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Gene Pages Team

The objective of this is to document the work, progress and efforts of the team during the Codefest. Members of the team should be able to check in to this document to find project details, instructions, design descriptions, etc. as needed fo the Codefest activities.

Team Lead

Name Organization Contact Time Zone
Stephen Ficklin Univ of Washington stephen.ficklin@wsu.edu US Pacific

Members

Name Organization Contact Time Zone
Monica Poelchau USDA ARS monica.poelchau@usda.gov US Eastern
Katheryn Buble Washington State Univ. katheryn.buble@wsu.edu US Pacific
Marta Silva CorkOakDB.org martacds07@gmail.com Western European
Blake Inderski United States Swine Pathogen Database blake.inderski@usda.gov US Central

Schedule

Team leaders should reach out prior to Jan 11-15th to schedule team meetings when members can meet to discuss project objectives and divide work.

Date Time Where
1/11 3pm US Pacific Transcript Field Design GatherTown Gene Pages Room
1/13 4pm US Eastern/1pm US Pacific Update Meeting GaterTown

Previous Comments

  • https://github.com/tripal/tripal/issues/100
    • @bradfordcondon: What im thinking is it should could list each child feature as a collapsible one, which could be expanded to view all children/grandchildren of that feature and annotations etc.
    • @lacey-sanderson:
      • Transcript listing: Shows all the transcripts for a given gene including all the functional information & annotation for each transcript.
        Could simply embed Transcript view modes (e.g. Teaser) allowing admin to change the view mode and completely customize what shows up in this sub-listing.
      • 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
      • Sequence Field: Shows the sequence for the Gene, any transcripts and proteins
      • Typical Interpro, GO, BLAST homology results
        should be provided by each Tripal Analysis Extension module

Considerations

  • https://github.com/tripal/tripal/issues/732 (Summary and thoughts below provided by @mpoelchau)
    • Child features – traversing feature relationships to display all child info information on gene page
        1. violates web service implementation,
        1. makes it hard for the page to load quickly (?),
        1. might put way more information on the gene page than we need
    • Do we need to have all the ’grandchild’ feature info display?
      • It seemed like the easiest thing at the time, but perhaps we should just have the child features (transcripts) show?
    • Glyphs – Bradford had problems using the Swissprot glyph library for this.
      • Perhaps do with Jbrowse embed for now, and save glyphs for next PAG hackathon?
    • Display choices:
      • I personally would like to have the sidebar have a ‘transcripts’ tab (probably could rename ‘Relationships’)
      • @spficklin: we have this now in Tripal v3. It simply lists the transcript names and the 'Relationship' field can be removed
  • @mpolchau
    • One thing I've been wondering about is if it is worth doing a usability study/test for the gene pages before embarking on any major UI re-writes. Not that I'm volunteering or have any experience with this but that might help pare down the development efforts in the long run. Perhaps something to discuss.

Possible Data Tree

  • gene
    • sequence
      • gene sequence
      • coordinate sequence
    • properties
    • blast results
    • interpro results
    • CV annotations
    • relationships
      • mRNA #1
        • sequence
          • gene sequence
          • FL mRNA
          • CDS
          • protein
        • properties
        • blast results
        • interpro results
        • CV annotations
      • mRNA #2
        • …

Possible Solutions

  • Option #1: Update the so__transcript field to include more information
    Image Not Showing Possible Reasons
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    • Each transcript gets its own fieldset.
    • Visualization?
    • What is the most useful information to include?
    • Pro:
      • it's straightforward to do.
      • We can make it compatible with web services.
    • Con:
      • what we choose to include and the layout we decide on may not be liked by everyone.
      • layout
  • Option #2: same as #1 but with configurable fields that should get included.
    • Pros
      • Let's users customize the fields they want shown their site
    • Cons
      • Layout may be come default.
      • Will may be difficult to intergrate with web services.
  • Option #3: Add a tab along the top with each transcript name.
    • Pro:
      • There's no incompatibility with web services
      • Drupal handles the page loading and
    • Cons:
      • If there are too many transcripts or the names are too long then the tabs can overrun one level.

  • Option #4: Add a new field that

Other Issues to address

Plans

Tasks

  1. Look into what a usabilty survey/interview looks like and what it would require.
  2. Code changes to the module
    • Katheryn and Stephen

Deliverables

  1. A pull request for an updated so__transcript
  2. Listing of resources for measuring usability and thoughts on how to proceed.

Accomplishments

Once the Codefest week is over, here is where the team documents the accomplishments that were made during the week!

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Tripal Codefest
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