Tripal Advisory Committee Meeting 2020/10/06

Community Highlights

Agenda

1. Hacktoberfest
   1. Details
   2. T-shirts and stickers!

2. No more January in San Diego. What to do about our annual meetup?
   1. Proposal: 
   2. Coordinate a virtual Hackathon (Stephen volunteered, anyone else want to help? Jill)
   3. Flexible timing to work across time zones - a self-organizing hackathon by zoom + slack on times that work best for the groups who want to work on different items.
      1. Provide some bounded hours - late morning in US for example, to create cohesiveness for break out groups
   4. Set aside one week and organize group sessions that work for each group during the week.
      1. Groups could rotate throughout the day 
      2. Topics - 
         1. Tons of T4 options! Fields will be done, will need importers, can pick functionality particularly useful for you, don’t forget extension modules! Working together to upgrade can be a powerful way to develop
   5. Have a final meeting at a time that works for folks to do reports on those efforts
      1. Doodle poll for scheduling? Second week of January!
   6. Here's a site with 8 tips for running a virtual hackathon: https://opensource.com/article/20/8/virtual-hackathon 
3. Tripal White Paper
   1. Ready for community review by October 20th: 
      1. Draft: https://docs.google.com/document/d/1w24HzOBJFKG4q3kvgAGwpEWEBgw9773jTcIqMp7bxsg/edit?usp=sharing
      2. Folder with supplemental files and draft:

https://drive.google.com/drive/folders/1AFSZxWPdcB6fCItdsZCJx87c9s3iErAi?usp=sharing

4. Tripal 4 Updates
   1. Lacey - hoping for alpha by Sept 30 -delay related to fields, fields in 8/9 are quite different. We’d like to make it friendly for extension modules. 8/9 has moved information into “annotations” ie. formatted comments at the top of classes. (related to symphony). The plan is to adopt an additional (optional) software called Drupal Console. Very cool for not only fields but many admin tasks. Drupal console will accept a T3 field and spit out a T4 field (yea!)
   2. Aiming for alpha in a few weeks. Everyone will need time to upgrade before losing security support in November 2022. Aiming to catch up with existing timeline: https://time.graphics/line/387503
      1. Plan is for everyone to go from D7 straight to D9 (9.0 and 8.9 testing). Everything in T4 is compatible with D9
   3. Repo: t4d8 - please go look at the repo and timeline, think about how you are going to tackle this for your database and your extension modules
   4. GFF Loader - much improved! (perhaps one bug left) - can load an entire genome in just a few minutes
      1. Functional testing needed - please help!
      2. Will get rolled into T4
5. Deleting features
   1. Not available in Tripal 3
      1. recent merge: https://github.com/tripal/tripal/pull/1061
         1. Good for deleting/unpublishing a small number of entities
   2. Staton lab: Feature Obliviator
      1. This Tripal 3 module provides a drush command that allows users to delete data from the chado.feature table by specifying the organism and the analysis for which features should be deleted.
      2. Command line only - no admin interface
      3. Depends on Tripal Manage Analyses
         1. This module creates browseable analysis and library lists for organisms.
         2. It also provides the obi__organism linker. This linker attaches to analyses and lists organisms linked to it.
      4. Sean will be expanding to work with other feature types
6. JBrowse fields for gene and mRNA pages: (not official, somewhat hacky) https://github.com/NAL-i5K/gene_jbrowse_field