Difference between revisions of "WBConfCall 2013.07.18-Agenda and Minutes"

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__TOC__
 
==Agenda==
 
==Agenda==
  
 
'''Models'''
 
'''Models'''
 +
If anyone wants to discuss anything, but nothing from Me (Paul D.)
 +
 +
'''Progress on Ontology Browsing'''
 +
 +
http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/amigo.cgi
 +
 +
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
 +
  
 
'''Upcoming Build'''
 
'''Upcoming Build'''
  
 
'''Post-IWM Discussion'''
 
'''Post-IWM Discussion'''
 +
*WormMine
 +
**Can anyone make templates public?
 +
**If not, should WB curators still be using the staff account to edit or publish templates?
  
'''Pending Helpdesk Issues'''
+
===Helpdesk===
 
*It would be helpful, for coordinating helpdesk responses, if we could assign issues to specific people.
 
*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...
 
** Either ourselves if we've picked up an issue to answer or...
Line 14: Line 33:
 
** We have a list of people and their responsibilities, but perhaps a more granular list for internal helpdesk purposes would be useful:
 
** We have a list of people and their responsibilities, but perhaps a more granular list for internal helpdesk purposes would be useful:
 
     http://wiki.wormbase.org/index.php/WormBase_Consortium
 
     http://wiki.wormbase.org/index.php/WormBase_Consortium
 +
 +
===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
  
 
==Minutes==
 
==Minutes==
 +
 +
===Upcoming Builds===
 +
*WS240
 +
**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
 +
 +
===WormMine===
 +
*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?
 +
 +
<code>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. 
 +
</code>
 +
 +
===Helpdesk SOP===
 +
 +
*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
 +
 +
===AmiGO2===
 +
*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

Latest revision as of 20:52, 23 July 2013

Agenda

Models If anyone wants to discuss anything, but nothing from Me (Paul D.)

Progress on Ontology Browsing

http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/amigo.cgi

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


Upcoming Build

Post-IWM Discussion

  • WormMine
    • Can anyone make templates public?
    • If not, should WB curators still be using the staff account to edit or publish templates?

Helpdesk

  • 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:
    http://wiki.wormbase.org/index.php/WormBase_Consortium

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

Minutes

Upcoming Builds

  • WS240
    • 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

WormMine

  • 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.

Helpdesk SOP

  • 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

AmiGO2