site?