extensions

Tripal User's Meeting 2017/05/05 Tripal Community Meeting Notes

Announcements:

 

 

Reminders:

 

 

  • Consider adding your modules into the Tripal GitHub organization.  

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

  • We now have "Powered by Tripal logos" if you'd like to add one to your site:  http://tripal.info/logos

  • 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:

 

 

 

 

 

 

 

  • Training

    • April Online Training:  bulk loader.

    • May Online Training

      • On Friday 5/26

      • Tripal v3 Development.  Converting template to entity fields.

    • Tripal Summer School?  

      • Interest in an all-day online hackathon (webcam encouraged) this summer?

      • Need to differentiate between "adoption" training and developers who want to collaborate on.  Documentation updating.  Have defined goals

  • Tripal v2.1

    • Any issues questions, problem?

  • Tripal v3

    • Support:

      • Example module already under development:  

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

        • Tripal legacy example module was like "drinking from a firehose".  This example module is broken out into common tasks.

        • Currently provides examples for creating custom fields.

        • Do you have an example you'd like to see provided as an example?  Please add an issue to the queue.

      • Updated API Documentation will be online

      • Tripal v3 User's Guide will be updated at the time of release, including developer's handbook.

    • Any questions about Tripal v3?  Upgrading, etc?  Conversion of custom modules?

  • Mailing list consolidation

    • Will remove gmod-tripal-announce and gmod-tripal-devel but keep gmod-tripal.

    • Major announcements will be made on the @TripalProject Twitter account and Tripal website for those who don't want to be on the mailing list.

  • Report on GO loading problem

    • Tripal v2.1 still has the GO loading problem

      • Problem in GO is a combination:

        • Of "has_part" and "part_of"

        • When updating an ontology old relationships can cause a cycle as well.  Action Item (Stephen)  Check on solution provided by Ethy for this.

      • Ontology loads fully, but cannot be added to the cvtermpath table.

    • We are working on a fix to detect cycles and avoid them.  We hope to have this fixed for Tripal v3 release.

  • Nic (Tree Genes):

  • Installation Profiles (Lacey, USASK)

    • Packages Drupal/Tripal/Extension modules needed into a bundle.

    • Simplifies Tripal installation.

    • Profiles:

      • Genomics (extensions and content types specific)

      • Breeding

      • Stock Collection (with eCommerce modules built in)

      • Headless Tripal with Loaders with privacy.

    • Current discussion on the issue queue:  https://github.com/tripal/tripal/issues/95

    • We would greatly appreciate any input on content types and/or functionality you would like to see included!

  • Wish List / Hate List

    • Gene/mRNA Pages: too chado-esque. Not as helpful to users as they could be.

      • Ethy: PeanutBase & LegumeInfo have an extension module to customize these pages. Example. Includes JBrowse image, mRNA, and protein sequences.

      • Monica: I5K has custom gene pages with a more EnSEMBL-like. Example i5k page: https://i5k.nal.usda.gov/OFAS001265

      • Transcript listing: Shows all the transcripts for a given gene including all the functional information & annotation for each transcript

        • Candidate Tripal3 Field that admin could add to their Gene pages

      • JBrowse Field to show a region of a JBrowse instance on any page.

        • This will be included in the JBrowse integration module when it has a Tripal3 release

        • And configuration to allow you to highlight a specific gene for example

        • (would be used in both LegumeInfo & I5K)

      • Sequence Field: Shows the sequence for the Gene, any transcripts and proteins (would be used in both LegumeInfo & I5K)

    • For suggestions see: https://github.com/tripal/tripal/issues/100

  • What can core developers to better help adoption/training/etc….

    •  

 

 

 

 

 

 

 
Tripal User's Meeting 2017/09/08 Tripal Community Meeting Notes

Announcements:

  1. Updated Tripal site:  http://tripal.info

  2. Tripal v3 API documentation coming in September.

  3. Online Training Events

    1. Sept 29th.  How to use Tripal v3

    2. Oct 27th.  Possible Topic Tripal + Galaxy Integration

    3. Nov 30th.  Topic TBD

    4. Possible week-long GMOD "Summer School" in November.

  4. 2-Day User's Meeting and Hackathon at PAG XXVI, January 11-12th.

  5. Add documentation for web services:  http://tripal.info/tutorials/v3.x/web-services

  6. Thank you!

Reminders:

  • 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:

 

Items not discussed:

  • Upcoming Training Meetings

    • September possible topics: Installation, migration from Tripal v2, content type creation, web services, development of fields, development of new web services.

    • October:  Tripal + Galaxy Integration, others?

    • November:  ??

  • Tripal Slack project?
Tripal User's Meeting 2017/12/08 Tripal Community Meeting Notes

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

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

      • 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?

  • 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

 

  • Explore CVTerm module.

  • Making Tripal FAIR discussion.

  • Documentation standards
Tripal User's Meeting 2018/02/02 Tripal Community Meeting Notes

Reminders

  • Consider adding your modules into the Tripal GitHub organization.
    • You can make your own team in the github repo.  Ask stephen/lacey/meg for permission to join the Tripal organization.
    • If not, please tag the repo as Tripal.  
  • Remember to update the status of your modules on the Tripal.info site.
    • If you need a login let us know. You have to email one of the admins.
  • If you have a new site or major updates to your existing site let us know and we can publish those on the Tripal news feed and twitter accounts.
    • http://tripal.info/sites_using_tripal 
    • We need to reach out to new tripal sites to encourage them to get their site on tripal.info etc.  
    • Let’s (Shawna please talk to Stephen) about who in the outreach team is responsible for reaching out.  Ethy will try to reach out to those present at PAG
    • Additional tripal.info needs?  We will add training videos.  
  • API in March
  • 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).
 

Agenda

Thank You to those who participated in our Hackathon, User's Meeting and Workshop in San Diego

  • 25 people attended the Hackathon/User's Meeting
  • 50-80 people were in attendance during the talks at the Tripal Workshop
  • Expect another Tripal PAG event next year!
  • Tripal workshop at ASPB in july/ASHS?
  • Would be nice to improve Tripal outreach efforts by giving talks at other conferences/sessions about Tripal3.  IE tripal talk in the ontology session.  Or include a standardized “Tripal slide” to include in all talks.  Could host on tripal.info.
  • Please fill out the survey about our PAG events: Even if you did not attend we'd like to receive your feedback about it.
  • https://utk.co1.qualtrics.com/jfe/form/SV_9tN0NUsNmv65Nat
 
Future Training/Tripal Therapy Events events.  
  • Need to videotape trainings.  Time is OK for those present.  Please add further training suggestions below and/or training topics you are willing to host (this is in the survey!)
  • Currently we have dev calls on the first Friday of the month
  • We could add a call on the third Friday of the month - does 8am US Pacific, 11am US Eastern, 5pm European Central work?
  • Perhaps offer two times… one for Americas and another for Europe?
  • Suggest alternating between organized training and tripal therapy topic
  • Training: Suggestions from last month's meeting:
  • 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).
  • Tripal Therapy Sessions
  • Bring your problems and we'll have folks to help debug. The idea is to meet all together and then break out into separate sessions to work together on a problem.
  • 3rd Friday of each month at the same time.
  • Is meeting 2x per month too much? Other suggestions?
 
Topics from the Hackathon that didn't get addressed
  • Is Tripal FAIR?
  • Findable, Accessible, Interoperable, Reusable
  • We can't enforce but can enable.
  • Findable: metadata support? can this be enforced? 
  • Who would enforce metadata?  Core? Extension modules?
  • PeanutBase/LIS has a genome metadata module based on MIxS and its plant extension from the Genomic Standards Consortium.
  • Upcoming module for genome metadata that adheres to some recommendations. 
  • Federated searching
  • Encourage module authors: Have to choose metadata standard. Tricky if none exist, or no standard.
  • Accessible: ?
  • Interoperable: ?
  • Reusable: shared modules.
 
Documentation standards for Tripal extension modules
  • We can allow for inclusion in the Tripal User's Guide for folks who want to put it there.
  • We can link from the User's Guide to your GitHub project page
  • Suggested standards
  • Insist that there be documentation (could use a dedicated support person here)
  • Step-by-Step setup instructions with screen shots
  • Step-by-Step usage instructions with screen shots
  • ?API guide if there is API
  • How does this module approach CHADO storage
  • New documentation.  The maps are helpful and you could use this to show where
  • Not just function description but also examples of use
  • Drupal.org has its own set of documentation standards: encourage people to look at them.
  • Tripal Core uses doxygen
  • https://www.drupal.org/docs/develop/standards
  • How to document API, with examples
  • Open Layers, http://openlayers.org/en/latest/examples/
  • GeoServer API, http://docs.geoserver.org/stable/en/user/rest/index.html#rest
  • Best practices for writing modules: handling updates and uninstalls (Ethy)
  • Recommendation is develop the uninstall as you write the install
  • Feedback on github issue template? https://github.com/tripal/tripal/issues/251  (click create new issue to see the template)
 
 
 
INSTRUCTIONS: The following template is meant to provide the information that will help other Tripal developers diagnose and reproduce your issue. Follow the directions below to complete the template. If the template is not appropriate for your issue you may remove it and describe your issue.
 
### System information
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Tripal User's Meeting 2018/03/02 Tripal Community Meeting Notes

Reminders

  • Consider adding your modules into the Tripal GitHub organization.

    • You can make your own team in the github repo.  Ask stephen/lacey/meg for permission to join the Tripal organization.

    • If not, please tag the repo as Tripal.  

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

    • If you need a login let us know. You have to email one of the admins.

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

    • http://tripal.info/sites_using_tripal

    • We need to reach out to new tripal sites to encourage them to get their site on tripal.info etc.  

    • Let’s (Shawna please talk to Stephen) about who in the outreach team is responsible for reaching out.  Ethy will try to reach out to those present at PAG

    • Additional tripal.info needs?  We will add training videos.

    • API in March

  • 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).

Agenda

  • Training and Help Desk Schedule

    • http://tripal.info/support

    • The first Friday of each month is reserved for a teleconference call for discussions about the state of Tripal with Tripal core developers and others developing extension modules. The goal is to improve the usability of Tripal, reduce duplication of effort, and  help find collaborations.

    • The third Friday of each month will alternate between a "help desk" open call and a training topic. Schedule below. All meetings are at 8am PDT/11am EST/4pm GMT.

      • Friday, February 23rd - Help Desk Call

      • Friday, March 2nd - User's Meeting

      • Friday, March 16th - Training  - Tripal v3 Fields

      • Friday, April 6th - User's Meeting

      • Friday, April 20th - Help Desk Call

    • Explore a Tripal Europe User's Meeting.

 

  • Tripal release schedule

    • A regular release schedule and corresponding notifications to the mailing list, website, and twitter account so that users know when to update their sites.

    • Perhaps just sent an update of what was fixed in an email.

  • Tripal Collection on FairShare.org  (Bradford Condon)

  • (Developer issue if time) - CI Testing framework.  [Discussion Thread]

  • Staton Lab working on Tripal Test Suite: Composter

  • Potential Training:

    • Development Best Practices -- May Training
Tripal User's Meeting 2018/04/06 Tripal Community Meeting Notes

Reminders

  • Consider adding your modules into the Tripal GitHub organization.

    • You can make your own team in the github repo.  Ask stephen/lacey/meg for permission to join the Tripal organization.

    • If not, please tag the repo as Tripal.  

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

    • If you need a login let us know. You have to email one of the admins.

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

    • http://tripal.info/sites_using_tripal

    • We need to reach out to new tripal sites to encourage them to get their site on tripal.info etc.  

    • Let’s (Shawna please talk to Stephen) about who in the outreach team is responsible for reaching out.  Ethy will try to reach out to those present at PAG

    • Additional tripal.info needs?  We will add training videos.

    • API in March

  • 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).

Agenda

  • Tripal v3 stable release update

    • Planned release for summer

  • Documentation, especially for installation, to help newbies, and for people investigating Tripal for the first time.

    • Might be helpful to have a statement indicating the overall philosophy of Tripal and the problems it is solving.

      • ACTION ITEM: What problems is Tripal solving → put this on the About page of Tripal

        • “Who is doing what with Tripal” ← When I (BC) solve a problem with Tripal, or I make a little module, I try to write a mini blog post about it.  We could encourage submissions from individual sites to blog about how they use tripal in their site for a specific problem etc

    • Could be interlaced in install process ("now you need to...")

      • ACTION ITEM:  Add an issue to issue queue for this.

    • Detect missing parts (e.g. "you have not yet created the necessary files in ...")

      • ACTION ITEM: combine with step above.

    • A list of FAQs would be helpful.

      • ACTION ITEM:  Add an FAQ to the Tripal website and an issue for this.

  • Related: could we re-visit Tripal discussions as the GitHub approach doesn't seem to encourage conversations around questions or ideas the way the e-mail list did.

    • Searchable archives of past discussions: information is now in multiple places (documentation, old e-mail list archives, GitHub, meeting notes, Twitter, ...)

      • TODO:  investigate if this is possible.

      • What are the best tools to get productive in the Tripal environment.

    • Encouraging conversations.

      • Stephen suggests Gitter

        • Used by galaxy and apollo

      • Stephen also mentioned the use of SLACK

        • Not allowed by the USDA

        • Discouraged but could be used through the web?

      • Lacey suggested adding to the template for issues to make them more welcoming to discussion (https://github.com/tripal/tripal/issues/251)

        • The concern seems to be that there are not enough people listening on github. You can’t do a shout-out to all tripal users

        • We can suggest to subscribe to the issue queue but then they get all the issue updates as well which could get annoying

          • Can you subscribe to issues tagged iwth “discussion” only?

      • ACTION ITEM:  Find a tool to encourage more discussion.

  • Someone from the LIS group could describe how gene families are saved in Chado, vocabulary used, et cetera.

    • Relates to the phylotree module -what version do we use?

      • In core is just the loader and tree viewer

    • Gene families started with the idea of displaying trees so they started with the phylogeny module

      • Create gene family definitions based on a HMM which is the basis for multiple sequence alignments

      • Try to follow the chado conventions for multiple sequence alignments

      • HMM defines the consensus sequence then everything else is aligned to that

      • Use featureprops to say that a given gene is part of the same family as everyone else

      • All members will be represented in the featureprop table to ensure that there is one consistent entry point for what genes are part of this family

      • There is a cvterm that indicates the featureprop is a gene family and the value the name/id of the tree (gene family)

      • Use materialized views for the gene search. This could be used to see how the data is stored and are part of the module definition

    • Tripal issue on topic: https://github.com/tripal/tripal/issues/308

    • GitHub Repo: https://github.com/legumeinfo/tripal_phylotree

    • Bradford: can use feature_relationship but then you have to create a feature for the gene family which feels like shoe-horning data into Chado

      • Andrew: If you think of a gene family as an ancestral gene that everything is derived from then it’s a feature like everything else

      • Bradford: feature table has not nullable organism_id so what is the organism for the group? Do you define the common ancestor in the organism table?

      • Sook: as long as we agree then it’s ok. We store populations in the stock table…

      • Andrew: problem with storing the common ancestor is the genus and species fields…

    • Stephen: Core tree loader downloads the full lineage from NCBI for the organisms in the organism table. The higher level nodes are only represented in the tree, not in the organism table.

      • Andrew: might this conflict with our idea of saving common ancestor in the organism table

    • Bradford: feels the phylotree is a pretty good model for a generic group model although it’s currently for trees

    • Stephen: if we can agree on a approach then it will make it a lot easy to share data

    • We should document Andrews method and propose it as a recommendation

    • Bradford: if you gene models are not external then do you have to create and maintain a db+dbxref collection for de novo gene models

    • Sook: Chado is also used by SGN (Naama) and the Venter Institute?

    • As far as suggestions go, we can form our own Tripal group to discuss and then suggest to the wider chado

    • Sook: comment on storing the gene families in the featureprop table.. We shouldnt use the value to link… Perhaps we need a linker table to phylotree for features

    • Andrew: what about people who want gene families but not trees?

    • Stephen: we should organize a meeting with the Chado community about gene families

    • ACTION ITEM: Bradford to organize a time to meet and follow up on his original email

    • ACTION ITEM: Andrew Farmer to make up a more formal document describing how LIS stores gene models

    • ACTION ITEM: Bradford: perhaps we need a blog section of Tripal.info for things like this.

      • This is done by Galaxy. Could be helped by us asking specific people to create blog posts ;-)

      • This could also help with creating a forum for discussion.

      • We do have to be mindful of the searching multiple sources problem

      • If you want to see my tripal posts, they are here: https://www.bradfordcondon.com/tag/tripal/

 

  • Testing

    • Test and Continuous Integration.

      • Runs all the tests and automatically builds a test installation to ensure they all pass. The status is then shown on the github page.

    • In tripal core

    • in your custom modules  

      • Use https://github.com/statonlab/TripalTestSuite

        • Composer tool which just downloads the needed files -doesn’t affect your system at all

      • Creates the testing environment

      • Really easy to install!

      • Provides a special Tripal test class

        • Transaction wrapping of tests

      • Data Seeders :-) to help with ensuring tests have the data they need

        • The test suite will provide a few general ones (like FASTA) but the hope is the community will contribute more

      • Factories allow you to generate 100’s of records in one line :-)

      • Travi-ci.org

        • Can be used to see the tests being run automatically

        • Also makes sure the module installs and builds correctly

        • Requires your module to be in github

        • NOTE: link you github account and it will detect new modules and once you say “test this module” it will detect code changes and re-run tests each time :-)

    • Lots of documentation on the github repo

      • Please submit any issues, suggestions, etc!

    • Meg: This would a Great training topic

      • Ethy: a help desk call with a slower walk through of setting this up

      • Next help desk call on April 20th

        • Divide up into groups and work with you one-on-one

      • Definitely have a break-out for testing if there’s interest

    • Allows us to all use the same testing! You can follow core’s lead easily using the Tripal Test Suite

    • Docker used for this available?

    • Please check out our developer docker manager tool if  you are interested in a tool to manage your docker (skip the learning curve):
Tripal User's Meeting 2018/05/04 Tripal Community Meeting Notes

Agenda

  1. Anything anyone wants to bring up?  Any questions?

  2. Moving Forward: governance

    1. Issue started on GitHub here: https://github.com/tripal/tripal/issues/344

    2. Identification of driving principles for future Tripal development

      1. Basics:  FAIR, Open-source, free

      2. Future changes should be for the benefit of the Tripal community, not any one group.

      3. Improved quality of Tripal core and extension modules of the community

      4. Prioritized development plan the transcends the goals for who has the most funding.  

      5. Develop a contribution process (commit standards)

      6. Avoid feature bloat

      7. Encourage others to more actively participate by

        1. helping respond to issues

        2. testing pull requests

        3. offering suggested changes to Tripal core.

        4. Health vs Unhealthy open-source projects (https://medium.com/the-node-js-collection/healthy-open-source-967fa8be7951)

          Users = orange; Contributors = green; Committers: teal; Technical Committee:  blue.

    3. Leadership structures for open-source projects: https://opensource.guide/leadership-and-governance/#what-are-some-of-the-common-governance-structures-for-open-source-projects

      1. Benevolent Dictator for life (BDFL) http://oss-watch.ac.uk/resources/benevolentdictatorgovernancemodel

      2. Meritocracy: those who demonstrate merit get formal decision making role.  Contributions are made by people not the groups they represent. http://oss-watch.ac.uk/resources/meritocraticgovernancemodel

      3. Liberal contribution:  those who do the most work get a more influential role (not based on historical involvement) https://medium.com/the-node-js-collection/healthy-open-source-967fa8be7951

    4. What do we want to avoid?

      1. One group, with the most funding, directing Tripal away from community needs.

      2. Bottlenecks in responding to users.

        1. Bottlenecks in accepting PRs

      3. Slow to adapt to changing technologies

      4. Dependence on one group for core changes.

 

thoughts:

  • Ethy:  There should be a keeper or keepers.  Concerned that "cruft" will get built up in the code.  With lots of people working on it in various directions there could be bloat.  A keeper of a vision may lock things down too tightly. Have a lead and give roles to others for certain areas.

    • e.g. lacey in Tv2 was the Views expert so it made sense to have issues go through her.

    • So it may make sense to have contributors become experts in certain areas.  

    • Area leads help decide what is appropriate for that area.

  • Bradford:  Have a blend of meritocracy with committers.  Adding major features can be controlled via a vote, provided they already follow set contributions guidelines.  He would like not every minor decision has to go through several people and requires a few weeks to get decisions made.

    • Contributors may not be writing code in core, they could be responding to the issue queue, or helping to write documentation.

  • Meg:  It's important give people "in the code" the power to do what they need to do. Higher-level decisions on steering should be in a committee.  Two types of folks represented: those who are not in the code, but contribute financially and making decisions for their own needs (PIs), those who code and are actively involved.

  • How to improve contributions

    • Meg: When writing grants if folks commit to support core development, including training their staff to contribute to issue queue.

      • Budget for training to help make their modules shareable.

    • Ethy: agreed the learning curve is very steep, because it takes a while to feel comfortable knowing if problems are issues with Tripal or personal understanding

    • Bradford:  how likely someone is to jump in and contribute if:

      • pull requests are being accepted

      • there is visible communication between others.

      • online rules.

      • BC- We respond to issues, kindly and punctually.  If there’s coding that needs to be done to resolve, we encourage user to try to submit themselves.  Offer to help them with their PR too. → training good contributors.

    • Meg:  work on our yearly hackathon.   We need new developers who need training.  

      • get some funds to help bring individuals to our yearly hackathon.

    • Ethy:  have a virtual training "hackathon" online to help folks get started.  For example "who wants to start a Tripal v3 field and let's work on it together"

    • Stephen:  how to include folks outside of North American time zones.  

      • Ethy suggested reaching out to these folks and see what they would suggest to help them feel more able to attend/contribute.

  • Action Items:

 

  • Complete the document for "Workflow for Contribution" containing acceptable guidelines for pull requests, what's the process is used to approve them.

  • Project committee:

    • Consists of coders and committers to help setup governance rules and develop the documents and manage the project

    • Pull request mergers.

    • Issue answerererers. (the ones who make sure all issues ARE answered ;-) )

    • Deadline for Contributions and decision making document:  July 1st. Governance document can follow.

      • Sooner we have a guiding document, sooner committers can start merging PRs that meet guidelines without having to funnell all decisions through BDFL.

      • Give a community comment period.

      • Specifically formalize how to contribute, who merges PRs, what PRs need to be to get merged, how to welcome contribution by our actions in Github, etc. by this deadline  

      • Broader topics of governance can wait to be decided by the formal committee

        • Try to make a start on things like what should be in core with the intent that it will be expanded upon and tweaked by the steering committee once formed?

  • Defining steering committee:

    • We need a set of guidelines to preserve long-term goals.

    • Should represent everyone.  Labs that use Tripal, people who contribute, etc.  

    • These are major directional decisions:  Meet once a quarter? Once a year? Could even just meet 1x at PAG….

    • Once issues are identified in terms of what Tripal needs to think about.  IE supporting new data types, Drupal 8…. We can assign committees. Now anyone who wants to write a grant, they can write it into their grant and take on a role on the committee.

    • Is this really any different than how we do our meetings at PAG?

      • Well now we’ve designated some people as responsible.

      • Formalized leadership role for users who aren’t necessarily coding…

    • We need to have a good representation

      • Roles (but don't actually label people see below):

        • Developer

        • “New community member?”

        • PIs

        • Biologist

        • Cyberinfrastructure

        • Technology specialist (Drupal, data management, etc).

      • Is categorizing people into roles bad?

      • Maybe instead we make part of the mission “we want to make sure each of these roles are presented:”.  SO instead, when we put out the call, we want people in all of these areas.

      • How many members?  How long will they serve?  Maybe the committee will decide these things when they meet.

        • 7 is the perfect number.  Also 10, 15. perfect.

    • First thing on the docket during the first meeting

      • Talk about the switch to D8 and how we will go about it.

      • Shawna is planned to start working on this in August.  Hard to get committee going before then. Maybe instead interim committee should be formed so we can discuss this issue before

    • Have an open committee meeting in August/September to discuss Drupal 8 and Tripal v4
Tripal User's Meeting 2018/06/01 Tripal Community Meeting Notes

Reminders

  • Previous meeting notes here: http://tripal.info/meetings/users/summary

  • Consider adding your modules into the Tripal GitHub organization.

    • You can make your own team in the github repo.  Ask stephen/lacey/meg for permission to join the Tripal organization.

  • Tag your modules on GitHub with the "tripal" topic so we can find them all.

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

    • If you need a login let us know. You have to email one of the admins.

  • Code with other users in mind, try to co-develop with others, submit issues when help is needed and try to help others

  • Please consider adding Unit Testing to your extension modules.

  • Help Desk call June 15th.

  • New releases of Tv2 and Tv3 this summer.

 

Governance Progress Updates

  • We have formed an interim Project Management Committee (PMC):  Stephen Ficklin, Lacey Sanderson, Bradford Condon

    • Reminder, the PMC ultimately should consist of coders and committers to help setup governance rules and develop the documents and manage the project

    • Please consider adding to our discussion about Governance here: https://github.com/tripal/tripal/issues/344

    • We have a slack workspace. Anyone who would like to be involved in governance issues can join.  Just let us know and we will add you.

    • Goal: July 1st have Code Contributions document.  

  • We will have an open meeting in August or September to discuss Tripal v4 design.

 

Open Meeting Agenda Items

Please add discussion items here

  • Help Desk or Training this month?

    • Didn’t have one last month for multiple reasons

    • Training topics?

    • Currently keeping with the schedule: help desk

    • Shawna sends out an email the week before asking if there’s anyone with topics

      • Most topics will be addressed, you get paired with a developer for one-on-one time

      • They’re awesome so please let us help you :-)

  • Nic:  Drupal question

    • Upload data via Tripal Galaxy

    • Proper way to pass data from Chado to a Galaxy instance

    • Drupal File API

      • Managing deletion of unused files

      • Tripal Galaxy ties into the Drupal File system

      • Stores some metadata about the file

    • Tripal integration with the Drupal File API uses HTML5 chunking to allow uploading and updating of very large files.

  • Ethy how to make collaborations better

    • ACTION ITEM: we continually encourage collaboration so tips/thoughts on how to make it happen would be helpful

    • ACTION ITEM:  Bring this back up for next month's meeting on 7/6

    • An example of collaboration working well is the Tripal BLAST UI (Ethy, Lacey, Sofia, Bradford). Perhaps it’s that we’re committed to collaborating?

      • This module was very broadly applicable so perhaps more people are invested

      • Very clearly defined what it is trying to do

    • Ethy's observations

      • Some highly committed groups have failed despite good intentions

      • It takes time and discipline that is challenging.

      • the person who was lead on the project did not give support when others needed it.

    • Ethy would love to collaborate on breeding support but it’s such an amorphous concept which makes it hard to find common ground

    • Barriers Stephen has encountered is

      • time

        • Can’t provide support

        • Need the functionality now

      • Culture: pride

        • Don’t want to ask for help

        • My way is better

    • Meg: Align priorities up front and throughout

      • Be transparent as to what you want and how much time you have

      • Also is the intent a general module or just “I’ll make and you can try it if you want”

        • Sometime there isn’t time to make it generic and it’s good to know if this is a goal from the start or if there just isn’t time

    • Bradford noticed he is contributed more to others but others are not contributing to his modules.  (he offers as a thought discussion, not because he is whiny. honest.)

      • How can he make it clear he is open to collaboration?

      • Are his modules not broadly useful?

      • Ethy commented: perhaps folks don't know what you're working on.

      • It’s hard to contribute to large projects since there’s a lot of code to become familiar with

    • Tripal Extension page

      • Much more community engagement?

      • This could be the portal to making these collaboration works

      • ACTION ITEM: Filter could include the lead on the project

      • If you’re curious what modules HWG maintains and uses: https://github.com/statonlab/hardwoods_site

      • ACTION ITEM: Add a help wanted tag, users wanted, etc.

      •  

      • Perhaps we should make the list as owners rather than require people to maintain it.

        • Use the github api?

      • It would be nice to have a listing of the Tripal sites and which modules each site uses.

        • This way if there’s functionality you like you have a shopping list of modules to check out

      • Github issue Created: https://github.com/tripal/tripal/issues/402

    • What is the search URL for all Tripal modules on Github ?

 

Summary of Tripal v3 Users and Available Modules

Please add your site/module to this list if you are upgrading/on Tripal 3
Tripal User's Meeting 2018/08/03 Tripal Community Meeting Notes

  1. Upcoming Events

    1. Tripal v3 stable release -- Sept 3rd.

    2. Tripal PAG Workshop committee requesting abstracts this Fall.

    3. Tripal v4 discussion at September's meeting.

  2. Support/Involvement

    1. SLACK discussion: https://join.slack.com/t/tripal-project/shared_invite/enQtNDExNDU1NzUxOTI3LTNlOTg1MTNjZGQ1NjRmNGQxMWRjOGVjN2IwMjQyOTc2ODZlYWM2OTQxM2Y1ZWM1MmFkNWJhOGEwN2RkZjdkNGU

  3. Introduction to GitHub Issue Discussions

    1. https://github.com/tripal/tripal/issues

    2. Choose label "discussion".  Quick link: https://github.com/tripal/tripal/labels/discussion

  4. Tripal Content Types

    1. Issue: https://github.com/tripal/tripal/issues/441

    2. Spreadsheet:  https://docs.google.com/spreadsheets/d/1wJbekYwaw4qULHdjh4hapWwrj82-w9IqiHs_1flr3iM/edit#gid=0

    3. Add fieldsets to organize content types… perhaps by module.

      1. If not fieldset, some organization method so that creating content isnt overwhelming.

    4. Sites have the power to remove/not install content types you dont care about.

    5. Sites can change the label to suit their needs, and the term will be the same across sites.

    6. Having default content types encourages use of similar terms for cross-site data sharing.

    7. Sites have the power to use different terms if they choose.

      1. But we discourage this since it reduces cross-site compatibility.

    8. Once we have a list of cv term assignments for all Chado tables/columns, we would like to put it to the Chado community for comment.

    9. Chris had wanted a

      1. linking table between organism and analysis

        1. There’s already a module! **Cheers -thanks statonlab!** https://github.com/statonlab/tripal_manage_analyses

        2. This module needs a bit of work to make it more shareable.  Considering there’s a couple of groups who want to use it, i’ll make that a priority. (bradford)

      2. Apollo/JBrowse integration

        1. JBrowse module:  https://github.com/tripal/tripal_jbrowse

        2. Made quite a bit of progress with JBrowse community to make it natively embededable! It should now be possible so that’s the next plan for the above module.

        3. Bradford had mentioned that the statonlab would be interested in collaborating on this since hardwood genomics would love it. Lacey is very excited about this :-)

    10. Ideas:  Core includes all definitions.  It seperates them into general topics via fieldsets.

    11. Discussion: bloat is a major concern.  Benefits: Now when someone installs tripal, they see that hey there’s a breeding module!  
      The bundles aren’t enabled by default but listed with links to “Install this module to use these contents?”
       

  5. PHP/Drupal/Tripal Pro's/Con's

    1. Issue: https://github.com/tripal/tripal/issues/461

    2. Spreadsheet:

  6. General discussion on what fields/formatters should go in core?

    1. Specifically, https://github.com/tripal/tripal/issues/523 :-)

  7. Project-wide style update

    1. formatting style (code style).

    2. Fear of breaking everything right before our stable release (stephen, shared by Lacey)

    3. Let’s do it after the stable release then :-)

      1. 3.1 or bust

      2. https://github.com/tripal/tripal/issues/310

 

https://laceysanderson.github.io/chado-docs/index.html