TableOfContents

2008

April

Thursday April 24, 2008
Allan, 
Notes: Allan

== 2.6 Release ==
 * 

== GSoC 2008 ==
 * 

== Retreat Update ==
 * 

== 3.0 Issues ==
 * Summary of graph/attribute model email thread is still needed
   - This needs to be reconstructed/organized on the wiki
   - Gary has started a page for this and folks can recontribute their points where appropriate
   - Look for it here: http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0#head-bfe4e806702979251d6c21d9e5e82fe51cf08730

Thursday April 17, 2008
Maital, Sarah, Alex, Peng, Kei, Allan, Kristina
Notes: Alex

== 2.6 Release ==
 * It's out the door!
 * Image export on the mac still has problems

== GSoC 2008 ==
 * We have the final 9!
 * Offer travel scholarship to retreat to Pekka, contact Tero
 * Start working with students on the 21st

== Retreat Update ==
 * http://www.cytoscape.org/cgi-bin/moin.cgi/CytoscapeRetreat2008
 * Any feedback on dates, etc?
 * Organizing committee is forming: send feedback
 * Online registration will be setup soon
 * Let us know if/when conflict with ISMB events arise, there is still flexibility in the schedule

== 3.0 Issues ==
 * Expect email on how to merge
 * Image of project plan now on wiki
 * Summary of graph/attribute model email thread is still needed
   - This needs to be reconstructed/organized on the wiki
   - Gary will start a page for this and folks can recontribute their points where appropriate
   - Look for it here: http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0#head-bfe4e806702979251d6c21d9e5e82fe51cf08730

Thursday April 10, 2008
Sarah, Mike, Kei, Peng, Brian, Noel, Gary, Kristina, Alex
Notes: Sarah

== 2.6 Release == 
 * Trunk of current Cytoscape is going to be the 2.6 "branch"
 * Few people have responded with some small bugs
 * Code has been checked into the trunk that will need to be tested if the release is rebuilt now
 * Will release now, 2.6.1 will come out shortly

== 3.0 ==
 * Look at plan on the 3.0 page
 * Note any fixes made in the 2.x branch will need to be fixed in the 3.0 branch, there will be no merges after the post-2.6 release merge
 * Encourage everyone to check out the 3.0 branch and get comfortable with maven
 * Break out the merge by package and everyone takes a piece.  Mike will send an email about how to do the diff/merge and assign pieces.
 * Sarah will link image of project plan on wiki (and keep it updated)
 * Everyone else will take a look at the plan and give feedback or just be aware

== Google Summer of Code ==
 * This week look at projects and request # of students
 * Need to be sure we have enough mentors for all the projects/students
 * Currently 7 mentors have signed up, need to know how many are definite by tomorrow (Friday)
 * Could use these projects as test cases rather than projects that will certainly be used
 * Need to think carefully about the projects proposed in case they are not useful for moving towards 3.0
 * Also need to talk to various groups that are have already done some of this (see NetworkAnalyzer)
 * Consider involving students who are interested outside the google program as well

{{{Thursday April 3, 2008 Sarah, Mike, Kei, Peng, Maital, Gary, Alex Notes: Alex

2.6 Release

• Any issues?
• Rework help docs in future

2.6.1 Release

• Changes should go to 2.6.x branch
• For the time being, don't bother with trunk since there is no 2.7 planned (may change...)

3.0 Planning Overview

• Separate repository due to major directory changes and build process
• Deprecations cleaned out, initial attempt at modularization, moved to Maven (i/o Ant)
  • - Initial organization to help see the potential modules and the major issues
• Strategy: start with current code and build in new architecture
  • - treat each module independently: impl, test, then continue - the ultimate test for each module is that Cytoscape still works, in addition to functional and architectural goals
• The refactoring strategy will be outlined on the 3.0 wiki page, including schedule, to encourage as much input as possible while also ensuring that things continue to move along

Google Summer of Code

• Mentors can now assign themselves to applications they *might* want to mentor (go ahead and sign up for more than 1 at this point)

• This action will begin to rank the applications (mentored > non-mentored).

• By April 8th, I want to see all applications ranked like this, then we can begin a round of scoring
• In the end, we will assign multiple mentors per student
• Mentors can work with multiple students, but can only be the primary mentor on a single project.

}}}

March

Thursday March 27, 2008
Sarah, Scooter, Alex, Maital, Mike, Ben, Kei, Peng, Trey
Notes: Ben

== 2.6 Release ==

 * A few outstanding bugs (see mantis):
  - inability to import vizmap.props
  - image export (pdf export from freehep is broken)
  - node size width
 * Scooter to make some user manual changes on Monday.
 * Put release files/candidate together early next week for internal testing
 * "Gold" release build files by next Thurs

== 2.6.1 Release ==
 * Scooter to cleanup UI and "hammer on" group node plugin with the goal of it becoming a core plugin for the release

February

Thursday February 28, 2008
Mike, Trey, Scooter, Sarah, Alex, Gary, Allan, Noel, Maital, Alex
Notes: Alex

== Google Summer of Code 2008 ==
 * Ideas Page looks good: http://conklinwolf.ucsf.edu/genmappwiki/Google_Summer_of_Code_2008
  * Keep adding ideas
  * Sign up as mentors
 * Will apply on Mon or Tue
 * Main focus now should be on attracting students to apply for our projects

== Bug Day Wrap-up ==
 * Lots of bugs: good and bad
 * $5 per person per bug; no cap
 * Will talk to Louis about execution

== Error Dialog ==
 * Scooter: managing session errors illuminated utility of a general ErrorDialog service
 * Error list you can append multiple errors
 * Task dialog currently only handles errors singly (an not very well)
  * Could improve on what already exists
  * But, error dialog is more user friendly
  * Can multiple tasks call addError to this dialog?
 * 2.6? Concerns about quick and dirty solution for long-term issues. On the other hand, slate will be cleaned for 3.0 anyways
 
== Case Sensitivity ==
 * Allan: identifier matching are case-sensitive 
 * Defer to 3.0 to find stable solution to broad problem

== CytoRetreat 2008 ==
 * Toronto: July 15-19: http://www.cytoscape.org/cgi-bin/moin.cgi/CytoRetreat2008Planning
 * Give feedback on schedule
 * Will open registration soon
  * Need to determine fee for symposium ($50 or $75, students and presenters free)

== Everyone should be fixing bugs ==
 * If a bug is a suggestion for a change in behaviour, you have the right to reject on principle. Just add note to bug, then close.
 * Cancellation of network and attribute download: leaves unwanted data behind 
 * Will implement if relatively painless. Real fix will come in 3.0

Thursday February 21, 2008
Trey, Mike, Scooter, Sarah, Alex, Gary, Allan, Noel
Notes: Sarah

== Category Names for Plugins ==
  * Mike at Agilent has the VistaClara plugin that doesn’t fit in any current category
  * Should we consider adding categories as requested or wait until we see more than one plugin that fits and then create a category?
  * Resolution: leave categories as they are, in 3.0 consider doing “tags” instead

== Plugins Page ==
  * Bug causing plugins to show up in lists multiple times (per each version)
  * Google for cytoscape plugins takes us to the old plugins page.  Alex will add link to the old pages back to the new plugin page.
  * Eventually move the plugins database to the cytoscape.org server

== Bug Day Friday ==
  * Thanks Alex!
  * Add info to the header for bug day, link to the beta release, bug tracker and the wiki page for testing.
  * Still working out how much and how we give out gift certificates.
  * Sign up on Skype to let people contact you for questions

== 2.6 Status ==
  * Bug fixing
  * Check any bugs you’ve reported, if something needs feedback please try to provide it

== Report ==
  * Trey had discussion with several NIH managers
  * Recommended NCBC (centers) grants, submission date isn’t until Sept 2009
  * Talked to Dan Galahan (NCI) and Genie Larken may be willing to permit a special grant application 
  * Plenty of groups are interested so should be able to get soemthing

== 3.0? ==
  * Wait until next week or until 2.6 is taken care of for further discussion

Thursday, February 14, 2008

Mike, Gary, Scooter, Allan, Noel, Gary, Sarah, Alex, Maital, Kristina, Brian
Notes: Ben

= Cytoscape 2.6 / Testing Day =
 * Must go out before testing day.
   + It's ok to get it out there with bugs as long as known bugs are announced
   + Concern about plugins not working with release, so we say beta is targeted toward plugin developers
   + Beta release 1 on 2/15.  Beta release on 2/22
 * Prize: Top 50 bug finders get $5 Amazon gift card - leftovers to be decided
 * Bugs entered in mantis
 * Use MeBeam and basic chatroom to facilitate communication during testing day

= Bugs =
 * Based on feedback, Mike has been moving bugs to postponed project & reassigning them
 * Hidden Cytoscape directory bug
   + Cytoscape dir gets corrupt if plugin has problem loading and cannot be started
   + Cytoscape needs to be able to startup regardless of what is in .cytoscape, check robustness of plugin manager
   + During testing day, make bogus track_plugins.xml
   + Possible problem with corrupt vizmapper.props file
 * Scooter made update to Task Manager to make it cancelable up to a certain point (before data structures start to get created)

= Cytoscape 3.0 =
 * 3.0 discussions to be postponed until after 2.6 release and testing day

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