WBConfCall 2013.07.18-Agenda and Minutes
Models If anyone wants to discuss anything, but nothing from Me (Paul D.)
Progress on Ontology Browsing
specifications: - given a goid, generate an svg graph with clickable nodes and make a separate html table of children if there's too many. - code is ~120 lines of perl - using GraphViz to generate an SVG with clickable links to other nodes in the graph. - using JSON to parse the json from berkeleybop - using LWP::Simple to get json from berkeleybop - currently limiting graph to 5 children, and suppressing GOIDs - arrows in graph follow colours used by amigo
- Can anyone make templates public?
- If not, should WB curators still be using the staff account to edit or publish templates?
- It would be helpful, for coordinating helpdesk responses, if we could assign issues to specific people.
- Either ourselves if we've picked up an issue to answer or...
- Someone else, which the helpdesk officer could do as part of their duties.
- I think this would help eliminate redundant efforts and/or responses and allow people to check to see if an issue is already claimed by someone before they start working on a reply.
- We have a list of people and their responsibilities, but perhaps a more granular list for internal helpdesk purposes would be useful:
Outstanding Helpdesk Issues
Since we didn't have a call on the 4th, I checked over the last month's worth of helpdesk issues.
Here are the issues that are still open, a brief summary, and anyone who's commented. Please check and close an issue if you can.
Also, issues that we haven't responded to at all are in bold.
- 1437 - still working on it- ky xEs12400 Vancouver large-scale strains and trangenes - Karen, Wen
- 1438 - RNASeq data access errors in GBrowse- needs help from GBrowse Dev, WebTeam or Hinxton?-ky Died links - Karen
- 1443 - BLAST with WS235 - Joachim, Chris
- 1462 - BLAST with suum - Kevin, Abby, Joachim
- 1466 - Multiple sequence alignments
- 1471 - Mary Ann proposed a solution through non-git e-mails (now pasted into git). Requires further discussion with curation group-ky n765 is lin-15AB - Karen
- 1484 - Download table from Interaction widget - Chris
- 1487 - Genome Browser images larger than 1024 pixels
- 1488 - had been moved to Helped-ky New widget on Process page - Karen
- 1500 - Genes in region of genetic map - Raymond
- 1511 - still working on it-ky Moving bacterial strain genotype - Karen, Mary Ann
- 1512 - Download list of Other_names - Wen, Chris, JD
- 1514 - Follow selected genes automatically via email
- 1517 - GBrowse exports out of frame
- 1518 - Follow up to 1517, only minus strand
- 1519 - Orthologs in WormMine - JD, Todd, Michael P.
- 1531 - Inline chat - Todd, Abby
- 1541 - Multiword string search Paper class - Michael P., Xiaodong, Karen, Kimberly, Abby
- 1556 - Widget placement and size - Kimberly, Abby
- 1557 - WormMine - unrecognized genes in list - Raymond, Chris
- 1563 - sp11 Downloads - Kimberly, Chris
- 1564 - BLAST/BLAT - Paul D., Joachim, Kimberly
- 1572 - Query Contains widget - Mary Ann, Todd,
- 1582 - Oliver - Submitting consecutive questions
- Will upload at the end of September and stay on two-month schedule for the time being
- Think about milestones for WS240 and start a github ticket to collect them
- Caltech is discussing a new, more process-focused approach to literature curation
- Will update group on what/how they decide to do this and if there's any coordination that should happen between sites as a result
- Panagrellus genome
- Michael P. waiting on Panagrellus submission to Genbank so we can incorporate this genome into WB
- JD currently on vacation; will need to confirm a few things with him when he gets back:
- Who can make things public (still staff account only)
- How often are things made public? Only with each new WormMine release?
- How often do existing lists, for example, need to be upgraded?
JD- Questions answered in order
- anyone with admin rights can make their own lists/templates public, although due to a bug only the primary super user if allowed to add their own public lists/templates to the frontpage as well
- Things can be made public anytime, however we may choose to release batches of new lists/templates following our current release schedule if we choose
- existing lists need to be upgraded if any of their members no longer exist following a data release. If the backend data doesn't change, lists will not have to be upgraded.
- Github may not be the perfect system for what we're trying to do, but it seems to have enough useful features to continue to use it
- Perhaps we can work on our existing SOP (http://wiki.wormbase.org/index.php/Github_Helpdesk_Working_Document) to help reduce redundancy in efforts and responses to users
- Some ideas:
- Everyone on helpdesk rotation should have a github account
- All issues should be logged in github
- If an incoming helpdesk issue is not automatically assigned an issue number in github, then the helpdesk officer, or person who answers that email, should add it to github
- If we can, assign issues to people, including ourselves, to indicate that someone is either working on, or is the point person for, responding to an issue
- If you've been assigned an issue and don't feel you can respond, you can re-assign it to someone else
- Users probably don't usually follow the github ticket, so make sure you reply to them via email
- Try to remember to cc everyone on a reply, so we all know what's been done about an issue
- If other sites have additional trackers they use, would be nice to have that all consolidated in github
Outstanding Helpdesk Issues
- Please look over the list again to see if you can close any issues
- Michael P. will respond to sp11 emails
- There seems to be two issues, one of missing protein sequences and the other with incorrect URLs
- Raymond and Juancarlos have been working on development of AmiGO2 for ontology browsing in WB
- Would like to start conversation with web team for implementation
- Juancarlos sent email to wormbase-staff with URL on account that doesn't require authorization http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/amigo.cgi