Tripal User's Meeting 2018/10/05

Reminders & Announcements

• New meeting time!  Tuesdays!  Same time/regularity.

• Next meeting: November 6th. (US Election Day)

  • Check if we want to postpone it a week.

• PAG is coming up!

  • Please submit abstracts to the Tripal session organizers bradford and Valentin!

    • bradford.condon@gmail.com

    • Accepting short and longer talks, just contact us!

  • Collaborationfest!

    • User tutorials

    • Python API (below)

• Tripal governance:

  • PRs require 2 reviews: You could be reviewer #2! Get involved!

  • Described in the Contributions guidelines here https://github.com/tripal/tripal/blob/7.x-3.x/CONTRIBUTING.md

  • Be on lookout for formation of Oversight committee.  PMC (Bradford, Stephen, Lacey) make code-level decisions, Oversight will discuss bigger vision issues.

  • Discussion thread: https://github.com/tripal/tripal/issues/344

• Stay connected: Follow us on twitter, join our slack space, watch the github repository to see issues/discussions, join the GMOD email list

• Slack: https://join.slack.com/t/tripal-project/shared_invite/enQtNDExNDU1NzUxOTI3LTNlOTg1MTNjZGQ1NjRmNGQxMWRjOGVjN2IwMjQyOTc2ODZlYWM2OTQxM2Y1ZWM1MmFkNWJhOGEwN2RkZjdkNGU

• Twitter: @TripalProject

• Github: https://github.com/tripal/tripal

• Mailing list: http://gmod.org/wiki/GMOD_Mailing_Lists

Discussion Topics (Open Agenda)

• Official Tripal 3 release!

  • Some parts of guide still need to be updated (functional annotation)

    • Gerard - Upgrade went OK(ish?)  A couple of errors at the end of the install.

      • Please share them on the queue!

      • Note we have continuous integration set up to upgrade a barebones tripal 2 site to tripal 3, so we can at least confirm that is behaving itself.

Im k

• Nathan

  • Blast, Interpro, KEGG

    • Cv_xray : visualizing ontology data across features

    • https://github.com/statonlab/tripal_cv_xray

  • GO → previously a page for visualizing GO terms.  

    • We’d love this contributed

• Valentin - add fields…

  • Feature_cvterm….

  • X_cvterm

    • The annotations field does this.

    • But isnt perfect for all needs:

    • Example use case: for stock table, with a CV ‘stock_status’ having the cvterms ‘active’, ‘lost’, ‘archived’,’..., it would be nice to define a new field “Chado cvterm” the way “Chado property” is, where you can select the CV to use for the available cvterms to select.

      • A custom field could be the answer

      • Alternatively a generic linker field that is an alternative to the existing annotation field.  It would behave more like the chado property field, allowing the admin to create a field using hte cvterm, but the term/value is stored in _cvterm instead of prop.

Docker images:

• https://github.com/statonlab/docker-containers (Old! Please see tripaldock instead)

• Tripaldock (development, Tripal 3 compatible): https://github.com/statonlab/tripaldock

• Helena Rasche docker containers (more for production): https://github.com/erasche/docker-tripal

• Store co-expression networks?

  • Old tripal 1 module?

  • Stephen Ficklin has some co-expression network data.

  • Shawna - Network module has fallen to the wayside and he’d love to work on it.

• Read the Docs (Earn your Hacktoberfest T-shirt!) (BC)

  • Tripal documentation: https://tripal.readthedocs.io/en/latest/

  • Hacktoberfest: https://hacktoberfest.digitalocean.com/

• Python API Library (Community)

  • Proof of Concept underway, please join us

  • Design meeting notes from 2018-10-02:

    • https://docs.google.com/document/d/1UUefbQUiMATjRr4o2LsN2McrvNZ1b6IPajkhclLiLiE/edit