Tripal User's Meeting 2016/11/04

Meeting Date: 
Friday, November 4, 2016
Attendees: 

Nic Herndon @ UConn - plan to attend, might be about 15 minutes late

Lacey Sanderson @ USask

Stephen Ficklin, Katheryn Buble, WSU

Ming Chen @ UTK

Andrew Farmer, NCGR

Ethy Cannon, ISU

Steven Cannon, ARS - Ames

Deepak Unni - University of Missouri (Apollo dev team)

Eric Rasche, CPT, TAMU

 

Sends Regards

Gerard Lazo, ARS - Albany, CA

 
Agenda: 

Agenda

  • Official Tripal Help Desk Hire

  • Hackathon at PAG: Jan 12-13, 2017

    • Will be two days.  Jan 12th is a typical hackathon.  Jan 13th is a round table discussion meeting.  Friday will only be half a day.  

    • What are some desired topics on the hackathon?

      • Tripal Download API

      • Help each other implement each other's modules or generalize them to make more shareable.Nic Herndon @ UConn - plan to attend, might be about 15 minutes late

      • Lacey Sanderson @ USask

      • Stephen Ficklin, Katheryn Buble, WSU

      • Ming Chen @ UTK

      • Andrew Farmer, NCGR

      • Ethy Cannon, ISU

      • Steven Cannon, ARS - Ames

      • Deepak Unni - University of Missouri (Apollo dev team)

      • Eric Rasche, CPT, TAMU

      •  
      • Sends Regards

      • Gerard Lazo, ARS - Albany, CA

      •  
      • SNPs and noSQL storage (Ethy)

        • Tripal 3 notes for how to do this.

  • Filter similar to Zappos.com (Nic Herndon)

    • Drupal Faceted Search uses Drupal Search API.  It integrates with ElasticSearch, ApacheSolr or Default Drupal Database.

    • ElasticSearch (Check with Valentin or Ming)

  • Training Meeting Dec 2nd

  • Legume Federation meeting Jan 13, 12:30 - 4:40 (quite a bit of Tripal discussion)

    • Half presentation / half discussion

    • Presentations will include show and tell of some Tripal related items.  Including phylotree implementation.  BLAST module (Ethy/Lacey).  Integration with Intermine and data store (H5AI; http://LegumeInfo.org/data). Integration with Cyverse (FTP style access) and mirror on Cyverse.

      • MetaData standards are a current challenge.

        • Provenance,  renaming, vocabularies to describe.

        • Still want navigation and directory structure to be intuitive.

        • Store on system for active work with files.

  • Main Lab (Sook)

    • Released 3 related modules:

      • Tripal Chado Loader:  comes with Excel templates for importing contacts, markers, map positions, QTLs, genotype, phenotpyes. Can generate the template for your needs and imports that data.

      • Tripal Mainlab Data Display:  provides Drupal theming templates to make a site look like and support data storage similar to GDR/CottonGen.

      • Tripal Mainlab Search Module: advanced search modules for genes, transcripts. markers, genotypes, QTL, MTL, image, germplasm, etc.

        • Based on materialized views.  If your data store is different you can modify the MViews to use the search module.

    • All three described on Tripal.info site with links to GitHub.

    • TripalMap module:

      • Javascript replacement of CMAP, integrates directly with Chado.

      • Will be presenting at PAG within CSFL website.

      • Released a few weeks after PAG.

      • Available on Tripal.info site with link to GitHub (code isn't yet posted, but coming soon).

  • Andrew Farmer

    • Tripal Phylotree module replacement. Released next week!

    • Visualized tree, sequence alignment, can subset tree to taxa of interest.

    • Integrates with Chado/Tripal by using Tripal API calls.  

    • Can be used for any species of interest.

    • Need to test compatibility with default phylogeny module with Tripal 2.1

  • Lacey

    • Getting close to releasing raw phenotype module.   Perhaps in the next few weeks.

      • Loaders and visualization of the data loaders and downloads for Excel (R-friendly format also available)

      • Loader is specific to the module to ensure data integrity constraints but allow flexibility to support user's specific needs.

      • Traits are stored in Chado… stores data from the field in custom tables that integrates with Chado which are created at time of installation.

    • Also working on Genotype functionality (maybe by PAG).  Handless 500M data points with quick responses!  Requires some database tuning, but tuning is built into the module.  Next test is 5B data points.  

  • CMap II (LegFed effort)

    • Prototype stage; aiming for “mature prototype” by PAG

    • Bokeh (python/javascript visualization library; http://bokeh.pydata.org/en/latest/)

    • Aiming for a standalone application, not dependent on Chado or Tripal, but capable of taking data from them or via REST methods

    • Will pull from REST web services for Tripal v3.