TableOfContents

2008

January

Thursday Jan. 31, 2008
Mike, Sarah, Allan, Gary, Noel
Notes: Scooter

= ISMB Tutorial =
 * Tutorial was not accepted
 * We should definitely propose a Demo ($400 for a 20 minute session)
 * Will also propose a BOF session covering "Network and Pathway Visualization and Analysis"

= 2.5.2 Release =
 * Release is available for testing
 * Will hold announcement pending backport of Vizmap class cast exception bug from 2.6
 * Goal is to release on Monday

= 2.6 =
 * In bug fixing mode
 * Goal for 2.6 is to make it a very solid release
 * Beta release (to allow plugin developers to port)
   + Sarah wants to do some fixes to the plugin manager first
   + Allan has some work to do on the workflow manager and themes integration
   + Goal is a beta in 2 weeks
   + Mike will do some bug triaging in the interim

= 3.0 =
 * Still waiting for use cases
 * What do we want our use cases to cover?
   + Want to put functionality in context
   + Want to have rationale for new functionality or things that are currently hard
   + Want to record reasons for design decisions
   + Put use cases up for areas of controversy or difficulty
 * Update Cytoscape 3.0 page on wiki
   + Specifically update new features list, 3.0 goals, links to RFCs
   + Include task/status table
 * Mike wants to look at Attribute interface
   + Look at Samad's proposal
   + Sarah will send along Hector's proposal.
 * Discussion points/shopping lists
   + HyperGraphs/HyperEdges -- are they worth it?
   + Break down by layers
   + Big issue: events
   + "Glue things"
     - Events
     - How layers interact with each other (e.g. Application and View)
       o Mike's idea:
         # Application is at top of heap.  Application depends on everything else, but nothing else depends on the application
         # Two examples
            - JActiveModules: pretty easy to see how it might work
            - Cytoscape Editor: more difficult to see how it might interact
         # Command layer is important in this context also
= Other Discussion =
 * Mike has been trying to remove all deprecation warnings
   + Definitely problematic given the current structure
   + Has identified areas where there are opportunities to clean up current code
   + Got deprecation warnings down to around 110

Thursday Jan. 24, 2008
Peng, Sarah, Allan, Gary, Noel, Brian, Maital, Ben
Notes: Sarah

= 2.5.2 =
  * Allan has been using it, no problems 
  * Maital has been using it, none to report

= 2.6 =
  * Bug fixing!
  * There are tasks on the wiki that need to be updated
  * Sarah and Allan will work to get the Workflow Theme up on the site
  * Pathway Commons plugin is nearly ready, may not be fully integrated with the web service API
  * On track for March 1st release

= 3.0 =
  * Use cases still need to be filled in.
  * Have comments on example code ready for Mike's return

= First Cytoscape Talk in Spanish =
  * Allan has been invited to give a talk on tropical diseases on Cytoscape and the Lit Search plugin.  Would like to give a dry-run for anyone who speaks spanish.
  * Cytoscape & List Search being used at a University of Antioch(?) for an interactome of a specific parasite

= Funding for Summer Intern =
  * Allan may have funding for a summer intern to work with him on a plugin of some sort
  * Has to be someone who does not need a visa to work in the US
  * If anyone has a student who would like to do an internship let Allan know

Thursday Jan. 17, 2008
Maital, Sarah, Allan, Kristina, Scooter, Noel, Peng, Gary
Notes: Sarah

2.5.2
-Sarah/Scooter have used it some, need others to bang on it a bit

2.6 March 1st Deadline
VizMapper
- Getting used more heavily now, but it's got some quirks.  
- There appear to be a lot of bugs on the VM
- Needs to be very robust before we release. Everyone needs to hammer on the VM
- When reading in the cys file would be nice to not apply every style as it gets loaded
- Kei is working on all VM bugs that are reported on Mantis so if you find new ones report them

3.0
- Waiting on use cases for graph model
- Samad has proposed a good API for attributes
- Mike's API is in his csplugins directory

Retreat
- Booking space
- Will be planning events shortly so send ideas to Gary

Thursday January 10, 2008
Scooter, Mike, Kei, Gary, Alex, Sarah, Trey, Allan
Notes: Scooter

== SBGN ==
  * Having a workshop in Okinawa.  Should there be a Cytoscape representative?  Costs are an issue for most of us.  Biopax will be sending Emek Demir.  Gary will ask Emek to represent Cytoscape at the meeting.

== 2008 Cytoscape Retreat ==
  * Strong preference for holding the Toronto retreat immediately before ISMB.  The retreat will be July 16-19 in Toronto, Canada, which overlaps with ISMB by one day.

== Cytoscape 2.5.2 ==
  * One outstanding bug (XGMML reader/writer problem).  Scooter is awaiting for feedback from user.

== Cytoscape 2.6 ==
  * Complete in terms of features, now on to bug fixing.
  * Outstanding "issues": Vizmap UI issues, Table import UI issues, Vizmap enhancement request
  * Tentative release date: March 1, 2008
  * Focus on really polishing and getting 2.6 to be a quality release
  * We are unanimous that postponing 2.6 release is the right thing and will be recommended to the board

== Cytoscape 3.0 ==
  * CyAttributes
    * Need both local and global attributes
    * What will the interface look like?
      * Mike is concerned that the code underlying CyAttributes has lots of boilerplate
      * Generics would be a good approach
      * Lists and Map attribute types complicate things significantly
      * Do we want runtime checks or compile-time checks
    * Arbitrary attributes vs. type-specific
      * Lean towards type-specific
    * API needs to be extraordinarily efficient
    * May need to avoid keeping large lists of attributes in memory
      * Interesting idea, but not an API issue at this point
      * Complex type:
        * Replace with the ability to recursively define attributes with the four basic types that you could combine into lists and maps
        * Primary direction: use generics, if possible.
      * What do we put into CyNode, CyEdge, vs. CyAttribute?
        * Everything goes into CyAttribute, including edge type
        * Will require work to provide better UI for merging allowing the user to distinguish between names and edge types
  * Need to develop use cases for Cytoscape 3.0

Thursday January 2, 2008
Scooter, Gary, Alex, Ben, Sarah, Maital, Mike, Peng, Trey, Allan, Noel
Notes: Sarah

== Grant Proposal ==
  * Trey is trying to put together a P41 grant
      * Part 1: Development of new technology
      * Part 2: Collaborative activities
      * Part 3: Service
  * Need info on the collaborative research being done using Cytoscape, list the one or two most important scientific collaborations you have (coauthoring).  Include some text (paragraph) about the project.

== 2.6 ==
  * Bug fixing!
  * Mike will assign some bugs

== 2.5.2 ==
  * Mike put out a release right before xmas
  * Gary’s lab has tested it, most bugs look fixed
  * Ben has checked in a fix to graphics export formats
  * Mike will put together another release after this
  * Need people to run through the test cases

== 3.0 ==
  * Scooter is putting together a 2 layer interface proposal
  * Lowest layer uses ints (Mike’s initial API)
  * Plugin API is all object based, allows for lazy-loading of CyNode/CyEdge objects for large graphs
  * Plan to discuss CyAttributes next week

== Large Networks ==
  * Mike implemented a mysql backed implementation of the API he put together, works, uses less mem etc. Got stuck on CyNode/CyEdge being held in memory