Tripal User's Meeting 2018/01/12 @ San Deigo -- PAG Conference

Agenda

Reminders

• Further PAG Events

  • Tripal Workshop on Sunday in the California room at 4pm https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4885

  • GMOD Workshop on Wednesday  in the Pacific Salon 4&5 at 10:30am.

  • Tripal Galaxy talk on Tuesday , 5:50pm, California room

  • AgBioData Booth -- Check it out if you aren't participating.  Booth #407

  • AgBioData Meeting -- Monday, 7:00-8:30PM, Pacific Salon 3-4.

• Post funded projects on the Tripal site

  • http://tripal.info/projects
    What we need:

    • A description of the project

    • Who does the project serve?

    • A description of your team?

    • Funded dates.

    • Use Cases if available.

  • Doesn't need to be funded by a large funding-agency.

• 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.

• If you publish on your site please remember to cite Tripal (Sanderson et. al. 2013). A Tripal v3 paper will be submitted this year. (We did not have a Tripal v2 paper).

Discussion Topics (Open Agenda)

• Any ideas to add to the agenda?

• Any new extension modules?

  • Knowpuse (Lacey)

    • ​Tripal Fancy Fields (USASK; beta released)

      • Single-series Chart Field Type: pulls data from a configurable mview and displays results as a pie, donut, or bar chart, as well as, a simple table formatter. Resulting chart is specific to the Tripal Content Page using configurable filter database column => Field mapping.

      • Future Development: Multi-series Chart Field Type, Pedigrees, Quick Search (search box which re-directs to existing search), Hierarchy/Relationship Chart Field.

    • Tripal D3.js API (USASK; beta released)

      • Call a single javascript function to draw a variety of charts. Highly configurable. All the charts in Tripal Fancy Fields are drawn by this module.

      • Already has a wiki started that shows how to use the module and documents options

      • README also shows how easy it is to use

    • ND Genotypes (USASK; release by the end of January 2018)

      • Marker x Germplasm matrix search (complete)

      • Tripal 3 Fields: Marker/Variant Genotype pie chart & Marker/Genotype flanking sequence showing all flanking variants (almost done)

      • See this module on our KnowPulse poster at PAG: #P0737

    • Phenotypes (USASK; release 1.0 coming soon;)

• Data upload & download

• Dynamic quantitative trait chart summarizing the data for a given trait/project combination. This chart keeps site-years separate but averages replicates.

• Version 2.0 will include trait pages and specialized Tripal 3 fields

• • Boyce Thompson Institute

    • Synteny Viewer

      • Circos plots, user's can click the blocks to show collinearity.

    • RNA-seq Module

      • expression viewer + DEG analysis.

  • Main Lab

    • Tripal Map

      • Replacement for CMAP.  Integrates with Chado directly. https://www.rosaceae.org/mapViewer

    • Breeding Information Management System

      • See the talk in the Tripal Workshop by Dorrie Main.  She'll discuss both modules.

    • Data templates and loaders for loading non-sequence data: markers, maps, genotypes, contacts, QTLs import into Chado. Data Display Chado Loader

    • Search module for faster Chado searches without Views Chado Search

  • Legume Federation

    • Link Out module (proposed). Allows you to link out to other resources for an entity (e.g. gene -> genome browser, synteny browser, gene pages, etc.)

      • Should they genericize this for other folks to use? Seems the answer is "yes".

    • Blast UI. Also USask. Working to convert to Tv3 to take advantage of web services.

      • overview images of hits on entire genome and local alignments.

      • Uses CViTjs for interactive whole genome view. Still beta. Code is here.

    • Phylogenetic Tree Viewer.  

      • Visible on LegumeInfo.org on the leguem families page

      • The code is available but needs some genericizing.  

      • Example here. Code here.

    • GIS Tool is available for placing germplasm on the map of the world

      • Also permits painting traits on to map (e.g. day length sensitivity.

      • Example here. Code here.

    • Vivek at JCVI is working on a Drupal module that queries across InterMine instances.

      • LegumeInfo uses InterMine by dumping Chado data into it.

      • Allows for cross-site InterMine searching.

    • Has an H5ai interface (non-Tripal sepcific) that can be used for providing a web-browser for files stored on the site. http://larsjung.de/h5ai

  • Staton Lab

    • ElasticSearch module to do cross-site querying

      • Integrates with Tripal v3 Data Collections

    • RNA-Seq Expression

      • mature for Tv2 but being currently updated for Tv3

    • Tripal Field Generator

      • Helps simplify generation of Tripal fields.

    • Entity converter

      • For Tripal v3 entities.

      • Allows you to transform one entity type to another type.

  • Ficklin / Staton Lab

    • Tripal Galaxy Module

      • Allows for integration of Tripal workflows with Tripal.

      • Can annotate the Tripal workflow and then share workflows across Tripal sites.

• Upgrading to Tripal v3. Who has started & how is it going?

  • KnowPulse: “cleaning” up our Chado, improving cvterms used & developing Tripal3 fields for our extensive customizations

  • PeanutBase

  • GrainGenes (non-Chado db interface; migration strategy; also ground-up dbs)

  • CSFL development site is in Tv3

  • Hardwoods + expression module will be fully upgraded very soon

    • Took longer than expected

    • Need more documentation!!!

    • Issues occurred with storing differently in Chado than what Tripal expects.

  • PeanutBase

    • upgrade a Tv2 to Tv3 relatively quickly!

• What is Tripal lacking?

  • Gene page how to create a single flat gene.

  • Is Tripal FAIR? -- We should have a discussion on this.

  • https://www.force11.org/fairprinciples

  • https://github.com/tripal/tripal/issues/94

  • Documentation to have a common method for accessioning data.

• What do you dislike about Tripal?

  • Debugging

    • Give a call stack with an error?

    • Fail early and often.

    • How to determine where the problem is especially if Drupal.

    • where do tripal_set_messages go.

• Long-term sustainability plans for your sites?

  • Tripal forms the part of sustainability

  • Tripal permits the site to be built with fewer people.

  • Have folks to build into their grants funding for people to curate data to work closely with the database.

  • Make data accessioned elsewhere if funding slows. To guarantee that the data has more permanence.

    • Get DOIs for dataset.  

• Training and outreach… what do you need?

  • regular online codefest to target coding issues.r Tripal Therapy.

  • Training topics:

    • How to write a Tripal Module to define a content and add some fields.

    • Web Services

    • Setting up Site-wide searching.

    • Intro to Chado -- where to put stuff.  

    • Visualization tools for Chado.

    • How to use the Natural Diversity module (or not use it).

  • There are programs to get transcripts off of videos to make searches.

  • Camtasia -- make Training videos. rather than

• API to pass files to Galaxy workflow (Nic).

• TODO: a future user's meeting or hackathon meeting today.

  • How to let folks evolve the documentation

  • Documentation for users and developers.

Hackathon Afternoon ideas

• Site debugging (before/after lunch)

• Tripal v3 site development.  (after lunch)

• How to store data in Chado. (https://iastate.zoom.us/j/8031935609)

• Explore CVTerm module.

• Making Tripal FAIR discussion.

• Documentation standards