Tripal User's Meeting 2017/12/08

Meeting Date
Attendees

Stephen Ficklin, WSU

Shawna Spoor, WSU

Valentin Guignon, Bioversity International (CGIAR)

Monica Poelchau, NAL/USDA

Meg Staton, UTK

Ming Chen, UTK

Bradford Condon UTK

Abdullah Almsaeed, UTK

Nathan Weeks, USDA-ARS @ ISU

Ethy Cannon, ISU

Blake Inderski, USDA-ARS

Yi Zheng, Boyce Thompson Institute

Malachy O’Connell, ISU

Junil Chang, Noble Research Institute

Gerard Lazo, USDA-ARS @ Albany, CA

Nic Herndon, UConn

 

Announcements & Reminders:

  • Tripal session at PAG will be Sunday January 11th from 4:00pm to 6:10pm in the California room

    • Yi Zheng: "Cucurbit Genomics Database: Integration Genetic and Genomics Resources for Cucurbit Breeding"

    • Dorrie Main: "Updates on Tripal Mapviewer and the Tripal Breeding Information Management System (BIMS)"

    • Stephen Ficklin: "The Tripal Gateway Project: Supporting Exchange, Transfer and Analysis of Large-Scale Data for Online Biological Databases"

    • Nic Herndon: "Tripal Extensions Facilitate Association Mapping Studies on Forest Trees with CartograTree

    • Abdullah Almsaeed: "Tripal Elasticsearch: Bringing Simple and Powerful Sitewide Search to Tripal Websites"

    • Sheri Sanders: "National Center for Genome Analysis Support (NCGAS) use and development of Tripal Genome Browsers on XSEDE’s Jetstream"

    • Alicia Talavera: "An Open and Community Oriented Web Portal for Subtropical Fruit Trees Genomic, Phenotype and Breeding Data Analysis"

    • Thanks to Meg Staton (Univ. of Tennessee) and Ethy Cannon (Iowa State) for putting together this year's workshop!

  • GMOD Workshop 10th-11th.  Both in the T&C. Brittany room

  • Tripal Hackathon and User's Meeting from 1/11-1/12 in the Garden Salon I at the Town and Country, meeting 9am-4:30pm each day with a group dinner Thursday night.  

  • We would like to post your funded projects on the Tripal.info site:  http://tripal.info/projects

  • Consider adding your modules into the Tripal GitHub organization.  

  • Remember to update the status of your modules on the Tripal.info site.  

  • If you have a new site or major updates to your existing site let us now and we can publish those on the Tripal news feed and twitter accounts.

  • Send us your logo if you have shared a module with the community and would like it showcased on the Tripal.info site

 

Agenda:

  1. Any generic or otherwise sharable Tripal efforts toward collecting and presenting gene function information (functional statements, ontology terms, et cetera, plus authority [typically a paper]). (Ethy)

    1. Function information derived from literature about genes.

    2. Perhaps check with GMOD schema mailing list.  

    3. PaperBLAST searches for papers associated with sequence

  2. Tripal Gateway Project Update

    1. Tripal v3 Update

      1. Completed online Tutorial coming

      2. Tripal v3 API documentation up by March.

      3. Data collections (shopping cart system)

      4. Demo site updated on tripal.info: http://demo.tripal.info/3.x/

    2. Data Exchange

      1. Tripal v3 Web services browseable with the HydraConsole: http://www.markus-lanthaler.com/hydra/console/?url=http://demo.tripal.info/3.x/web-services

      2. ElasticSearch from Staton Lab:  https://github.com/tripal/tripal_elasticsearch

        1. Working on integration with Data Collections and Tripal v3.

        2. Cross-site querying already working in dev, but will be released by January.

        3. Cross-site querying can work on Tripal v2 as well!  Both Tv2 and Tv3 can cross-site query.

    3. Galaxy Integration Resources

      1. Tripal Galaxy Module Released in October.

        1. https://www.drupal.org/project/tripal_galaxy

        2. https://github.com/tripal/tripal_galaxy

      2. Workflows compatible: https://github.com/statonlab/dibbs

      3. Documentation: http://tripal.info/tutorials/v3.x/galaxy

      4. Videos

        1. Basic set up of jetstream galaxy https://www.youtube.com/watch?v=clTyLMbUGho&t=2s

        2. Set up of Tripal V2 docker on jetstream:

https://www.youtube.com/watch?v=KUcsdCv35PY&t=14s

  1. Anthony Bretaudeau@BIPAA: Sorry I can’t attend, but some news if you’re interested:

    1. Working on updating https://github.com/erasche/docker-tripal to tripal 3 (v3.x branch) -- For Production

    2. Updating https://github.com/abretaud/python-tripal too, work in progress, changes needed in tripal: working on WS: https://github.com/tripal/tripal/pull/211

  2. For Development Docker image and Galaxy form Staton group.

    1. TripalDock: https://github.com/statonlab/tripaldock

  3. I (Ethy) am giving a talk on Tripal in the GMOD workshop at PAG. I plan to focus on how the Legume Federation is using Tripal but will also give a general update re: Tripal 3. If there is some aspect of Tripal 3 that you think should be mentioned, please email ekcannon@iastate.edu.

    1. Will put slides in a Google Doc for folks to provide input

    2. Please Email ethy if you'd like access to these slides.

  4. BrAPI (Breeders API):  

    1. Perhaps integration with Tv3 Web Services.  Perhaps talk in February/March.

    2. Uses Chado as the data store.

    3. MCPD (Multi Crop Passport Descriptor) http://www.cropontology.org/ontology/CO_020/FAO-Bioversity%20Multi-Crop%20Passport%20Descriptors

  5. Other Project Updates?

  6. Add agenda to the Tripal User's Meeting in San Diego the Issue about "Is Tripal FAIR?"

  7. Valentin's group is working on a phenotyping module.

  8. Analysis Expression module Tripal 3 release this month?

Meeting Type
Users