Tripal User's Meeting 2016/10/7

Meeting Date: 
Friday, October 7, 2016
Attendees: 

Lacey-Anne Sanderson (UofS)

Nick Booher (Iowa State University)

Chris Childers, Vijaya Tsavatapalli, Monica Poelchau (USDA-ARS-NAL)

Nathan Dunn (LBNL)

Valentin Guignon (Bioversity International, CGIAR)

Meg Staton, Ming Chen (UTK)
Katheryn Buble, Sook Jung, Taein Lee (WSU)

Eric Rasche (TAMU-CPT)

 

Sending Regards

Anthony Bretaudeau (INRA)

Ethy Cannon (Iowa State)

Gerard Lazo (ARS, CA)

 
Agenda: 

Quick Announcements

  • Tripal Workshop at PAG

    • Sunday January 15th 2017 from 4pm-6:10pm in San Diego, CA

    • Abstracts can be submitted by email in MS Word or PDF to pag-abstracts@tripal.info by Friday October 14th.  

  • Module Releases

    • Tripal JBrowse API: exposes your chado features table as a JBrowse compatible REST API

      • Credit to Sascha Steinbiss (wrote the SQL queries that make it it work in the parent project by Eric Rasche, kind enough to re-license to make PHP port possible), Nick Booher (ported to PHP)

    • Tripal Download API: provides a framework for downloading Tripal/Chado data

      • Credit to Lacey-anne Sanderson

    • Tripal Docker image: Docker image was updated to Tripal 2.x

      • Credit to Eric Rache and Anthony Bretaudeau

    • Chado 1.31 Database Dumps: there are no pre-built chado database dumps available for v1.31

    • Python Tripal Data Loader: a python module that allows you to load data into a Tripal instance from command line (or python code).

      • Credit to Anthony BretLacey-Anne Sanderson (UofS)

      • Nick Booher (Iowa State University)

      • Chris Childers, Vijaya Tsavatapalli, Monica Poelchau (USDA-ARS-NAL)

      • Nathan Dunn (LBNL)

      • Valentin Guignon (Bioversity International, CGIAR)

      • Meg Staton, Ming Chen (UTK)
        Katheryn Buble, Sook Jung, Taein Lee (WSU)

      • Eric Rasche (TAMU-CPT)

      •  
      • Sending Regards

      • Anthony Bretaudeau (INRA)

      • Ethy Cannon (Iowa State)

      • Gerard Lazo (ARS, CA)

      • audeau

    • Tripal Jobs REST API: a simple REST API exposing job information and an interface for non-PHP scripts to submit Tripal jobs.

      • Credit to Anthony Bretaudeau

    • Python Chado Tools: a small set of tools for interacting with chado from python

      • Credit to Anthony Bretaudeau and Eric Rache

    • blend4php: A PHP library for Galaxy integration. Currently being used for creation of a new Tripal Galaxy module.

      • Credit to Connor Wytko, Brian Soto, Stephen Ficklin

    • Others?

  • Coming Soon:

    • Tripal Expression Module: visual representation of gene expression.

      • Credit to Staton Lab @ Utenn

    • Tripal Elastic Search Module: Provides site-wide searching using Elastic Search

      • Credit to Staton Lab @ Utenn

    • ND Genotypes: Provides an interface and more efficient data storage model for genotype calls

      • Credit to Lacey Sanderson @ UofS

    • Raw Phenotypes: Provides an upload/download interface for raw phenotypic data

      • Credit to Lacey Sanderson @ UofS

    • Tripal Map Module (replacement for CMAP)

      • Credit to Main Lab @ WSU

    • Main Lab Tripal and Main Lab Search

      • Credit to Main Lab @WSU

    • Multi-Chado:  Support for multiple instances of Chado within one Tripal instance

      • Credit to Valentin

    • Updates to Tripal Blast, GO, InterPro:  

      • Credit… fixes courtesy of Anthony Bretaudeau (INRA)

    • Ontology search module: for finding children, siblings, and/or parents for trait searching (i.e. QTLs). Use ontologies to expand searches

      • Credit:  Ethy Cannon

    • Network Module: visualize interaction or co-expression networks

      • Credit:  Ficklin Lab

    • Tripal Galaxy Module: Integration of Galaxy and Tripal.

      • Credit Ficklin Lab

    • Breeding API: Breeding API implementation for Drupal (currently being rewritten)

      • Credit: to Valentin

  • Please fill out the GMOD JBrowse & Help Desk Survey!

  • A Big Thank you to everyone who has contributed bug fixes and features! For anyone else who wants to contribute to core Tripal development, we welcome pull requests and would Love to hear from you :-)

Agenda

  • Tripal Hackathon and/or Developer/User Meeting before PAG (Lacey)

    • We are looking for feedback from the community on interest in attending a Hackathon and/or Meeting for Tripal on the Thursday and/or Friday before PAG

    • http://doodle.com/poll/qqkwm3x4zrsqqinz

    • Possibly come up with a list of topics for "hackathon"

    • Possibly start early (8am) on Friday… 8-2pm

  • Tripal Download API Views Support (Lacey)

    • This API currently provides generic support for custom downloads

      • You register a Download Type using hook_register_trpdownload_type() and a URL that will trigger download using hook_menu()

      • The API provides a generic download page with ajax progress bar that calls your custom download function to create the file.

    • I would like some input on what would be the most useful/performant/flexible with respect to views integration:

      • A) Most flexibility: Use the API to get the views query but you handle executing it, processing results and generating the file yourself.

        • Ensures that the user downloads the same results they saw but allows you full control to manipulate the views results while generating the file.

        • Requires more developer effort to get it going.

      • B) Most Functionality: The API programmatically executes the view, iterates through the results and generates the file. All you need to do is tell it how to transform a single query row into a string to write to the file.

        • Could be too restrictive depending on how much processing is needed to generate your file.

        • Do you need access to more than one row at a time?

        • Additional functions could be made available to customize the header and footer of your file.

      • C) Any other ideas?

        • Even programmers don’t want to write yet another fasta bed gff bam file formatter / writer

        • Implement a) but some support for b)

  • Tripal Related Job openings

  • Google Summer of Code Report

  • Neo4j implementation of Chado

  • Tripal 3 update

  • Questions

    • Anyone used Tripal with Drupal 7.50 or Drupal 7.51? (Nick Booher)

    • Tripal 2.1 final release date?

    • Any questions on the Tripal Docker image?

  • Action Items

    • Stephen: send out information about Sequence Retrieval Tool build in Chado.  Add documentation to User's Guide (perhaps break out into a separate module)

    • Stephen:  Test Drupal 7.50 or 7.51

    • Stephen & Lacey:  Set a target date for 2.1 release.

    • Add Tripal Docker to User's Guide.