extensions

Tripal Users Meeting 2020/12/01 Tripal Community Meeting Notes

 

Agenda

  1. Plan the January Hackathon/Codefest-
  2. Advisory Committee Updates
    • Still working on Tripal White paper
  3. Tripal Release
  4. Overview for how the Codefest will work
    • Jan 11-15
    • We will organize teams today
    • You may meet prior to January, with your team, if you want, to maximize productivity for the Codefest.
      • Our official gather.town room is available for such meetings
    • With your team, set aside on your calendar about 8 hours (similar to in-person event in San Diego)
      • Can be one day, multiple hours throughout the week.
      • Arrange to meet in Gather
    • Will have kick off meeting Monday and wrap-up meeting Friday
  5. Potential Topics:
    • Chado
      • Improve efficiency for storing some data types (e.g. Genotyping, Phenotyping).
      • e.g. mimic ElasticSearch functionality without the need for ES.
    • Tripal 4:
      • Core development
      • Fields: Upgrading existing fields (Core/Extension) 
      • Drupal Console commands for easy upgrade/development 
      • Automated Testing!
    • Tripal 3:
      • Glyphs for gene/mRNA pages
      • BrAPI, (upgrade module to current version of BrAPI)
      • phenotype filtering module (want to make existing MGIS module generic and cooperate with BrAPI - See "Morpholigical descriptor > Selection interface/Display graphical interface" at https://www.crop-diversity.org/mgis/accession-search )
      • Chado-related Tripal 2 to 3 upgrade issue
    • Extension Modules
      • Tripal Galaxy:  improvements and upgrade to T4.
  6. Volunteers to lead a topic?
    • BrAPI/Phenotyping filtering
      • Lead: Valentin
      • Participants: Lacey
    • Tripal Galaxy
      • Lead: Stephen
      • Participants: Jill
    • Chado Improvements
      • Lead:  Valentin
      • Participants:  Lacey, Jill, 
    • Tripal 4
      • Lead:  Lacey
      • Participants:  Stephen, Sean, Valentin
  7. Time Zones
    • Central European (GMT+1) 4pm
    • Western European (GMT)  3pm
    • Atlantic Time (GMT-4) 11am
    • US East (GMT-5)  10am
    • Regina (GMT-6) 9am
    • US Mountain  (GMT-7) 8am
    • US Pacific (GMT-8)  7am
  8. Schedule
    • Kick off Meetings
      • European: 
      • North America: 
  9. Slack
    • #codefest
    • If you want a slack channel let us know.
  10. Tripal Advisory Committee
    • Delay to February's User's Meeting.
  11. Gather.town as a potential “Venue”
Tripal Users Meeting 2021/10/05 Tripal Community Meeting Notes

Agenda

  1. NSF’s Cyberinfrastructure for Sustained Scientific Innovation (CSSI) solicitation for FY22 has been released and can be accessed at the following link: https://www.nsf.gov/pubs/2021/nsf21617/nsf21617.htm.
    • Lets add this to codefest. Dedicated time.
  2. PAG Workshop Organizer Committee
    • Who will be in the committee this year.
    • Historically, we rotate this between 2-3 individuals.
    • Attendance at PAG may be quite low.
      • Likely to go: Dorrie, Sook, Scott Cain, Mathieu Rouard, Jill W, Stephen F
      • Maybes: Sophia, Surya, Sean, Monica
    • Jill will spearhead PAG effort -  is this happening? But she needs more time to decide. She’ll put out another call on where people stand. Even if we have presenters, will we have an audience?
      • Ideas: lightning talks
  3. PMC: Hackathon will be held online this year. We may have to schedule differently so as not to conflict with PAG.
    • Focus on T4! Need community support. Need to be at a point where the community can help. How do we get there?
    • January 13th and 14th
    • Online, the whole time
  4. TAC Chair 
    • Meg's nearing the end of her 3 year tenure as chair
    • Propose elections in January (or appointment in January if there is no need for an election)
    • Nominations? Be thinking about it!
      • Jill could do it (maybe co-chair) - next term focus on grant!
  5. Community topics for Hackathon/TAC on January 13th and 14th
    • development priorities - T4
    • funding strategies
    • community growth
Tripal Users Meeting 2021/11/02 Tripal Community Meeting Notes

 

  1. Reminders
  2. Any Updates from the Advisory Committee?
  3. Any Updates from AgBioData (if steering members are present)?
    • https://www.agbiodata.org/ 
    • The research coordinated grant has started
    • A project coordinator has started. This person will support the activities in the grant.  She starts part-time in Nov and full-time in January
    • Working groups will form around special topics 
      • 5-10 people per working group
      • These groups have been formed by community involvement
      • See website for proposed topics.
      • Working group signup has closed but attend the Dec webinar if you want to get involved.
      • Sign up on Slack space 
  4. Tripal Updates

 

  1. January Codefest
    • Tripal page (under construction): https://tripal.info/events/codefest_2022
    • Registration Form (coming after today's meeting)
    • Review of this past year's survey responses
    • Preliminary Decision
      • Format? 
        1. Week long again?
        2. A few full days?
        3. Jill: shorter but more concentrated is better
        4. Lacey: shorter and more concentrated 
        5. Valentin: early or late on days for just 2 days should be okay.
        6. Add to registration page: time blocks for when time works for each attendee.  Days 18-28
      • Topics
        1. Tripal v4
          1. Field Implementations in Tripal v4
          2. Search in Tripal v4 -- Views may not work well we may need an alternative (i.e. ElasticSearch)
          3. Default theme for Tripal and perhaps documentation for how to deal with themes in Tripal 4?  Upgrading the theme is problematic.  
        2. Tripal File (Stephen Leads)
        3. Tripal v4 Docker Production Ready (Lacey leads)
        4. Tripal nf-core Integration (Stephen/Jill)
        5. Sustainability discussion group
        6. User Feedback Panel discussion
          1. What do they want to do that they can't do?
  2. December's Meeting
    • Codefest prep
    • Send out a single document with zoom links.
  3. Advisory Committee Meeting
    • Day after the codefest?  Jill will talk with Meg about that meeting.
    • Jill is the new chair in January
  4. PAG (Jill)
    • Extensions to submit an abstract through Friday
    • There is the opportunity to give virtual talks (not sure how that will happen)

Submit your abstract here before Friday! https://docs.google.com/forms/d/e/1FAIpQLSeHteXWGASXYDtBSHscoB6hdZ_GjAYqRpYOtaRhe5HQqIgtXQ/viewform

Tripal Users Meeting 2021/3/02 Tripal Community Meeting Notes

Agenda

  1. Reminders
  2. TAC Announcements (Jill)
  3. Demonstration of the Tripal File Module and request for input
    • https://github.com/tripal/tripal_file
    • For sharing data files with collaborators through a Tripal site
    • Working towards FAIR data standards for making files available:
      • Files are findable and accessible via Tripal's content web services.
      • Metadata about files use globally unique controlled vocabularies. These metadata can be assigned as properties of each file.
      • License and usage details can be assigned to each file.
    • There is online documentation available through readthedocs: https://tripal-file.readthedocs.io/en/latest/ 
    • Needs Tripal version 3.6 or higher (currently use the dev branch until 3.6 is released)
    • Uses a number of custom tables to associate files with various chado data
    • Handles a lot of file metadata including the license for the data 
    • Use the Tripal ontology loader to import the EDAM vocabulary (it will be added to the drop-down for you)
    • Creates a file and license Tripal Content Type to allow adding through the UI.
    • First add your License for the file (examples in the document)
    • Next, create the file page: 
      • the types are available via EDAM, 
      • you can use contacts to associate the source of the file (create the contact first)
      • Supports both local and remote locations for the file
    • If the file is associated with Tripal pages (chado data) then the link to those pages will appear on the file page.
    • The license is actually embedded on the file page including the human-readable description
    • If you use the Tripal Managed File Interface to handle your files for download then the size and md5sum will be provided to the user.
    • You can associate a file with a Tripal content page, you edit it and scroll down to the file section near the bottom and select the file to be associated. For example, go to the analysis page from the Tripal Tutorial and clicked edit then select the file on the analysis edit page.
      • Note: Add the field to the content type by clicking “Find new fields” on the Manage fields page for the content type you want to add it to.
Tripal Users Meeting Fri. Sept 7th. Topic: Tripal v4 Announcement

We will be holding our Monthly Tripal User's Meeting on our usual first Friday of the month.   Anyone who uses Tripal is invited to attend and provide input at any of these meetings.  This meeting will be a bit atypical as we have one agenda item:  Tripal v4. You can find the exact time for the meeting in your area at this link:

https://www.timeanddate.com/worldclock/fixedtime.html?msg=Tripal+User%27s+Meeting&iso=20180907T08&p1=2035&ah=2

We would like to focus on the future of Tripal, what it should look like and how do we ensure a productive, active community of users and co-developers to ensure long-term sustainability of our respective databases and for the Tripal software itself.   This is timely as we anticipate the Tripal v3 official release this week! We encourage everyone to attend and voice your opinion.  We may go longer than the typical 1 hour.

Google Doc for Notes: https://docs.google.com/document/d/11cuzGkI_V1G5FMvUw-J54LNcqFbzw1WPZhI…

Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/455940438

Or iPhone one-tap :
    US: +14086380968,,455940438#  or +16468769923,,455940438#
Or Telephone:
    Dial(for higher quality, dial a number based on your current location):
        US: +1 408 638 0968  or +1 646 876 9923  or +1 669 900 6833
    Meeting ID: 455 940 438
    International numbers available: https://zoom.us/u/cXre9E3v8

Hope to see you there!
Tripal v0.3.1b Released Announcement

Several extension modules have also been re-released with bug fixes as well for this new version.
Tripal v1.0 Released Announcement
Tripal v1.1 Released Announcement
Tripal v2.0 in Docker Announcement

For those who want to quickly explore a lightweight instance, Docker images offer a nice alternative to full VMs.  You can find the Docker GitHub project here:

The project  on Docker Hub:

If you have any problem or suggestion please open an issue on the project's GitHub issue tracker.
Tripal v2.0-alpha Released Announcement

This release is expected to have bugs and there is some functionality still under development.  However, this release is made to help early adopters of Tripal for Drupal 7.   Reports of bugs or other issues are highly welcomed.   Below are available resources for Tripal 2.0a

The Installation tutorial is still under development but should have enough information for complete installation of Tripal v2.0a as well as loading of organisms and features.