Meetings

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Agenda for next Meeting

Contents

[edit]

Wednesday Sep 3

  • Minutes - email - who will take them?
[edit]

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
[edit]

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
[edit]

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.
[edit]

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)
[edit]

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
[edit]

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
[edit]

Wednesday May 14

  • Newsletter
  • LinkChecker now online: [1]
  • PV article
    • osteoclasts pathway
  • Add zebrafish? user request (from a user that actually filled in the user page!)
  • Plan for tracking WP stats: pathways, genes, users -> table -> graph
  • Curation round protocols, example
  • Toronto
[edit]

Wednesday Apr 30

  • PathVisio article
  • mailing list status
  • GSOC students
  • Efficiency
  • GenMAPP pathways don't open after updating (this bug?
  • Connectors
    • Testing
    • Applying Sjoerd's work
    • Converting all pathways
[edit]

Wednesday Apr 16

  • Ready to release?
    • blocked users deleted from database?
  • Bugs to discuss:
    • ...
  • Are our categorie safe?
  • WP paper revision, due 6/3
    • sticky edge plan
    • user/talk pages
    • portals
    • categories and tags
    • other issues...
  • RFC review
  • GSoC status
  • Travel plans:
    • updates to dates?
    • flight itineraries?
[edit]

Wednesday Apr 2

[edit]

Wednesday Mar 19

[edit]

Wednesday Mar 12

  • Milestone 2: release
  • Major bugs
  • uncommitted changes
  • Wikipathways promotion plan
  • Gramene project: collaboration?
  • Portals
  • Backup/Test site progress
  • Sticky edges: when and how?
[edit]

Wednesday Feb 27

[edit]

Wednesday Feb 13

  • Wikipathways paper: feedback and timeline
  • PathVisio paper: update
  • Feature freeze for WP milestone 1
  • Review Bugs and RFCs
    • yeast id conversion: [2]
  • Webservice example walkthrough: example in perl, example in php, rpc api-doc
  • Onotolgy report by Alex from recent meeting with Nigam
    • 1. BioPortal webservices; write our own applet; populate categories
    • 2. Return flatfile of ontology tagged pathways to BioPortal for 2-way links
    • 3. Integrate cross-ontology mappings to perform ontology suggestions based on gene ontology terms associated with pathway datanodes
  • KEGG and Reactome updates
  • Ideas for including other immutable content, i.e., network analysis results
  • Yugma [3]
[edit]

Wednesday Jan 30

  • Wikipathways paper: next step?
  • PathVisio paper
  • wikipathways automated backups
  • developers mailing list
  • release cycle agenda
[edit]

Wednesday Jan 16

  • WikiPathways Paper #1: Status on tasks
  • Latest WikiPathways Features
  • Testing Protocol
  • Major Known Bugs?
  • New and Updated RFCs
  • NuGO microarray course is 14-18 July 2008
  • Status on Various Other Issues:
    • KEGG
    • Reactome
    • Flat file [Andra's work]
    • Ontology Widget
    • FC Response (none so far)
  • PathVisio paper draft
  • Openstreetmap: [4][5]
[edit]

Wednesday Jan 2

  • WikiPathways Paper #1: Tasks to completed before submission or publication
  • PathVisio Paper: Update and prioritize development
  • Reactome Conversion: Reestablish contact with Reactome collaborators and outline proposal
  • KEGG Conversion: Update
  • Assess OntologyWidget for structured category selection
  • Factoid Capture: Present mock-up
  • new GenMAPP format and conversion
[edit]

Monday Dec 17

  • Dropdown menu testing
  • Factoid RFC
  • ISMB
[edit]

Thursday Dec 6

  • factoid rfc
  • organism names
  • search problems
  • main page refactoring
  • applet deployment problems and fullscreen applet (or webstart)
  • WikiPathways tutorial, any ideas?
[edit]

Wednesday Nov 28

  • Paper outline
  • Server specs and plan
  • Factoid capture
  • Some minor wikipathways things
    • New export file types
    • Sidebar layout
    • View old revisions -> diff viewer?


[edit]

Wednesday Okt 31

[edit]

Wednesday Okt 17

  • Plan for private / hidden / draft pathways on wikipathways
  • Plan for curation / trust levels
  • Plan for supporting full version of PV (and other tools) from WikiPathways
  • Plan for publication
  • Collaborations: Journals (Nature, PLOS) / Chris Sander / WikiProfessional
  • Speed check (server and js loading)
  • KEGG KGML to GPML conversion (maybe other sources for gpml import: NCI PID database)
  • BioPAX update:
    • level 3
    • semantic mapping OLS iHOP
    • PV and GPML changes
[edit]

Wednesday Sep 26

  • Private/group pathways on WikiPathways
    • Compare to private datasets on GEO
  • WikiPathways test bugs
[edit]

Wednesday Sep 12

  • documentation update
  • backpages in new gdb's
[edit]

Wednesdag Aug 29

  • remaining bugs / features
    • nudge
    • ungroup
    • mac version
    • gene databases
  • testing, esp.:
    • c/p
    • undo
    • grouping
    • sticky edges
  • next meeting, about tool integration
[edit]

Wednesday Aug 22

  • PV1.0 Release Schedule
    • Features to include before freeze
    • Bug review
    • Coordinated WikiPathways release?
  • RFC on WikiPathways editing workflows
  • Derby Databases
  • PV 2 development plan: Which features to include.
  • Jar signing certificate
[edit]

Friday Aug 17

  • GSOC
  • New PathVisio features & bugs
    • Undo / Redo
    • all GenMAPP Shapes
    • Groups implementation - ungrouping
    • Snap-to-grid, Snap-to-angle
  • PathVisio + WikiPathways RoadMap, including
    • MIM
    • v1.0 release
    • new Release Schedule
  • Derby Databases
    • the making of
    • integrating with wikipathways
[edit]

Wednesday July 25

20:39, 25 July 2007 (CEST)

  • Bug reports on WikiPathways
  • GSoC Progress
  • PathVisio Dev
[edit]

Wednesday July 18

Time: 11.00-12.00 PDT, 20.00-21.00 CEST.

  • (Andra) Pathway annotation with whatizit.
  • Mapp archive update & Patch testing
  • Groups: Arrow to group?
[edit]

Wednesday July 11

Time: 11.00-12.00 PDT, 20.00-21.00 CEST.

  • GSOC mid-term evaluation
  • New Gene database structure (to enable search on symbols / description), see GeneDatabaseLayout
  • wikipathways TODO list
  • Logistics of WikiPathways-to-GenMAPP MAPP transfer: How do we transfer new MAPP content from WP to GenMAPP archives? (how often, when is a pathway finished etc).
  • Problems with groups in latest PathVisio checkout (StackOverflowError)
[edit]

Wednesday June 6

Martijn:

  • GSOC progress: Martijn and Thomas
  • mailinglist wikipathways & pathvisio
  • pathvisio new release candidate

Chris:

  • Tissue-specific versions
  • Gene name: display and search (see GeneDatabaseLayout)
  • Cytoscape-style selection of downstream genes

Alex:

  • Low hanging fruit: align
  • Groups update
[edit]

Wednesday May 25

GSoC:

  • Second Life: June 20th
  • setup svn branches and diffs for code submission

PathVisio:

  • mac swt.jar --> place each swt.jar in a named subfolder
  • compile error with new libs --> Thomas
  • Groups - update

WikiPathways:

  • GPML info transferred to wiki pages for future development
  • Plan for WAJAX version


[edit]

Wednesday May 9

Time: 11.00-12.00 PDT, 20.00-21.00 CEST.

Thomas:

Martijn:

  • google analytics for wikipathways?
  • pathvisio daily build script now also produces webstart
  • my google blog: http://www.helixsoft.nl/blog
  • wikipathways motto
  • GPML update

Notes from this meeting here

[edit]

Wednesday April 25

Time: 11.00-12.00 PDT, 20.00-21.00 CEST.

PathwayConversion <-- claim your pathways here.

[edit]

Thursday April 12

Time: 11.00-12.00 PDT, 20.00-21.00 CEST.

  1. PathVisio
  2. Google Summer of Code
[edit]

Wednesday March 21

Time: 12.00-13.00 PDT, 20.00-21.00 CET.

  1. Google Summer of Code
  2. WikiPathways
    • windows server for GPML->MAPP conversion
  3. GroupIDProposal
  4. PathVisio & GPML
  5. Databases
  6. results TNO meeting
[edit]

Wednesday March 7

Time: 11.00-12.00 PST, 20.00-21.00 CET.

[edit]

PathVisio

  • Release candidate 1 released
  • Revisit "low hanging fruit?" LowHangingFruit
  • GPML update
  • request system codes for pubchem, chebi and CAS
  • Still need to troubleshoot PV on a mac
[edit]

WikiPathways

[edit]

Databases

  • Did last .zip version will all ID systems work in PathVisio?
  • Update: still working on building Derby automatically, then will crank through all species. Est 1-2 days work, then a species per day.
  • Request for C. elegans gdb
[edit]

Thomas' Visit

  • All set here. Any questions?
  • review Thomas' tasks.
[edit]

Wednesday February 21

Time: 11.00-12.00 PST, 20.00-21.00 CET.

  • Changes to GPML and PathVisio
    • Proposals
    • Division of labour
  • WikiPathways
    • Upload script for GPML & MAPP files
    • Use of templates
[edit]

Wednesday February 7

Time: 11.00-12.00 PST, 20.00-21.00 CET.

  • Stem cell portal
  • Thomas' visit
  • Wikipathways
  • PathVisio changes for converting GenMAPP pathways to full GPML
  • Proposed GPML.xsd changes: GPMLChangeProposal
  • recent changes in pathvisio
[edit]

Wednesday January 3

Time: 11.00-12.00 PST, 20.00-21.00 CET.

  • The new bug tracker
  • opportunities for beta testing
  • future of biopax xsd
  • return of the wiki items
[edit]

Wednesday December 6

Time: 11.00-12.00 PST, 20.00-21.00 CET.

  • The PathVisio 1.0 Beta release
  • Switch to new subversion server
  • Derby databases
  • result UCSF library meeting?
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