Tripal Developer's Meeting 2014-12-02

Reminders

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

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

3. 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

Funded Projects:

1. NSF DIBBs (PI Ficklin)

   1. Tripal Exchange Module:  REST web services.  Work begins now. First developer’s meeting held mid December. All invited. Watch for forthcoming email.

      1. Andrew farmer implemented API for gene family module (based on phylotree module).

      2. Ethy has had requests for web services for QTL module.

   2. Tripal Galaxy Module:  Work will begin later in 2015.

   3. Tripal SDN Module:  exploration of SDN technology for faster data  transfers between Tripal databases.

2. USDA NRSP (PI Main). Formal list of items coming next month.  Started in October.

3. USDA SCRI (PI Main). Formal list of items coming next month.  Started in October.

   1. NCBI parser/loader/Gene/Gene family module (year 1)

   2. Tripal module for RightField (done in year 1)

   3. Tripal Module for Field Book (breeding data application for collecting phenotype data (pictures, measurements)) (year 2).  Any relation to IBP field book?  Will be completely open-source.

   4. Customizable Query builder tool (year 1 & 2)

   5. Conversion of Breeders Toolbox to be Tripal compatible.

      1. breeding data management (year 1-3)

      2. other breeding decision tools (year 2-5)

4. Andrew, Ethy, Steve,... NSF PGRP proposal outstanding.  Legume database federation.

5. Nobel Foundation: Alfalfa. Extension of Chris Town Medicago database.

Job Postings:

1. Post on Tripal Site (with expiration date) if desired.

2. Post on GMOD Site (coordinate with Scott).

3. Current Openings:

   1. Web Developer at WSU for DIBBs project.

Upcoming Activities:

1. Posted on Tripal Website. Let us know and we will add them.

2. Tripal PAG Workshop. Jan 11th, Sunday at 4:00-6:15pm PST.

   1. Extension Modules presented by Lacey:

      1. ND Natural Diversity Genotypes (U Sask)

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

      3. Tripal Germplasm  (U Sask)

      4. JBrowse module (U Sask)

      5. Tripal Daemon module (U Sask)

      6. EImage module (if finished in time)

      7. Phlyotree module ??

      8. QTL module ??

3. GMOD PAG Workshop.  Jan 14th, Wed 10:30-5:00pm PST.

4. GMOD Online Training / Summer School ?

5. GMOD Annual Meeting ?

6. Others ??

   1. BOSC:  Dublin Ireland. 2 days before ISMB conference. Provide support for hackathons.

7. DIBBs web services design meetings (Start mid Dec 2014)

8. Any conferences where your work will be presented?

9. Continued Tripal Developer Meetings (change to every other month rather than monthly?)

   1. Interleave… some more topic and every other month the larger broader meeting.

Extension Modules Under Development

1. QTL Module (Iowa / WSU / USask)  

2. Main lab Customizations (WSU).

3. Network Module / Expression data (WSU / Clemson; Discuss with Mara & Kris).

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

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

6. VCF Loader (WSU).

7. Pedigree/Relationship Viewer (USask).

   1. Does anyone need tree-like views of relationship data.

   2. Ontologies are configurable via the interface.

   3. Using JavaScript InfoViz Toolkit (JIT).

   4. Check the phylotree module from Andrew’s group.  Visualization based on D3 libraries.

8. ND Genotypes (has a Released version; documentation needed) (USask)

9. Tripal Germplasm & Cross Management (USask)

10. Genbank Parser. Includes search tool. Will implement in group module. Includes bulk loader templates for importing Genbank files (WSU)

11. Phylotree Module (NCGR/Iowa)

12. Shopping Cart style data store (NCGR). Generating lists of items to do operations.  

    1. Light-weight list generating tool in Tripal and passing those/integrating with iPlant.

    2. Uses LightShop Drupal module.

    3. Implemented for BioMaterial module already.

Tripal Core Future Developments

1. What is core functionality?  Should web services be incorporated as core functionality?  What data loaders should come with Tripal by default (i.e. VCF, GenBank)? Should only Tripal Core module be Tripal and all other modules be extensions?   

   1. Reason for the question:

      1. Too much stuff, is it overwhelming?

      2. Takes a long time to convert to new Drupal version & Release updates.

      3. Currently, Tripal is heavy on the whole genome / transcriptomics which may confuse folks who may be looking to construct a resource for storing stocks/germplasm, breeding resources, etc.

      4. Maintenance: hard to keep up with all these modules on the same release schedule.

   2. Pros for separating

      1. Allow for more releases, more often

      2. Simplified code base to convert as new versions of Drupal are released.

      3. Users only need download modules they need. They don’t get a bunch of other modules they don’t need.

      4. Forces dependencies to be properly specified (currently all come together).

   3. Cons:

      1. Increases the difficulty for installation:  users’ must be more aware of dependencies and which modules to install.

   4. Concerns:

      1. The core modules must remain generic for common usage.  By making other modules not “core” (e.g. feature) there is the risk of losing oversight and loss of generic functionality.  Who maintains?

   5. * TODO:  plan out what should go into core, what should be separate (specific to a certain subgroup).

2. RSS feed on Tripal.info that lists extensions available.  

   1. Add to the Tripal core module a web interface to parse read that RSS feed and show users all available modules.

   2. Tag modules with categories to help select modules for installation.

3. Installation Profiles:  

   1. RSS feed provides profile setup details.

   2. pre-configured set of modules by need (e.g. genomics site, breeding site, genetics site, etc…).

   3. functions just like a manually installed Tripal site with the ability to add additional modules, disable core ones, etc.

4. Data access permissions.  

   1. Proposed expansion of web services to include authentication/access NSF PGRP (PI Main @ WSU)

   2. Current solution:  chado controller

5. Expanded Drush commands for full command-line management -- no current funding to do this.  Must be done step-by-step.

6. Tripal changes for Drupal 8

   1. Use of Drupal Entities (object oriented)

      1. Provides an API for every chado table.

7. Store results of queries into a “Shopping Cart” style.

Chado

1. Updated release

   1. List of new tables

2. * Progress getting into git.

3. Group Module

iPlant Data Commons (Steve Cannon)

1. A new feature at iPlant.  Website development toolkit within iPlant.  Tools for sharing managing, publishing data to be used with iplant analysis tools.  Connects to workflows metadata, etc.

2. Looks like a new GMOD-style toolkit.  For creating custom websites within iPlant.

3. * Talk with iPlant during development to have design interaction.

4. Perhaps PAG Meeting to discuss.

Issues

1. Tripal GFF3 loader doesn’t create polypeptide features.

Topics for future meeting

1. Open up discussion of germplasm / cross management / breeding.

2. Javascript graphing visualization library.