Tripal Developer's Meeting 2014-10-07

Meeting Date
Attendees

Andrew Farmer (NCGR)

Stephen Ficklin, Chun-huai Cheng, Sook Jung, Taein Lee (WSU)

Lacey Sanderson (U Saskatchewan)

Mara Kim, Kris McGary (Vanderbilt)

Valentin Guignon (BIOVERSITY)

Scott Cain (GMOD, Ontario Institute of Cancer Research)

Monica Poelchau, Chris Childers, Vijaya Tsavatapalli (USDA / NAL)

Steve Cannon, Deepak Bitragunta, Sudhansu Dash (Iowa State Univ.),

Nelson Nazzicari (Parco Tecnologico Padano)

Those Sending Regards
Ethy Cannon (Iowa State)
Meg Staton, Nate Henry (Univ of Tennessee)
Alex Feltus (Clemson Univ)
Gerard Lazo (USDA/ARS)

  1. Recently funded projects for Tripal development.

    1. NSF DIBBS:

      1. http://www.nsf.gov/news/news_summ.jsp?cntn_id=132880

      2. http://nsf.gov/awardsearch/showAward?AWD_ID=1443040&HistoricalAwards=false

      3. API for cross-communication and web services.

      4. Integrate Galaxy with Tripal.

      5. Software defined networking.  

    2. NRSP: Breeding resources, Customizable query building, open-source applications for field collections of breeding data and linking with Tripal.

    3. NSF PGRP

  2. Tripal Workshop at PAG: Call for Extension Modules to be presented

    1. Existing modules

      1. ND Natural Diversity Genotypes (U Sask)

      2. Blast Tripal Modules  (U Sask/Univ Iowa/WSU)

      3. Tripal Germplasm  (U Sask)

      4. Functional Annotation Modules (KEGG/InterPro)

      5. JBrowse module (U Sask)

      6. Tripal Daemon module (U Sask) (forgot to mention in call, added afterwards)

    2. What’s coming

      1. EImage Module (WSU)

      2. QTL Module (Iowa / WSU)  (See demo later today at PeanutBase under QTL tab).

      3. Main lab Customizations for Genotypes/Searching (WSU).

      4. Network Module / Expression data (Discuss with Mara / Kris)

    3. Modules included in other talks: Andrew’s Phylotree module (NCGR) in Ethy’s talk.

  3. Module Development:  Drupal "git vetted user role"

    1. Please email mailing list to have other users review your modules.  We can review each other’s code.

    2. To place your module on Drupal.org and to have permission to release full projects follow the steps on this page: https://www.drupal.org/node/1011196

  4. Other ongoing projects

    1. GenSAS: automated and manual structural and functional annotation of genomic sequence. Integrates with WebApollo.  Probably release Q1 of 2015.  With Tripal integration coming later. (WSU)

    2. WebApollo Tripal module (needs lots of work)  (WSU)

    3. JBrowse Tripal module for integrating JBrowse with Tripal (Univ Sask)

  5. What else is needed?

    1. Nelson:  Issues of access permissions for specific data types.

      1. Valentin: uses chado controller, works with feature table primarily, and allows you to restrict access to specific records.  Thinking about creating a Tripal module for install for chado controller.

      2. CHADO Controller URL: http://www.gnpannot.org/content/chado-controller

      3. Added Issue to track issue: https://www.drupal.org/node/2352859

  6. Feature requests.

    1. Mara:  More command-line ways to interface with Tripal.  Specifically because she has pipelines to interact with Chado database. (i.e. creating organism/feature pages, etc). Issue added at: https://www.drupal.org/node/2314235

    2. Mara:  Blast loader requires a database cross-reference.  Can we handle blasting without specifying a database.  Issue added at https://www.drupal.org/node/2352329

    3. JBrowse integration example: http://coffee-genome.org/jbrowse

  7. Chado

    1. Scott: Updated release perhaps by end of 2014.

    2. Mara: Group module, new update with Flybase requests.  

  8. TODO:

    1. Next meeting have a shared google doc.  

 

 

Next Month’s Agenda

 

 

  1. Inclusion of new extension modules as part of Tripal (if they are generic enough)

  2. Should Tripal be broken into separate modules?
Meeting Type
Users