1. Conference Call Instructions
    2. Wednesday, July 28, 2010
    3. Wednesday July 7, 2010
    4. Wednesday June 23, 2010
    5. Wednesday June 2, 2010
    6. Wednesday May 10, 2010
    7. Wednesday April 28 2010
    8. Wednesday April 7 2010
    9. Wednesday March 10 2010
    10. Wednesday February 17 2010
    11. Wednesday February 3 2010
    12. Wednesday January 20 2010
    13. Wednesday January 6 2010
    14. Wednesday December 2 2009
    15. Friday Nov 20 2009
    16. Tuesday Oct 27 2009
    17. Wednesday Oct 7 2009
    18. Wednesday September 16
    19. Tuesday August 26
    20. Tuesday August 11
    21. Wednesday July 29
    22. Wednesday July 15
    23. Wednesday July 1
    24. Wednesday June 10
    25. Wednesday May 20
    26. Wednesday May 06
    27. Wednesday Apr 22
    28. Wednesday Apr 1
    29. Thursday Mar 19
    30. Wednesday Mar 4
    31. Thursday Feb 18
    32. Thursday Feb 5
    33. Wednesday Jan 21
    34. Wednesday Jan 15
    35. Wednesday Dec 10
    36. Wednesday Dec 3
    37. Wednesday Nov 11
    38. Wednesday Oct 29
    39. Wednesday Oct 22
    40. Wednesday Oct 8
    41. Tuesday Sep 16
    42. Wednesday Sep 3
    43. Wednesday Aug 13
    44. Tuesday July 29
    45. Wednesday July 10
    46. Wednesday June 25
    47. Wednesday June 11
    48. Wednesday May 28
    49. Wednesday May 14

Conference Call Instructions

  • Request to join the conference call notification list via the  discussion group
  • You will receive schedule details and instructions via email from  TeleJunctions
  • Bascially, if you are in the US, you can call in to the FreeBridge system for free. If outside the US, we'll call you and patch you in.
  • Typically, we meet every 2-3 weeks for an hour starting at 11:00AM Pacific Standard Time.
  • Note: we have access to WebEx via the Pankaj Lab, if we have a need to share a screen.
  •  chat applet embedded in the wiki or via IRC at chat.freenode.org, channel #wikipathways.

Wednesday, July 28, 2010

  • Bug review
  • BioPAX progress
  • GSOC status
  • CIRM and Wikipedia

Wednesday July 7, 2010

  • GSOC
  • NuGO Metabolomics Workshop
  • What's up with LibSBGN

Wednesday June 23, 2010

Wednesday June 2, 2010

  • New Derby databases ready for production (version 58 released for all species!)
    • new species?
    • integer links worthwhile?
    • synonyms parsed as separate attr values - done.
  • New species and pathways for WikiPathways??
  • GSOC update
  • Roadmap

Wednesday May 10, 2010

Wednesday April 28 2010

  • Release schedule
  • SBGN Workshop report
  • GSOC
  • Community binding curation event.
  • References & Comments & MIM

Wednesday April 7 2010

  • BridgeDb webservice reliability.
  • SBGN Workshop
  • GSOC
  • Mouse pgdb - descriptions
  • Milestone 23 progress

Wednesday March 10 2010

  • Newsletter
  • M23 release focus features
  • Commenting on private pathways?

Wednesday February 17 2010

Wednesday February 3 2010

  • Curation Jamboree planning: spread the word!
  • M21 status and testing
  • BridgeDb and GPML release plan
  • Feature ideas for discussion:
    • displaying shape labels
    • datanodes representing pathways ( step 1: adding WP identifiers to next build of databases)
    • supporting multiple pathways per session

Wednesday January 20 2010

Wednesday January 6 2010

  • Mapping SNP data on Pathways?
  • Patches
  • Databases:
    • Maize db ready for testing
    • Release 56 databases ready for testing
    • Scheduled for Release 57: late Feb
    • automatic sync of SQL sources?
  • BridgeDb web service status/issues
  • M20 status

Wednesday December 2 2009

Friday Nov 20 2009

  • M19 status
  • Review [ M19 bugs]
  • Database update (more affy probesets than we know what to do with)
  • BioPAX meeting recap: action items for PV, WP and GPML?
  • BioPAX plugin BiopaxPluginHelp
  • Vector drawing example:  http://www.xaraxtreme.org/
  • Interactive pathway views (a la Google maps)
  • MIMs update
  • PharmGKB update
  • OSU update
  • Reactome update

Tuesday Oct 27 2009

  • BridgeDb paper response progress (Nov 10th)
    • Labrador server move (Nov 18th)
  • BioPAX meeting
  • pharmgkb progress
  • Time for GPML change? -> Reactome / SBGN use case

Wednesday Oct 7 2009

Wednesday September 16

Tuesday August 26

  • Welcome new developers: introductions
  • PharmGKB patch, trunk questions, BioPAX strategy
  • M17 status
  • Wormbase follow-up
  • Vanderbilt Conte update
  • GSoC, Mentor summit
  • BridgeDb status
    • MIRIAM submission status
    • Meeting tomorrow
    • REST web service status (any help needed?)
      • MIRIAM support & changes to url structure

Tuesday August 11

Wednesday July 29

  • BridgeDb paper
    • MIRIAM
    • REST Webservice
    • Editorial review
  • SBIR grant update
  • Ensembl release 55
    • changes to schema
  • Milestone 16 status
  • Inferred pathways
  • Community updates?
  • GSOC

Wednesday July 15

  • BridgeDb paper
  • SBIR grant update
  • Ensembl release 55
    • changes to schema
  • Milestone 16 status
  • Inferred pathways
  • Community updates?

Wednesday July 1

  • Which ID systems are supported in latest set of databases? => Some PV users are having problems getting data to import (RefSeq?/horse).
  • Reset test site content. Make sure nobody has useful content left there.
  • BridgeDb paper status
  • Potatoes
  • Mirror options - Squid caching or backup?

Wednesday June 10

Wednesday May 20

Wednesday May 06

  • M14 Status
  • homology script
  • gpml rename script
  • nathan's serotonin signaling pathway
  • wormbase
  • bridgedb
  • gsoc (id mapping, biopax, superpathways)

Wednesday Apr 22

Browsable archive:  http://www.genetrap.org/dataaccess/pathways.html

  • Chris' topics
  • Inferator: human-rat
  • changes to sidebar links on wikipathways

Wednesday Apr 1

  • GSoC 2009
  • M13 status
  • KEGG pathway plan
  • Publication Plan: Pankaj
    • Gene database system (Martijn/Alex) June-Aug
    • WikiPathways community and general report (Thomas/Alex/Martijn)2010

Thursday Mar 19

  • GSoC 2009
  • wp-dev subscription requests
  •  Low hanging fruit
  • M12 review
  • M13 status
  • Publication Plan
    • Gene database system (Martijn/Alex) June-Aug
    • WikiPathways community and general report (Thomas/Alex/Martijn)2010
  • Alitora

Wednesday Mar 4

[Image(Image_Munin-memory.png), center]

Thursday Feb 18

Thursday Feb 5

Wednesday Jan 21

  • M10 bugs review and nomination
  • Announce new features
    • New species
    • Private pathways

Wednesday Jan 15

  • M10 bugs review and prioritizing
  • Web service article
    • figure 1
  • Private pathways
  • Moving the WP Server
    • Temporarily switch to test server?
  • test/backup server - remainging issues:
    • (1) img_auth (no images unless logged in!)
    • (2) port 80 open to world (set to happen soon after the 15th, UCSF IT lockdown)
  • plant pathway support and new developer

Wednesday Dec 10

Wednesday Dec 3

  •  Milestone 9
  • Launch Meeting Canceled - industry funding has dried up
  • At database - contact Philip Zimmermann?
  • Ce database - symbol search working?
  • WikiPathways at ISMB'09
  • Switching search from CSE to web service
  • NAR paper
    • Author list
    • Images?
  • Trac
    • Severity: major, minor, feature
    • Components
    • Milestones
  • Checkstyle

Wednesday Nov 11

  • NBIC Workshop "Scientific Software as an asset" report.
  • Bug Nomination:
    • commit wpi/MetaTag.php changes (removal of updatePathwayCache)
    • stable id migration script issues
    • unnecessary debug statement, may cause log file to grow too large
  • 6 new plant databases!

Wednesday Oct 29

Wednesday Oct 22

  • Newsletter - yay!
  • Doing point releases
  • Rate of development
  • Contacting GenMAPP authors
  • Two new plugins: features and consequences
  • Stable Identifiers update
  • Bug review
  • Thomas' visit
  • SBGN Meeting

Wednesday Oct 8

  • Bugs:  609  623  624  654
  • GPML Changes: GpmlChangeProposal?
  • Stable identifiers (integers, padding, prefix...)
  • Milestone release
    • Go or no-go?
    • Send email to wp-discuss announcing new features? (Idea from Bruce: include short demo video, like the tutorial videos)
    • Update the tutorial with curation tags
  • BBC Abstracts (Suggestion Box)
  • Genes & Nutrition paper
  • PathVisio paper
  • Contacting new contributors
  • Proposed extensions for M8  646  647  649
  • Chicken gene database request
  • Gene databases & Gene database schemas

Tuesday Sep 16

  • Launch meeting
  • Funding
  • CC license and trademark
  • Author list

Wednesday Sep 3

  • Minutes - email - who will take them?
  • CC License
    • Scenario 1: redistribute live or stable version of content
      • free
      • charge
    • Scenario 2: augment content with proprietary content, then...
      • keep internal
      • distribute free
      • distribute for charge
    • Get input from Nature, Aglient, Reactome
  • Wikiprofessional
  • GPML proposal for Reactome
  • Launch meeting agenda
  • Database master: new hire Sept 5th!
  • GSoC mentor summit - visit to Gladstone?

Wednesday Aug 13

  • Funding plans
    • Bruce: SBIR
    • Chris: education/tutorial company
  • Launch meeting plan: early Feb '09
    • push for participants and sponsors in Sept
  • 6.0: Web API
  • 7.0: Meta-tag implementation
  • groups fix
  • contact new contributors
  • collection of presentation, flyers, posters, tutorials, workshop materials; centralize repository; FTP at BiGCaT

Tuesday July 29

  • Cytoscape Retreat update
  • BioPathways SIG: not really about biological pathways
  • BioPAX BOF: call for Factoid Ideas; positive reception of WikiPathways; discussions with Emik
  • ISMB: Kam and John - database production and E.coli pathways; poster not too active
  • PV1.1 + Paper
  • ChemSpider - must be open and free; Martijn will follow-up
  • Arabidopsis via Gramene? Wait for Kam + John?
  • Portals for species -> subpages for databases; discussion forum
  • Make databases for bovine, chicken, dog, pig,...; Isaac Ho
  • Release cycle on wiki:
    • 6.0 = Web API/SOAP, My Experiment; design tagging impl
    • 7.0 = tagging infrastructure; tagging bots flagging pathways; user tagging for test pathways
    • 7.0.1 (parallel?) = BioPAX import/export; Alitora collaboration (tab in node dialog)
  • Review RFCs on Tagging and (optionally) stable IDs for M7

Wednesday July 10

  • Review recent emails about WikiPathways Feedback
  • PathVisio Paper update
  • Last minute issues prior to P-day (publication day)?
  • Connections in other species - plan?
  • Major bugs before July 18 code freeze
  • Martijn's apartment at  19th and Judah! Other side of Parnassus campus. It's an "in law" apt on the ground floor of a larger house, which includes a private kitchenette/living room, bathroom and bedroom, plus access to a little backyard.

Wednesday June 25

  • Reset the test site content?
  • Reset Sandbox periodically?
  • Factoid capturing, ever got a reply? --> Nope.
  • Funding Plan?
  • Capacity testing, e.g., simultaneous editing
  • WikiPathways Paper #2
  • Portals and Pathways in the works?
  • BioPAX conversion
  • M5 release
  • M6 goals and timeline? (still before PLoS publication!)
  • WikiPathways and Wikipedia (see user suggestion at  http://www.wikipathways.org/index.php/WikiPathways_talk:About)
  • Martijn's summer visit - housing, poster, cytoscape application showcase?
  • Lucene search progress (see  demo)

Wednesday June 11

  • Release M5
  • Bug status
  • M6 goals
  • Portal status
  • BioPAX+ planning
  • Help:Guidelines
    • discussion items
    • additional upgrade needed prior to publication?
  • WP achievement awards and points
  • Martijn's summer visit: flights + housing
  • GenMAPP Workshop for Mike Vanderhaar

Wednesday May 28

  • Community Curation event evaluation
  • 1st & 2nd wp article
  • Getting rid of SWT
  • PathVisio paper status
  • ISMB / Cytoscape retreat / Travel plans
    • Cytoscape application show case?
  • GSOC Status
  • Portals: Zebrafish, E. Coli?
  • PANTHER / WIkiProfessional

Wednesday May 14

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