Agenda

please submit your agenda items here

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?

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.

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

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.

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

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.

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.