WBConfCall 2016.01.07-Agenda and Minutes

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Agenda and Minutes

1. SAB schedule

Submitted by Kevin

  • more strategic
  • needs to address budget crisis
  • fewer but more pointed talks
  • more time for discussions
  • provide document summary
  • cut uninteresting waffle (?)

Paul's comments

  • more Mod interactivity
  • new SAB member Brian Oliver (flybase)
  • emphasize getting funding from non-mod funding sources
  • scaling, flexibility, community annotation
  • bring everyone up to the best resource
  • metrics - more than just site hits and publications.

"How many lives has WB saved"


  • should give a brief overview of WB organization for the benefit of the new SAB members
  • what and how we prioritize our efforts


  • mention SVM and textpresso helps curation

2. WormBase exhibit at the GSA meeting Dev., Cell Bio and Gene Expression Meeting

Submitted by Chris

Anne Marie Mahoney wants to know if we're interested in having a booth at
the Orlando meeting in July:
It looks like the cost is $3,000 USD for an 8'x10' non-profit exhibit
space. Do we have any definitive plans for attending this conference? I
would like to attend and am happy to represent WormBase.

Reply from Todd

We should certainly have people attending and presenting at this meeting.
Various Intermine groups (probably including WormMine) will be presenting as a consortia. It makes sense for WormBase to be there, too. Whether or not we need an exhibit space probably hinges on what we will present and how many are attending.
We could always be creative and organize things like WormBase breakfast/lunch/dinner meet ups although it is hard gather too many people around a lap top.
I know I'd be happy if you help organize the WormBase contingent.


  • Mike Cherry said we can share SGD space
  • one or two WB people
  • will want a Textpresso person
  • as a topic meeting - not as many elegans community members
  • more about educating other people, mods, etc about what we are doing - not so much about educating worm community members
  • Overall, want one person at each of the elegans topic meetings this year as well as a couple at the Orlando Mod meeting - different focus for each meeting.

Other meetings


  • Janelia Farm meeting-
  • need to find new funding sources (other NIH departments or international sources) or cut costs by 2019
  • work together with other MODs to build more efficient projects


  • regional meetings
  • push community participation in pathways, Reactome


  • Reactome hold minisymposia at meetings, getting the experts together- ended up with skeletal pathways, reactome curators would end up doing the most work afterwards to put it together, onus on curator

Chris - review of community outreach for phenotype curation and gene concise description

  • user friendly forms
  • ask for small chunks of data
  • curator tool for tracking requests and responses
  • updates to curator curation forms to accommodate user submissions
  • 80-100 people (~20%) response rate
  • responding users ask for being able to submit different types of data - so good community feedback
  • close to 600 annotations receive
  • authors do not curate their whole paper

Bottom line for community annotation

  • what is the level of precision that is necessary, useful, and sufficient
  • Recotome experience with working with community, what curators curate are do not fit the models - cycles
  • LEGO curation - one goal is to generate reports about what is missing in a pathway - to help prioritize data gathering, and guide users to submit more atomized chunks of data. LEGO pathway models will be built using all of the existing GO annotations - will work as a scaffold, or seed for pathways

3. Data submission forms

Submitted by Paul D.

Should we have a more centralised place or have some form of webforwarding for the user submission forms rather than exposing the machine and username of one of the WormBase Caltech staff?
The following is used as the root of most/all user submission forms.

Reply from Juancarlos

We've had the forms on tazendra ~azurebrd since 2001 (tazendra was minerva at the time, until 03 or 04) and haven't had any problems, so I'm okay with leaving things as they are (if the issue is the safety and privacy of my account and machine).
A lot of the forms interact with the local postgreSQL server directly, and for speed and potential network issues, it's nice that they're in the same machine. If we wanted to move things to a different centralised place for user submission, we could, but I don't know where it would be, and how much benefit we'd get from it. If someone wants to pilot that, I could move some non-postgreSQL forms and see how that works.

Reply from Todd

Personally, I think it looks more professional to have everything hosted from the same domain.

Reply from Kevin

The service could still be physically hosted on tazendra (and maintained by @azurebrd ), but have a WormBase domain URL root, right? e.g. www.wormbase.org/submissions, or even submissions.wormbase.org.

Reply from Todd

Yep! It could be configured either way. The first would require a transparent reverse proxy, the second either proxy or direct traffic to host.

Need to decide on the URL

4. WS252 on staging

Submitted by Todd

WS252 is now available (again) on staging.wormbase.org for testing.

5. WS253 model call

Submitted by Paul

As the SAB has a major impact on the WS253 build schedule could I get an idea of what models are going to be touched and how complicated a change they are likely to be. A brief summary that would be great.
I am aware that Mary Ann is in the process of preparing a simple change to the Transcription_factor::Feature connections but I believe that is the only one.

A build schedule will be made at the SAB meeting.

Outstanding helpdesk issues

  • ticket #4463 user is trying to find all genes encoding the proline tRNA that recognizes "CCC" codon - assigned to Paul D.
I am trying to find the gene (or genes) that encodes the Proline tRNA that recognizes the "CCC" codon. I know previous versions of Wormbase annotation (for example, WS230) used tRNAscan-SE as the source for defining tRNA genes. However, the currently published versions of the tRNAscans for WS220 show no tRNAs that recognize the CCC codon. C. elegans clearly uses this codon for Proline, so there must be a tRNA for it. Can you tell me whether there is now a known Proline tRNA (CCC), and if not, how I might go about identifying it? (I will soon try to run tRNAscan on the latest genome release, but I'm guessing that's already been done).

  • ticket #4455 -assign to OICR
I sent a message a while ago. Apparently the problem is that your Blat only works with short input sequences? With 400 bases it wotked,but BLAT is supposed to accept up to 20000 bases.
Please advise
  • Bug Report: Server Error: 500

should people who report these be responded to - consensus,

    • if takes more than a day to fix-
    • perhaps a notice should be posted on the homepage,
    • or a more informative automated reply for certain errors,
    • only need to reply to non-anonymous users
    • modify the Error 500 page include all the bugs that are being worked on, based on github tickets
    • 500 error pages are probably being tracked
    1. 4467
    2. 4452
    3. 4458
    4. 4454