Tripal Developer's Meeting 2015-08-04

Meeting Date

Tue, 08/04/2015 - 12:00

Attendees

Lacey Sanderson (Usask)

Stephen Ficklin, Chun-Huai Cheng (WSU)

Meg Staton, Nathan Henry, Ming Chen (UTK)

Nathan Weeks (USDA-ARS/Ames)

Vijaya, Chris Childers (USDA/NAL)

Andrew, Pooja (NCGR)
Gerard Lazo (USDA-ARS/Albany)

Non Chado Data?
- Andrew Farmer: a bit of prototyping trying to associate URLs to BAM files via biomaterial table. Metadata for experiment for RNA-seq data would be stored there. Focusing on importing data from NCBI BioSample/BioProject.
- Stephen Ficklin: a file module.
- Nathan Weeks: Brilliant Gallery for showing image data. Also using customized version of FileBrowser Drupal module, for browser based access to Excel spreadsheets with metadata.
- Chris Childers: documents (tutorials/guides/etc.) including flat files, PDF documents and other documents.
- Gerard Lazo: Drupal wrapper around GrainGenes. Looking to migrate.
RNA-Seq Module (Meg Staton)
- Adding RNASeq expression data to chado is not intuitive. Here is a google doc describing some potential ways forward.
- Andrew Farmer: was importing XML from BioProject/BioSample and meta data fit nicely into existing Chado tables. Did not represent experimental design. Interested in pursuing work on RNA-seq.
- Should we request table changes or new module for RNA-Seq Data
- Perhaps a link between biomaterial + library and biomaterial + stock.
- SolGenomics Network is developing and RNA-Seq module. Perhaps not in Chado but is willing to talk Chado.
- Where to put quantitative information. Link features to samples and linking expression quantities.
- Meg can make available to the code for others to see.
- Andrew’s group can share the code with importing form NCBI BioSample/BioProject.
Page redesign & gene pages.
- Would folks be interested in i5K templates for gene pages? They can share.
Site-wide indexing
- Meeting notes from 2015/7/24
- Meeting notes from 2015/7/16
- Summary:
  - Goal: provide a recommended method, perhaps a module, and set of documentation to help others setup site-wide indexing on their site.
  - Discussed different implementations for a site-wide searching method: Drupal default search, Apache Solr, Elastic Search
  - Needs:
    - Only data made available to end-user should be indexed. Not necessarily everything in Chado
    - Search results should highlight matched words on page.
    - Would like to integrate with a “basket” system for later transformation of data.
  - Vijaya Tsavatapalli of USDA/NAL working on an Apache Solr module
  - Valentin Guignon (Bioversity International, CGIAR) working on an Elastic Search module.
- Action Items
  - Vijaya will work on administrative section of her Apache Solr module to provide more customization.
  - Documentation for the module on tripal.info
  - More input from Valentin.

Chado/Tripal Sustainability (Stress Testing)
- Meeting notes from 2015/7/22
- Summary:
  - Goal: plan for, test and attempt to resolve issues related to poor performance:
    - Syncing takes too long
    - Setting URL alias takes too long
    - Loading GFF?
    - Missing indexes in Chado
    - Bulk loader can be slow for large data sets.
    - ND tables: takes a large number of records for a single genotype/phenotypes.
    - MViews bloat the database.
  - Ideas:
    - Stress test by creating dummy data to explore limits of Chado.
    - Improved interface for MViews: better way to share, track FK constraints between them.
    - Improve accessibility of documentation for solutions to common problems.
    - Maybe something similar to testing (https://travis-ci.org/, https://jenkins-ci.org/). Looks like a Drupal module also available for testing. https://github.com/sonnym/travis-ci-drupal-module-example
  - Action Items
    - Chris created a python script takes a GFF and set of FASTA files (assembly/CDS/cDNA/peptide) and generates a set of new data.
      - https://github.com/NAL-i5K/test_data_gen
    - Andrew is working on a test server at iPlant.
    - Lacey: it will likely be a month before I get some time to work on this :(
    - Stephen: will see if there’s another solution. Can we get AWS credits for it.
    - Stephen & Chun-huai to discuss creating data for data at Mainlab.
    - Some needed improvements
      - Stephen try to fit in improvements the Materialized Views + documentation in the coming months.
      - Restrict setting url alias to a limited set of items. Crashing because of memory issues.
    - Stephen to work in patch into Tripal package so folks can at least apply the patch for syncing that Nathan created.

Meeting Type

Users