Tripal Advisory Committee Meeting 2021/02/1

Meeting Date
Attendees

Sean Buehler
Lacey Sanderson
Irene Cobo
Stephen Ficklin
Meg Staton
Monica Poelchau
Noah Caldwell
Valentin Guignon
Sook Jung
Jill Wegrzyn
Risharde Ramnath
Rodrigo Ortega Polo
Lilia Mesina

Agenda

  1. Update on the Tripal Codefest
    • 19 participating, 25 registered (JBrowse will join next time!)
    • Breeders API - 
    • Tripal 4 - 9 PRs!
    • Tripal Galaxy
    • Gene Pages
    • Please fill out survey if you participated in codefest!
    • PMC - weekly development meeting will be more in person coding, all welcome to join in
    • 3.5 with many bug fixes close to release
  2. Tripal White Paper
    • We received USDA approval last week, its going in this week
  3. Tripal Grants and Priority Development
    • Jill
      • CartograTree - (becoming CartograPlant!) - natural populations with georeferenced coordinates, adding environmental layers, Galaxy workflows, visualization, genotypes + phenotypes for landscape genomics
      • TreeSnap mobile app
      • Genome Annotation - deep learning approaches - functional info + RNA folding - at the end of the grant (3ish years) move the workflow in Tripal
      • Methylation proposal - perennial species - best practices for comparing across data sets, how to integrate into Tripal
      • Gene families and orthogroups
      • Pangenomes
      • Core Tripal!
      • Focus on solid use cases
    • Stephen
      • NSF -  SciDAS  - workflows on the cloud - RNASeq particularly 
        1. Integrate tripal workflows (nextflow, easy to dockerize, run on kubernetes or slurm or PBS or other)
          1. Future nextflow tripal module?
        2. Working on tripal file module - ready for testing!
          1. license/usage
          2. associate files to data types
          3. Make files available through web services
      • NRSP10 (PI Dorrie Main)
        1. Tripal core development and outreach
        2. Full time - Josh coming to Tripal this month 
        3. Part time - Risharde 
      • Multiomics data integration, metagenomics, microbiomes, all the omes!
      • Network  module - close!
    • Docker - a popular solution for dev and production Tripal sites
      • Singularity - supports docker images and friendlier on HPCs
      • Lacey - her group uses Docker entirely for development and for production in one project
      • Monica - moving toward docker for production
      • This might make a great future dev or user meeting topic!
    • Main Lab (Sook)
      • NRSP10 - core (see above) Oct 2019 - Sept 2024
        1. 3 developers for
          1. epigenome module
          2. Map viewer w/ genome view
          3. TripalBIMS themes to support phenomics data and BrAPI compatibility and GWAS tools
          4. Curation module 
      • Preproposal - USDA SCRI - application in
        1. Curation of data
        2. 1 developer for modules - pangenome module, map viewer, SNP genotype and haplotype module, synteny viewer and Community gene curation - enable community members to contribute (like TAIR GOAT)
        3. Focus on linking module to facilitate more integrated display
        4. Funding for Training and outreach
      • PGRP - pending
        1. Project database for rice
      • In discussion for funding support for developing a bacterial database for Metabolomic and proteomic data
    • USDA - consistent messaging from plant and animal communities about database support - 
      • Team up with Fiona (idea from Monica)
    • Lacey
      • Genome Canada
      • Evolves - not just Tripal, KnowPulse and resources
        1. Integration of 3rd party tools - JBrowse2, SynVisio, Genotype matrix tool to support haplotypes and haplotype views
        2. EVOLVES Project page: knowpulse.usask.ca/evolves
        3. We are beginning year 3 of a 4 year grant
      • DivSeek Canada pilot project - focused more generally (not just pulses) 
        1. https://www.divseekcanada.ca/ 
        2. Completely focused on Tripal
        3. Docker container for breeding/variant focused Tripal site, already configured, Tripal Crop Docker, first version done
          1. https://www.divseekcanada.ca/tripal-crop-docker/ 
        4. Funding covers documentation, already has an administrative guide, videos showing functionality
        5. Image -> container -> script pulls down all modules based on an environmental file -> run configure w/ crop info -> modules are configured automagically 
        6. Pilot portal for smaller crops can use this as a central repo without having to maintain their own site
          1. Example data already loaded for 3 species
          2. https://staging.divseekcanada.ca/ 
        7. Lots of outreach to breeding/variant focused community in Canada
      • Our group is focused on third party tool integration, structural variation, pangenome, and breeder support, as well as, outreach
    • Monica
      • Sean Buehler - funded by USDA cooperative agreement
      • AgBioData - RCN - 
        1. Identify priority issues
        2. Include stakeholders and funders
        3. Education component - FAIR data
        4. Sustainability analysis - how databases can continue to exist with more data but less funding (Phoenix Bioinformatics)
      • Comparative genomics, gene family display, building on legume community (Valentin - greenphyl.org - not Tripal, maybe one day :)
    • Valentin
      • Moving from 2 to 4 (skip 3!)
      • Moving drupal 7 to 9
      • Less reliance on chado - nice that its normalized and standard but complicated queries are a problem and not fast - materialized views or drupal solutions (data in Drupal sync with Chado data) may be implemented (or other approaches… still in progress)
      • Chado for loading but not querying
      • Banana genome hub v2 on T3 just released! https://banana-genome-hub.southgreen.fr/ 
        1. New modules - plant genome viewer, next year 
      • BrAPI module - need to move to T4 - no funding for Valentin but can work with Lacey
    • Rodrigo - AgriFood Canada - PI Genome Alberta project 
      • Bee microbiome
      • Switzerland, Germany, large international group!
      • Just began, beta version of portal developed - considering adopting Tripal 
      •  
  4. Opportunity to collaborate or build on resources from AGR   
Meeting Type
TAC