Difference between revisions of "WBConfCall 2013.07.18-Agenda and Minutes"
From WormBaseWiki
Jump to navigationJump to search (→Agenda) |
|||
(28 intermediate revisions by 5 users not shown) | |||
Line 1: | Line 1: | ||
+ | __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''' | ||
Line 10: | Line 26: | ||
**If not, should WB curators still be using the staff account to edit or publish templates? | **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. | *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 18: | Line 34: | ||
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. | Since we didn't have a call on the 4th, I checked over the last month's worth of helpdesk issues. | ||
Line 25: | Line 41: | ||
Also, issues that we haven't responded to at all are in bold. | 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 | |
− | *1437 - 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 |
− | *1438 - Died links - Karen | ||
*1443 - BLAST with WS235 - Joachim, Chris | *1443 - BLAST with WS235 - Joachim, Chris | ||
*1462 - BLAST with suum - Kevin, Abby, Joachim | *1462 - BLAST with suum - Kevin, Abby, Joachim | ||
*'''1466''' - Multiple sequence alignments | *'''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 | *1484 - Download table from Interaction widget - Chris | ||
*'''1487''' - Genome Browser images larger than 1024 pixels | *'''1487''' - Genome Browser images larger than 1024 pixels | ||
− | *1488 - New widget on Process page - Karen | + | *1488 - ''had been moved to Helped-ky'' New widget on Process page - Karen |
*1500 - Genes in region of genetic map - Raymond | *1500 - Genes in region of genetic map - Raymond | ||
− | *1511 - Moving bacterial strain genotype - Karen, Mary Ann | + | *1511 - ''still working on it-ky'' Moving bacterial strain genotype - Karen, Mary Ann |
*1512 - Download list of Other_names - Wen, Chris, JD | *1512 - Download list of Other_names - Wen, Chris, JD | ||
*'''1514''' - Follow selected genes automatically via email | *'''1514''' - Follow selected genes automatically via email | ||
Line 44: | Line 57: | ||
*'''1518''' - Follow up to 1517, only minus strand | *'''1518''' - Follow up to 1517, only minus strand | ||
*1519 - Orthologs in WormMine - JD, Todd, Michael P. | *1519 - Orthologs in WormMine - JD, Todd, Michael P. | ||
− | *1531 - Inline chat - Todd, Abby | + | *1531 - Inline chat - Todd, Abby |
*1541 - Multiword string search Paper class - Michael P., Xiaodong, Karen, Kimberly, Abby | *1541 - Multiword string search Paper class - Michael P., Xiaodong, Karen, Kimberly, Abby | ||
*1556 - Widget placement and size - Kimberly, Abby | *1556 - Widget placement and size - Kimberly, Abby | ||
Line 50: | Line 63: | ||
*1563 - sp11 Downloads - Kimberly, Chris | *1563 - sp11 Downloads - Kimberly, Chris | ||
*1564 - BLAST/BLAT - Paul D., Joachim, Kimberly | *1564 - BLAST/BLAT - Paul D., Joachim, Kimberly | ||
− | *1572 - Query Contains widget - Mary Ann, Todd, | + | *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
Contents
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
- 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