Tripal Developer's Meeting 2015-11-03

Last Month’s Notes

TODO items from October:

• Ontology loader needs fixing. It does not properly load the new Relationship Ontology.  Work has started on this… still working on it..

• Stress Testing Plan:  test atmosphere on IPlant, look into Jenkins/Travis CI. No movement has been made on this issue.

• Remove recommendations for Views Data Export on Tripal documentation. Verified no longer recommended on the documentation.

• Status of GFF Downloader:  Initial code exists for it.  But it needs further development and testing.

• Add to Tripal v3.0 design the topic of data export and filtering.   Export of Entities (e.g. genes) and attached fields (properties, dbxref, locations, etc) has not yet progressed to design exporting and filtering.  But it will be kept on the TODO list.

Expect the following:

• Trying for a Tripal v3 alpha release before PAG.  Will not support all Chado tables but will give folks opportunity to explore initial functionality with entities and web services.

  • Any experience with cross-origin request (e.g. how will work with future Tripal web services)?  How to setup Drupal server to allow these requests to be made.

  • https://www.drupal.org/project/cors

• Integration of Chado v1.3 into Tripal 2.x.  We will try to have this ready before Jan 1st 2016.

• Fix for OBO import problem. Possibly an OWL parser for ontologies as well.

• Tripal PAG workshop.  Jan 10th at 4pm PST.

Tripal PAG codefest.  Friday Jan 8th.

• Tentative agenda, please edit!!!: https://docs.google.com/document/d/1jarLU2EwzQ2Gl9LiHVTfDW9ju-MmP-LPTJsDPeNqJHk/edit?usp=sharing

• Will there be ability to login and remotely attend.

Drupal 8 Release:  Nov 19th.

• Porting Modules and themes: https://www.drupal.org/drupal-8.0.0-rc1#porting

• Conversion of PHP tpl.php template to twig: https://www.drupal.org/node/2025313

• Tripal v3.0 will be Drupal 7 compatible.   This will give the Drupal community time to catch up with porting dependent modules (and give us time as well).

Status of extension modules

• Blast Module (Ethy/Lacey).  Visualization of hits, can edit and resubmit a blast analysis job. Keeps track of previous results.  

  • Stephen will explore merging two blast modules after Ethy & Lacey’s module is released.

• Bibtex importer for the publication module.  Not quite support of full Bibtex.  Currently a separate module.  Could potentially be imported into Tripal pub module.  Only has drush not yet a web interface.

• Expression Module (Meg/Nate).  Will be available in beta from by PAG.  Using MAGE tables.  

  • In future work on setting up meeting for modifying MAGE module or create RNA-seq module for Chado… and also perhaps an interaction module.

• Phylogeny module (Andrew):  working on ability to interact between synteny viewers and trees.  Synteny viewer uses AngularJS.  Andrew will give demo if someone is interested.

  • In January -- perhaps merge in genericized code into Tripal v2.x core.

  • Anyone interested in discussing how to genericize code feel free to contact Stephen, and we can talk specific for your project.

  • TODO:  a demo for Andrew’s synteny viewer (see news items on legumeinfo.org site for links).

    • An Example displaying segments of genomes with similar gene content to that surrounding the example “Fin” gene: http://legumeinfo.org/lis_context_viewer/index.html#/search/phavu.Phvul.001G189200?numNeighbors=8&numMatchedFamilies=6&numNonFamily=5&algorithm=smith&match=5&mismatch=-1&gap=-1&threshold=15&order=distance

• Protein Domains (Andrew):  goes further than the existing InterPro Analysis module but goes a bit further.  Hits becomes pair-wise alignments between protein and domains and adds features to Chado.  Those features are linked to gene records.

• Apache Solr site-wide indexing (Chris/Vijaya): still working on genercizing the module.  

• Elastic Search (Valetin): Meg’s group is communication to hopefully merge efforts.

• Breeding Management System:  converting previous breeders toolbox to Tripal and adding new functionality.  Breeders will be able to import their own data. Will have preliminary information by PAG.  

Future Discussion:  How to code such that you can make your module shareable but at the same time tailored for your own needs.