Tripal User's Meeting 2018/11/13

PAG Events

1. Dec 3rd.  Last day to update abstract text

2. Will let speakers know if they will be invited to give a talk at the workshop at PAG.

3. Thursday-Friday Jan 10-11th.  Codefest + User's Meeting

   1. Goal: more coding than discussion

   2. Current Topics:

      1. Topic 1: Tripal v4 Python Proof of Concept.  Leader: Stephen Ficklin

      2. Topic 2: Tripal + BrAPI Integration.  Leader: Valentin Guignon

      3. Topic 3: Chado Updates.  Leader: TBD

      4. Other Suggestions Welcome

         1. I’d also be happy to continue the discussion on gene pages with a larger group (Monica P).

   3. Sign up Sheet: https://docs.google.com/spreadsheets/d/1agEK8S4yxphTOC7cojvsVjTxsPH5PenvtHDBDz5XotE/edit?usp=sharing

   4. Plan for remote attendance at the sessions.  

      1. We need to coordinate with T&C for better internet and power.   The Codefest committee will get that organized.

4. Sunday Jan 13.  4:10pm Tripal Workshop at PAG

5. Monday Jan 14th: AgBioData Meeting.  Garden Salon 2 , 10-12am.

User's Meeting Dec 4 to prepare for Codefest.

1. Group leaders will connect with their groups to organize tasks.  Watch for multiple online conference links.

Reminder: Slack Workspace. https://join.slack.com/t/tripal-project/shared_invite/enQtNDExNDU1NzUxOTI3LTNlOTg1MTNjZGQ1NjRmNGQxMWRjOGVjN2IwMjQyOTc2ODZlYWM2OTQxM2Y1ZWM1MmFkNWJhOGEwN2RkZjdkNGU

Consolidate documentation for core and extension modules

1. Use Read the Docs  https://github.com/tripal/tripal/tree/7.x-3.x/docs

2. We will link to extension modules with RTD docs in the Tripal User's Guide

3. Two options

   1. Use Sphinx to import docs from other projects

   2. Link to repo or documentation, or a one sentence description with a link out.

If something comes to your mind that you want to discuss add an issue!  Ask to have it tagged with 'Discuss in User's Meeting' tag.

New Module Announcements (please add your own):

1. Tripal Headquarters (Bradford)

   1. Provide an administration layer so users can submit content to your site pending approval before it goes into Chado.

   2. Allows you to define chado-specific permissions.

2. Tripal Apollo (Bradford)

   1. User management service for Apollo: connect your apollo server(s) to chado records and auto-sign users up for apollo-side permissions.

      1. Gensass has their own apollo integration with some potential overlap of interest.

      2. Should Monica/Bradford reach out?

3. JBrowse Management Module (Abdullah)

   1. manage jBrowse completely from Tripal to choose an organism from your Chado database and create a JBrowse instance.

   2. Provides forms for adding tracks without having to deal with perl or command-line.

   3. Different from https://github.com/tripal/tripal_jbrowse which adds a field on an entity page.

4. Coexpression networks module (Stephen)

   1. Not quite ready to be released, but please get in touch if you would be interested.

Gene Page Improvement (Bradford)

1. https://github.com/tripal/tripal/issues/732

2. Perhaps we should reach out to a collaborator in computer science to help direct us on human computer interaction.

3. Book recommended by grant reviewer: https://www.springer.com/us/book/9781493903771

4. Quick solution

   1. ONE: just write one field (thats what i started doing)

      1. Problem: its really hard to display so much info in one field.

   2. TWO: Make providing the child info the responsibility of each individua lfield.

   3. Asking each field to recursively travel the feature_relationship table on its own, and not sharing wiht other fields, seems like a major problem to BC/AA.

   4. Therefore, you also provide a feature_relationship lookup.  This would be in the form of featurepath (think: cvtermpath), OR in the form of a cached, shared child relationship lookup.

5. Things to consider

   1. Fields go to web services

   2. Page and web services should avoid providing different information.

6. Look at Intermine pages for examples, TAIR, Ensemble

Code Coverage Integration (Bradford)

1. https://github.com/tripal/tripal/issues/714

How to improve and increase collaborative coding (Stephen)

1. https://github.com/tripal/tripal/issues/540

2. What are you working on this week and are you open to collaboration if another group is interested?

Advisory committee. Who should be on it?  What is its role? Let's formalize by PAG

1. https://github.com/tripal/tripal/issues/344