Tripal Developer's Meeting 2015-02-03

Thanks to PAG speakers!

Status of Chado

1. Ideas for changes: changes to organism table for infraspecific names; Group module needs some looking at further; adding property tables for existing tables (also how to deal with units);  Eimage table; db table in it’s own module. And some changes requested on the mailing list.

2. Will make document of changes public for other comments.

3. Idea: deal with easy issues (organism table, property tables) for a quick release and more difficult issues in future release.

4. Move to GitHub… request for any further commits.

GMOD Summer School (Tripal workshop) + GMOD Meeting

GMOD/Google Summer of code

1. “Google Summer of Code is a global program that offers student developers stipends to write code for various open source software projects”

2. http://gmod.org/wiki/GSoC

Status of Tripal v2.0 stable release.  Look for release in March.

Tripal extension modules currently under development

1. QTL  (U. Iowa, WSU, U. Sask)

   1. Need to pull together a vocabulary and then a list of requirements for feedback from other groups.

   2. Waiting on feedback of template file.

2. BLAST (U. Iowa, U. Sask)

   1. plan to put development code in GitHub and move to Drupal repository once it’s ready for general use.  

   2. Separate but somehow combined to reduce confusion.

3. Networks (WSU, Clemson)

4. Web Services (WSU + community)

   1. Demo currently online, using AGAVE + HAL format.

   2. Need to address data privacy issues within the web services.

      1. differential access (different groups have access to differenet things).

   3. Anonymous registration to track usage.

5. Phylogeny (NCGR, U. Iowa)

   1. Make public soon.

6. Pedigrees (U Sask)

7. d3 support (U Sask)

   1. want to support basic pie/bar charts, feature location diagrams, etc.

8. KEGG module issues (WSU)

9. Ecommerce style shopping cart (NCGR) for collecting data. Currently gene oriented has some sequence download functionality.

Searching?

1. Add a section on how to deal with searching to the online documentation?

2. Valentin Guignon provided a suggestion for integration with ElasticSearch and Solr and provided some example code: https://www.drupal.org/node/2214775

3. Need a single search box capability (google type approach).  Perhaps something like Entrez.

Setup Improvements?

1. Installation, ease of use, recommended improvements?

2. Installation profiles vs Distribution

   1. Installation profiles can be executed after Drupal is setup to download everything needed.

   2. Distribution is a full package with everything need that can contain an installation profile to complete some additional steps.

3. What kind of “Tripal” Distributions/Installation profiles should we offer?

   1. Genomics site for whole genomes transcriptomes?

   2. Breeding-specific site?

   3. E-commerce/stock site?

   4. Need tutorials for these.

   5. Other thoughts

      1. Not include default organisms, analyses. Or ability to control what data gets preloaded.  

      2. Ethy offers to provide feedback from her group.

      3. Include a tour in distributions: https://www.drupal.org/project/joyride

      4.  

Change to gene/mRNA default page:  merge into a single gene page?

1. difficult to traverse feature relationships (mostly gene centric).

2. Yes, combine, at least for genes, into a single gene page.

3. Chris Childers: i5K would be willing to share their efforts as a potential default solution.

TODO:  

1. Add a section to the Tripal tutorial about permissions… how to make some date private for certain groups.