Community Highlights

Please add anything you would like to highlight about your Tripal-based projects: publications, new extension modules, new collaborations, newly funded grants, project update, etc.  We won't talk about these in the meetings but may tweet them from the Tripal twitter account if you approve!

Agenda

1. Messages from the PMC (Lacey Sanderson, Bradford Condon, Stephen Ficklin)

   • Tripal 4 development update (https://github.com/tripal/t4d8)

   • Community engagement for Tripal 4 Development:

     • Docker available for quick start-up

     • Documentation available for Drupal 8 from a Tripal perspective: https://tripal4.readthedocs.io/en/latest/dev_guide.html

     • Issues describing a current set of manageable tasks to help you jump in: https://github.com/tripal/t4d8/issues 

2. Messages from the TAC Chair (Meg Staton)

   • At PAG meeting had discussion about how to expand 

   • White paper and movement on grants.

   • Next month is the advisory committee meeting we may need to move a week or two later as Meg may be out of town.

     • Talk about grants and white paper

       1. Ethy and Monica had indicated support to lead the white paper discussion/work.

     • Everyone is invited!  Even if not a TAC member.

3. Demo of Tripal HQ by Sean Buehler

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

4. Brief update on gene pages (Monica Poelchau)

   • see https://github.com/tripal/tripal/issues/100, https://github.com/tripal/tripal/issues/732

   • i5k and HWG are picking up the gene page issue again. I suspect that we will tackle individual components in stages, and will seek feedback for each one

   • will start with Jbrowse field for feature pages

   • will abandon the idea of populating gene page with 'grandchild' info 

   • what considerations should we have in developing this for Drupal 8/Tripal 4

     • Lacey:  

       1. currently tripal fields are being ported now to D8 so once that is done we should have a better idea of what considerations there might be.  

       2. we're working to make sure that upgrading is as easy as possible and there will be as few requirements to update a field as possible.

5. AgBioData meeting tomorrow to discuss GFF3 format.  See if there are enough use cases to identify the main issues in the format to see if we can get the AgBioData community to rally around a way to represent structural and functional data across databases.

Agenda

• Messages from the PMC (Lacey Sanderson, Bradford Condon, Stephen Ficklin)
  • Tripal 4 Development (https://github.com/tripal/t4d8) update
    • We have had some great contributions from the community -Thank you!
    • We are currently working on upgrading Fields and adding Chado integration
  • Tripal 3 Updates
    • We released Tripal v3.3 this month which includes a lot of bug fixes and the following new functionality:
      • The ability to find and delete orphaned Tripal content (pages whose Chado content was removed).
      • Improvements to the error messages from the FASTA loader.
      • Additional functional testing for web services.
    • Thank you to everyone who contributed issues, code fixes and testing to make this release happen!
• Messages from the TAC Chair (Meg Staton)
  • White Paper outline 
  • Doodle poll to work on outline and assign sections (please fill out before Thursday)
  • OR put your name in document and we’ll keep you up to date via email
• Demo of Tripal Contact Profile and Colleagues Directory by Risharde
  • Tripal Contact Profile: https://gitlab.com/TreeGenes/tripal_contact_profile
  • Tripal Contact Profile Display Fields: https://gitlab.com/TreeGenes/tripal_contact_profile_display_fields
  • Colleagues Directory: https://gitlab.com/TreeGenes/colleagues_directory 

Community Highlights

Please add anything you would like to highlight about your Tripal-based projects: publications, new extension modules, new collaborations, newly funded grants, project update, etc.  We won't talk about these in the meetings but may tweet them from the Tripal twitter account if you approve!

Agenda

1. Messages from the PMC (Lacey Sanderson, Bradford Condon, Stephen Ficklin)

1. Tripal 3 Updates
   • Community Contributions in review includes GFF3 importer performance improvements.
   • Please consider reviewing this PR if it’s of interest to you!
2. Tripal 4 Updates
   • Will be covered in the demo portion of today’s meeting
   • Drupal 7 end-of-life is November 2021: https://www.drupal.org/psa-2019-02-25 
   • Tripal 4 will be compatible with Drupal 9 although its currently being developed on Drupal 8.8.x

2. Messages from the TAC Chair (Meg Staton)
   • There is a draft version of the whitepaper outline: https://docs.google.com/document/d/1w24HzOBJFKG4q3kvgAGwpEWEBgw9773jTcIqMp7bxsg/edit?usp=sharing
   • The white paper writing group has started working on sections.
   • We welcome additional contributors! Just let us know if there are items you would like to add to the outline or if you want to sign up to write a section!
   • Tuesday June 9th, 9am pacific/ 12pm Eastern
3. Tripal 4 Development (https://github.com/tripal/t4d8)
   • Live demo of a current Tripal 4 Drupal 8 site
   • Introduction to the current documentation: https://tripal4.readthedocs.io/en/latest/dev_guide.html 
   • How to contribute to Tripal 4 -everyone welcome!
     • Issue Queue: https://github.com/tripal/t4d8/issues
     • Current Focus: https://github.com/tripal/t4d8/issues?q=is%3Aissue+is%3Aopen+label%3A%22Current+Focus%22 
     • Assign yourself to an existing task issue to indicate you will work on it
     • Comment on existing task issues to 
       1. Indicate if you will work on part of it.
       2. Share your opinion on implementation
       3. Provide any documentation you’ve found to help others
       4. Anything else you think will be helpful!
     • Tripal Code Meetings (every other Monday at 4PM EST, next Jun 8)

Agenda

1. Notices for the Advisory Committee
2. An introduction to the Main Lab Breeding Module by Taein Lee
   • Breeding Information Management System
   • BIMS Overview
     • secure and comprehensive online breeding data management system.
     • store, manage, backup private breeding data.
     • comparable with the field back app (an android app for collecting data in the field)
     • BIMs is installed on all Main Lab databases, including GDR under the Tools menu.
     • Online documentation at https://www.breedwithbims.org/ 
     • You can access public data and there are private data only accessible to breeders.
     • Mange Breeding
       1. Manage Program
          1. Can add users
       2. Manage Traits
          1. Can manage all traits used by the program 
          2. Can view plots of usage of each trait
       3. Accessions
          1. You can view details about each accession (organism and parental information).  
       4. Trials
          1. You can view information about trials
     • Data Import
       1. Can import data using the BIMS t template file. There are various templates for different data types, or you can download a single template of all.
       2. Templates are excel files with headers.  Users can add data to the template files and use those to import data into BIMS.
     • Field Book Management Page
       1. On this page you can import data from the field book.
       2. Export field file from the field book app and import it on this page.
     • Archive page
       1. Allows you to retrieve previously uploaded data files.
       2. Can create new archive files for download so you have a backup of data in BIMS
     • Search
       1. You can search for phenoyptes, crosses, genotypes (SNP/SSR), Haplotypes. 
       2. Search results show histogram of selected trait.  
       3. Search results page has a default set of columns but you can add any column of interest to expand the results table.  
     • BIMS is currently available at https://gitlab.com/mainlabwsu/bims
     • It is a Drupal 7 module.  
     • Limitations
       1. Does not currently handle the organism table of Chado v1.3 (due to addition of infraspecific name).  
       2. Uses BrAPI 1.3 but currently BrAPI is at 2.0
     • Requirements
       1. Mainlab Chado Loader
       2. OAuth 2 SErver
       3. Breeding API module
          1. Druplal 7, BrAPI 1.3

Agenda

1. Reminders
   • Tripal Dev meeting every Monday
     • Location: https://gather.town/app/6QHlnxNUK2JBVKKF/tripaldev
     • Time: https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+Development+Meeting&iso=20210201T17&p1=1440&ah=2 
     • Activities: https://docs.google.com/document/d/1KKRzPffcV1PkBXohLiAAo1CFhQL9u927NjoMPCN52q8/edit#heading=h.n42jpnjoy4z5 
2. Any Updates from the Advisory Committee?
3. Next Month's Meeting:  Advisory Committee Meeting.
4. AgBioData Research Coordinate Network (RCN) Award
   • https://www.nsf.gov/awardsearch/showAward?AWD_ID=2126334&HistoricalAwards=false
   • Monica and Meg are both on the steering committee!
   • Will hold an online meeting in 2022 and there will be some working groups for folks to join.  Meg hopes Tripal can be involved!
     • Meg:  Education
     • Monica: Data Federation
   • Looking to hire a project coordinator.
   • Kick-off meeting was held Sept 1st.
   • Please watch for AgBioData notices and news for further information.
     • https://www.agbiodata.org/
   • Any updates from folks in the leadership team?
   • Chado and the Semantic Web paper
     • If interested please consider volunteering with this.
5. Tripal Hackathon and PAG Workshop
   • Currently the Tripal Workshop is scheduled with PAG.
   • Due to international travel restrictions, the PMC has decided to hold the annual Hackathon/Codefest online again this year.
   • Suggestions:
     • pre-record talks
6. Presentation by Stephen Ficklin.  Tripal Network Module Introduction. 
   • Purpose: stores and integrates gene co-expression, protein-protein interaction and other network data within a Tripal site to help researchers explore gene function through relationships. 
   • It is still under development. We are hoping to offer it for use early 2022.
   • History: the module has been in use as a Tripal v2 site at http://gene-networks.org/. The site and the module have languished but with the release of the new KINC workflow (https://kinc.readthedocs.io/en/latest/) we wanted a place to display the networks we and our collaborators are constructing.
   • Features
     • Integrates with the Tripal file module for sharing network files and data with licenses.
     • Designed to support multiple network types with nodes as genomic features:
       1. Gene co-expression
       2. Protein-protein interaction
     • Fully supports controlled vocabularies for edge and node annotations.
     • Supports KINC workflow (https://kinc.readthedocs.io/en/latest/)
     • Database and Code Review
       1. A new set of tables in Chado for storing network data
       2. New Content Type:
          1. Network content types
       3. New Fields
          1. For the Network content type
             1. Network attribute
          2. For the feature-based content types (e.g. gene)
             1. Network Neighborhood Viewer   
       4. New Importers
          1. Imports networks in GraphML format (http://graphml.graphdrawing.org/) 
       5. New Bulk Loader Template
          1. Functional data importer
     • Website Review
       1. Example network data source:
          1. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA301554/ 
       2. Network Content Type
          1. View existing
          2. View creation form
       3. GraphML Loader
       4. Interactive whole network 3D viewer application
          1. Fully Drupal compatible
          2. Uses Plotly for interactive networks
          3. Feature review
             1. Network selection
             2. Network layering
             3. Selected node and edge
             4. Network filtering
             5. Help and info
       5. Interactive gene neighborhood
       6. Web services
   • TODO:
     • selecting networks by data source.
     • Integration of expression data (perhaps in conjunction with the Staton Lab Expression module)
     • Improvements to the gene neighborhood viewer
     • Better graph layouts
     • Bug fixes!
     • Step-by-step installation and usage documentation.
     • Functional enrichment of the filtered network.
   • Thoughts or feature requests?
     • How to do cross-species comparisons.
     • Add the ability to turn on and off node labels

This Friday, July 13th 2018, 11am EST 8am PST, we will have our Tripal User’s meeting.

Friday, January 13

8am - 12pm Round-table Discussion

12pm - 1pm LUNCH

1pm - 5pm Free Collaboration, continued Round-table Discussion

Agenda

1. HacktoberFest with Free T-Shirts! 
   • 5 commits to core (?) = a free shirt in the mail 
   • Anyone handy with design?
   • Creating issues
   • Advertising
   • Commits count twice! You could also get a github t-shirt
   • Stickers too!
2. Update on the white paper and community survey results - Meg Staton
   • Slides: https://docs.google.com/presentation/d/1gvHxhSXISa0lFwiW0B7pkcMroOyXvce36NLKY7_cDVw/edit?usp=sharing
   • Getting a broader perspective:
     • GMOD and AgBioData mailing list
   • It’s not too late! Take the surveys:
     • Tripal Impact Survey: https://forms.gle/EjySFMm9cG3YkMGu7
     • Tripal Community Survey: https://forms.gle/vnhxAsTBP37Jwbse8
3. Updates to Phylotree and Demo of Use for Orthogroups - Noah Caldwell
   • Drush command for loading batches of Newick files- https://github.com/statonlab/phylotree_loader_cmd
4. Consider joining the Tripal Dev Calls weekly

Agenda

1. Messages from the TAC
   • The whitepaper is still in progress. It is a bit long and so needs some further changes.  
   • If you're interested in reviewing please ask for the link and it can share.
2. Oct 6th User's Meeting is a TAC meeting.  
   • possible discussion items are the annual CodeFest
   • OctoberFest.
3. Tripal 4 updates
   • Repository: https://github.com/tripal/t4d8 
   • README on the tripal 4 developmental repository with a timeline.
   • We are running about 1 month behind so we need help from the community
   • Our plan is to release the beta on time
   • We've updated the documentation to make it easier to jump in. 
   • If you want to contribute but feel lost please reach out on Slack or comment on GitHub.
4. Tripal File Module Discussion (Stephen)
   • Let's make a module everyone can use… we need your thoughts!.
   • Distribution of flat file data in a FAIR manner and association with site content
   • Github repo: https://github.com/tripal/tripal_file (this is a Tripal v2 version started several years ago but not finished).
   • New Tripal v3 Design Spec of the Tripal File Module: 
     • Note:  comments that were in the agenda prior to the meeting were moved to the document above).

Agenda

1. HacktoberFest Wrap Up - how’d we do?
   • PRs made to Core Tripal: 20
     • Ferrisx4(1), michizhou(2), risharde(4), katherynbuble(1), spficklin(5), dsenalik(4), laceysanderson(2), bradfordcondon(1)
   • PRs made to Tripal 4: 4 (plus two that haven’t been accepted yet)
     • Ferrisx4(1), spficklin(1), laceysanderson(2)
   • Don’t forget to fill out the form: https://forms.gle/Pp737HjruK9roCph8 
     • Only 3 so far: michizhou, dsenalik, laceysanderson
     • Stephen and Rish need to fill out the form :)
2. Tripal 4 Status & Call for Help
   • You can check out our current task list here: https://github.com/tripal/t4d8/projects/1
   • We are still behind schedule and urgently need help!
3. Next Month's Meeting: Preparation for the annual Tripal Codefest
   • We will be sending out a form requesting topics of interest
   • We will organize into groups, with each group organizing their session with a combination of Slack/Zoom 
   • Hackathon will proceed Jan 11-15th 
   • We will hold a final get-together to review progress Friday 1/15.
   • Coordinating with GMOD?
4. White Paper Update
   • Thanks Valentin for additions! (Val: you’re welcome ;) )
   • Sending out soon. If you would still like to review let Meg know.
5. Demonstration of AnalyzedPhenotypes & ND Genotypes by Carolyn Caron
   • AnalyzedPhenotypes provides a researcher-friendly importer, violin plots and histograms, trait pages and integration on germplasm pages for phenotypic data. Additionally there is download functionality in R-friendly formats.
     • For more info: https://github.com/uofs-pulse-binfo/analyzedphenotypes/
   • ND Genotypes provides integration of large-scale genotypic data on sequence variant, genetic marker, germplasm and project pages. Additionally, there is a genotype matrix view with download capabilities.
     • For more info: https://github.com/uofs-pulse-binfo/nd_genotypes/
     • For import: https://github.com/uofs-pulse-binfo/genotypes_loader/ 
   • These modules provide Tripal support for large-scale Genotypic and Phenotypic data in a proven generic manner with both modules having gold badge status! There is extensive configuration with sensible defaults to get you started quickly!