WBConfCall 2015.07.16-Agenda and Minutes

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Agenda

please submit your agenda items here

Ticketing System

  • Where should we submit internal work tickets
  • Should there be a project wide choice
  • Doesn't feel that the website/helpdesk system is the natural place....or is it?
    • webcode and can attach tickets to code commits for tracking why development was necessary.
  • Hinxton have:
    • Jira - working to consolidate information here.
    • Bitbucket (old washu/sanger retired and in process of migrating into jira
    • RT - Sanger worm-bug@sanger.ac.uk - Poss retirement? Effect Caltech paper submissions for Hinxton/UK curators
    • GitHub - retired and consolidated into
  • Caltech have:
    • WormBase wiki?
    • Other internal trackers?
  • OICR have:
    • GitHub main tracking system/HelpDesk
    • Other internal trackers?

RNASeq Expression Graphs

  • In the IWM, Julie Ahringer expressed a wish for RNASeq expression graphs like Gexplore.
  • Gary Williams has been working with Julie to produce graphs using a subset of the modENCODE data.
  • When she is satisfied, what is the best way of transferring this work to the Web Team?
  • It currently consists of a perl script that queries an acedb database for data from Gene, CDS, Transcript and Pseudogene classes to produce png images.

Naming of cis-regulatory sites

  • Tim Schedl brought up last week in response to naming of "rex" sites (Recruitment Elements on X) from Barbara Meyers group
  • Do people have strong opinions about how/if we could/should standardize names of sequence features or cis-regulatory elements in particular?


Minutes

Ticketing System

  • Paul Davis - I'm trying to get a feel for what other sites in the project are using - can we consolidate what we use?
  • Kevin - GitHub is not designed for tracking general non-code-related tasks.
  • Raymond - I would prefer one system used by everyone.
  • - we use wiki a lot which is not ideal.
  • Todd - GitHub requires creative use of labels. Most issues it tracks tend to be website issues. GitHub could be leveraged a little more.
  • Raymond - we should encourage site-spcific projects on GitHub.
  • Todd - we pay for GitHub and all our project management should be publicly available.
  • Kevin - all the Hinxton code is on GitHub and we use it for code-related tasks, but a lot of our issues are not code-related.
  • Todd - using a dummy project means you lose being able to close with a commit.
  • Paul Kersey - Jira at Hinxton can be made public - but you will have to login.
  • Todd - It should be publicly accessible. It is possible to to make sections visible by default.
  • Paul Kersey - I would feel more comfortable with a project management system that is not public.
  • Kevin - we would like to consolidate systems. Is there a recommended or agreed way to consolidate?
  • Todd - I would be happy to use GitHub and Jira for a while.
  • Kevin - if we are to fix on something it should be something we can control.

RNASeq Expression Graphs

  • Sibyl and Gary agreed to exchange the code for RNASeq expression graphs, rather than transferring the image data.


Naming of cis-regulatory sites

  • Gary explained the current situation where the authors' names for regulatory sites are stored in the Public_name tag of the Features that mark them.
  • Chris - if names like 'rex-1' were to be used in a lot of sites it would pollute the namespace.
  • Raymond - we have unique identifiers - they are the Feature IDs.
  • Xiaodong - we only show the public name on the browser.
  • Chris - users are not going to search for the WBsf number ID.
  • Raymond - is it necessary to have an official name? Use the full name like "Recruitment Elements on X" in the Public_name tag.
  • Paul Sternberg - we should have a plan in place. Maybe we should look at what other people are doing.

Wormbook Chapters

  • Paul Sternberg - could I have a resume of where people are with the Wormbook Chapter? Mary Ann has submitted. I am waiting for the other chapters before writing the Introduction.
  • Xiaodong - maybe we should just email you.
  • Kevin - In the "instructions for authors" there are requirements for figure formatting. Is this necessary for the review process?
  • Paul Sternberg - it should be done now. The review should be quite quick.