TableOfContents

2008

February

Thursday, February 7, 2008

Mike, Noel, Gary, Sarah, Alex, Maital, Kei, Allan
Notes: Gary

Stanford Medical School (Allan) – Agilent collaboration using LitSearch. Needs ~1800 attributes, which is slow. Wondering if anyone else has dealt with this many attributes before? It doesn’t seem so. Open questions: Could Gaggle manage this and just import the attributes you want? There is also the old data matrix code, but that . This is a use case for 3.0.

Cytoscape 2.5.2 – no one has any outstanding bugs. Mike will publish this today.

Cytoscape 2.6 – do we need a contest for fixing the most bugs? People don’t think they need motivation, but rather help with time management. We need to find a way to motivate people outside of the core team to do testing. Alex suggests scheduling specific time to get together virtually to fix bugs e.g. open up an IRC chat. People feel we don’t need a prize. Testing could involve undergrads, but they may not be able to test well – they need some training on Cytoscape first. We should do this early to give us enough time for bug fixing. Also, would be nice if all participants could get a prize, not just one person. Decision: Alex will organize a virtual testing session, likely on Fri.Feb.22.

Status: we are feature complete, just need to test and fix bugs

Cytoscape 3.0 – Mike updated the 3.0 site. Please add your use cases. Mike has been working on his own branch to clean up code and remove deprecation warnings, mostly related to an external library. Did things like remove references to the rootgraph. Mike will keep experimenting on the branch, simplify visual styles. Noticed that current GUI is very spread out, so would be interesting to see how it could be moved into one code area. Merge model layer with CyNetwork, then extract it into an OSGI bundle.

Planning the next stages of 3.0. Mike will create a plan for the model layer on the wiki to focus discussions.
Regroup around the model discussion and finish that up
Attributes
Identifiers

Deadlines: schedule a call to discuss each proposal to ensure people all review the proposal by a given date.
Open issues that are dependent on other layers can be identified and returned to later.

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