Thursday, December 20, 2007
Participants: Gary, Mike, Sarah, Allan, Noel, Brian, Kei, Trey, Scooter, Ben
Notes: Gary

Scheduling – no call on Dec.27th.  Next call on Thurs.Jan.3.2008.

Book chapter – Book chapter opportunity on Cytoscape from ISB if anyone is interested, speak to Sarah.

2.5.2 – Code has the required fixes. Just need to be tested. Question: should we release this given 2.6 is out the door? Yes, so we can fix some basic bugs even though 2.6 is nearing release.

Multiple UI issues with Vizmapper. E.g. it is easy to lose a mapper by mistake and there is no way to get it back. We should really hammer on visual mapping for 2.6 and push 2.6 release out e.g. to February.

Test plan on wiki is being put in place to better test 2.6.  E.g. Sarah found a Windows specific bug.

Allan workflow panel – it is basically ready to go. 1. It is strictly keeping to what’s in Nature Protocols, but some other workflow elements like saving work are not part of this, so Allan will add it. 2. Doesn’t have importing networks from other sources e.g. IntAct.

CyNetwork – Mike Smoot – Waiting for round 2 of update and feedback.
View thoughts – Mike Smoot – API under discussion on list, Mike will check in later today
Identifiers – Gary Bader – seems ok – but open policy issues to be resolved later. Two major issues: 1. support for local vs. global attributes – need to define an API for accessing these. 2. Shared vs. non-shared attributes.
Attributes – Mike Smoot – waiting for feedback on attribute typing issue.

Things to do next: Groups, Hyperedges and Projects
Main issue is separation of groups, hyperedges, network. We want basic graph algorithms to work. UI is important to avoid complexity for users so they don’t have to choose one set of e.g. group aware plugins given a graph that has group information.

One hyperedge use case is representation of metabolic networks.
Scooter proposes have a 2 layer model. 1 layer is basic graph, 2 layer contains hyperedges and groups that could be given for plugins.

One problem with putting graphs, groups, hyperedges together is that the API becomes too complex to implement, as happened for Cytoscape 2.0.

Idea of a core vs. plugin APIs. Everything is made public via OSGI. Current assumption is that everything we’re building is public.

Thursday December 13, 2007
Sarah, Alex, Scooter, Maital, Hector, Brian, Mike, Kei, Peng, Gary, Allan, Trey, Noel
Notes: Sarah Killcoyne

== Model ==

What broad functionality do we want the model to expose in the interface?

- Group, Attributes are part of the model layer
What happens when I remove a node?
        Edges get deleted
How do we inform other model aspects (groups, attributes etc)?
        Fire an event (Mike)
        So the Group for instance would have to listen to an event and update itself.
At what layer of the model should a plugin layer traverse the network?
        At the model layer.

Scooter: challenges
Network traversal with metanodes (special imp of groups?).  Have to add and delete group node into the model, seem to have to keep my own separate model

Trey: attributes can/should track it’s set of nodes, references etc.

The answer to groups may be recursive networks. Do not need special model to handle groups/hyperedges.

Hector: Interface to be exposed needs to be clean and simple ASAP, the implementation can change underneath and it should not matter to the plugins.

Need to classify what types of things are being done or types of things people want to do with a graph.  Look at the CLR algorithms book, think out some pseudo code and write to that.

2 ways to do this:
1. Design from the plugin developers point of view, abstracted from the graph
2. Design from the underlying implementation of our graph, abstract at a low level to allow for performance

Thursday, December 6, 2007
Attendees: Maital, Brian, Sara, Gary, Piet, Kristina, Mike, Kei, Peng, Noel, Ben, Allan
Notes: Gary

Cytoscape 3.0
        -Maven: Cytoscape is using modules – Brian recommends moving away from modules to make things simpler. Either move to a single POM where everything is one src directory and compiles from there OR each module could be its own project with dependencies between them. The modules add unneeded complexity.  Also, there is a project called artifactory – a web enabled Maven repository that would allow us to put our libraries in one place for all projects.
        -Setting up a list for cytoscape 3.0 discussion – let’s use the cytostaff list with a subject prefix e.g. ''[Cyto3]''. We will publish something on Cytoscape discuss only when we have something that we’re happy about for review, since broader review will require better documentation, etc.
        -Model discussion – 2-3 bigger issues identified by wiki discussion at http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/Model, many smaller issues resolved – discussion of these bigger issues will move to cytostaff mailing list and conference calls as needed.

ISMB tutorial – dates for retreat? Gary will organize. How many people going to ISMB? Seems like quite a few. Tutorial is on Google Docs ready for input. Speak to Mike if you want to access the document. Contact with Yeyejide will be reinitiated by Piet and Mike.

2.5.2 maintenance release – anyone tested 2.5.x release branch? No, but people can check it out from svn and start testing. Mike will check if the XGMML bug has been fixed in the 2.5.x branch, will let Gary know and Gary (and maybe others) will start testing.

Cytoscape 2.6 – filtering is almost done. 2-3 day ETA
Themes: Nature protocols would be the main one.
Multiple network selection is checked in. Delete, layout actions are implemented.
Modal label positioning – not likely part of 2.6
Workflow panel – this is close and will be part of the Nature Protocols Theme.
Pathway Commons – no updates in past week, but more work to be done by Ethan and Ben required.

Dec.20 is the code freeze date.


Thursday November 29, 2007
Sarah, Scooter, Alex, Piet, Brian, Gary, Mike, Peng, Kei, Allan
Notes: Alex

== Agenda ==
 * Session Bug
 * Cytoscape 3.0
 * ISMB Tutorial
 * Cytoscape 2.5.2 and 2.6

== Session Bug ==
 * Scooter and Mike are making some progress on dissecting examples from Matthais and Paul, however, no one has been able to reproduce the error
 * Clues: 
   * xGMML filenames don't match manifest file
   * old filenames are not updated within xGMML
   * there may be a parsing issue dealing with "-0" somewhere

== Cytoscape 3.0 ==
 * Sarah and Mike have 'model' compiling and are now tackling 'view' and 'i/o' which will be slow going; Mike will send out a link
 * Sarah got advice on MVC: any data that is being saved should go to 'model' (i.e., coordinates), while the 'view' decides what to do with the data
 * Scooter has a model of 3.0 classes at http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/Model
   * Brian will update with model with a clearer separation of nodes per network
   * Scooter's current model will be versioned for future reference
 * Brian will review progress with bundling and Maven; Sarah will send out a link
 * For 3.0 we are removing ALL depricated code, so delete at will

== ISMB Tutorials ==
 * Deadline for submission Dec 12th: anyone want to take the lead?
 * Plenty of materials available from the tutorials at the retreat
 * Submission materials will be sent around to the cytostaff list

== Cytoscape 2.5.2 and 2.6 ==
 * 2.5.2 is a maintenance release: next couple weeks, just in time for the holidays!
   * bug fixes: session file, xGMML saving bug, slow selection due to undo
 * 2.6 features: should be in beta before xmas
   * Mike has in-memory saving and label positioning lined up for 2.6
   * Kei is making progress with web services
   * Peng is looking into QuickFind bugs related to listening for NetworkFocused and updating deletion events(?)
   * Themes are ready to go once the Perl script and database are updated
   * Allan has a bit of work left on workflows
   * Allan is researching hooking licensing into the website 

Thursday November 15, 2007
Noel, Maital, Gary, Mike, Sarah, Scooter, Brian, Piet, Peng, Kristina, Ben, Allan, Kei
Notes: Gary

Plot course for 3.0
Two tracks – start modularizing, define model

Modularizing track:
Osgi vs. spring vs. felix vs. equinox
Determine package structure without

Raven doesn’t have a broad user base.

Decision: start an SVN branch, push code where you want it just under the five major blocks, then clean up, handing out to multiple people. Eclipse refactoring tools will help.  Goal: keep code compiling while we’re relayering, although it will break every now and then.
Mike will set up SVN for clean slate, with Maven, and basic package structure
Sarah will move code into main packages.
Target: next conference call, 2 weeks from now (after Thanksgiving)

Do people like Maven?  Yes, but mainly for code and library versioning support. Not for documentation yet.

Core plugins will be their own bundles.  Core libs – not sure, but eventually seen as part of the overall package, but will probably be bundled up and moved around with e.g. osgi.

Model track:
Start javadoc of interfaces for review – create RFC for the model and link to javadocs. Scooter will do this and have it up in 2 weeks.

Licensing and plugins – two issues. Logging downloads for plugin writers – need this for plugin manager. Allan and Peng will work on this. Network analyzer (Mario Albrecht) plugin also wants this.

Testing - http://www.cytoscape.org/cgi-bin/moin.cgi/CytoscapeTesting – developers should volunteer to write test procedures for all of the menu options – email Mike. Goal – we should be able to run this test plan for 2.6, so there is some urgency.  Unit tests would also be useful.  Should send this out to the Cytoscape users list after it is complete. Test procedures should be written with specific data/networks listed.

New maintenance release 2.5 – XGMML + event handling
Have this as an agenda item for next call – should we release a 2.5.2

Status 2.6
Filters – ongoing - Peng
Biomart – fixed web service changes - Kei
Event fixing - Mike
Pathway Commons – Ben will send a movie of the latest Pathway Commons plugin. Wondering how this will interact with Kei’s web service API.

Topics for next time
Wiki spam
2.5.2 maintenance release

Next conference call in 2 weeks.


Thursday October 25, 2007
Present: Scooter, Mike, Ben, Allan, Sarah Killcoyne
Notes: Sarah

  * Scooter sent Piet abstracts on tutorials for CyGroups and Layouts
  * Mike doing vizmapper and web services
  * Discuss properties/config wizard

  * Themes: pretty close, have a couple of bugs to work out in deleting themes.  Code is checked in may demo through Allan’s workflow in Amsterdam
  * Properties: not started
  * Workflow needs tooltips and a front page, mostly done
  * XGMML: done
  * Network from Pathway Commons: API is working, UI in construction
  * Undo & performance issues fixed

Board Report
  * Sarah working on putting the RFC’s that were put up into a report form for the board.  It will be sent out to the core group first no later than Monday morning for any  comments/edits then to the board on Tuesday.

Error Handling: New RFC - Scooter
  * Macs/PCs loses output because we use ad-hoc methods
  * Would like instead to write to a log
  * Mike suggests we wait until we’re using OSGi because they offer a logging service
  * Put up RFC for discussion of adding just a logging system or a full exception handling system

Message on Helpdesk
  * Degrees on nodes, are there plugins that handle this issue already?
  * Does degree-sorted layout handle it, check with Samad or look at code?
  * Wait until discussion in Amsterdam regarding network analysis plugins

Thursday October 4, 2007
Present:  Mike, Kei, Peng, Gary, Kristina, Allan, John, Bruce Herr
Discussed items

Discussion about problems arising due to conflicts between XGMML and vizmapper
-Scooter and Alex have a fix, involving toggling a flag to save states, but there are defects. 
-This is fairly early in the process, and further issues may arise.

Discussion about meeting in Seattle
- Alex asked about which RFCs people should concentrate on for the meeting. 44,46 and 47 and related RFCs were suggested.
-The agenda will be on the wiki and will include details about what should be covered in the over view of other products session.
-If there are any problems/questions then people should email sarah and john

Discussion about the retreat
-there will be an informal discussion session on the monday

Features for Cytoscape 2.6
-Pang will work on filter redesign (should take about a week to refactor the GUI)
-Mike's work is action event firing is on hold
-Kei has checked in his web service client manager, have had conversions with Pathway Commons group as well (Ben and Ethan are working on it)
-Mike will go through bug list and assign tasks
-In memory session saving is completed (but requires testing)
-Workflow panel work is ongoing (and is checked in "natureprotocalsworkflow")
-Scooter is fixing defects on XGMML parser
-Scooter has checked in code for loading a network from a URL (requries testing)
-Plan is to have an alpha by the retreat


Thursday September 27, 2007
Gary, Mike, Ben, Peng, Kei, Sarah, Alex, Allan, Scooter
Notes: Sarah

== 2.6 ==
  * Themes - code in progress, implementation plan on RFC.  
  * Workflow panel -Workflow plugin may be generalizable for use in other themes.  For architecture group Taverna’s workflow should be researched for future development (NOT 2.6)
  * Filter UI - design document written, coding will begin next week.  Dynamic filters are almost done, gui next week
  * Refactor  Network Mgr - code in progress, working on retrofitting areas that use getCurrentNetwork() to getSelectedNetworks().  Messy code in the Cytoscape class!  Goal is to have initial event handling code checked in by the end of the week.
  * Web Service Client Mgr - First draft of RFC is up please make comments. Implementing sample clients based on the RFC design.  BioMart nearly done, currently working on clients for network import (IntAct, NCBI).  How will attributes be named from different network imports?  Some sort of standardized naming scheme?
Core changes, WebServiceClientManager - lists clients currently available.  Working on UI for the mgr.  
  * Modal Label Positioning - no progress
  * Bugs - everyone!
  * In Memory Session Saving - done
  * Properties - not started
  * XGMML - mostly done, some bugs being worked on
  * Pathway Commons - discussion on Friday, Ethan has been working on some mockups
  * Load Networks from URL - working on it, needs to be done for GML and SIF.  New method added to the FileReaders to get the mime types

== Status update Ethan: ==
PhD student at Cornell, working part time on Pathway Commons currently.

== Bruce Hurr(??) ==
Network Workbench architect visiting UCSD.  Mike will be working with him to learn OSGi.

== Paper/Book chapter Status ==
  * Gary working on the chapter
  * Trey hasn’t heard about the Protocols paper, not yet published

Thursday September 20, 2007
John, Sarah, Alex, Ghislain, Mike, Kei, Peng, Kristina, Ben, Allan, Scooter
Notes: Alex

== Seattle Pre-Retreat Meeting ==
 * Who? Allan, Mike, Scooter, Alex
 * When? most arriving Wed night, sharing a rental; Scooter arriving on Saturday via Portland; Alex on Monday, staying with friends
 * Prep work: Look at other apps for a distillation of key relevant features
   - PathwayArchitect - Allan
   - VizAnt - John
   - BiologicalNetworks - Mike
   - GeneGo - Sarah
   - TerraNode - Sarah 
   - Ospre - Scooter
   - Pajek - Sarah
   - CellDesigner - Sarah
   - Patika - Emek/Ben?
   - Ingenuity (IPA) - Alex
 * Timing: start around 9am?  Sarah is working on schedule and will coordinate by email.
 * Mike will meet with BioWorkbench guy just prior to the retreat
 * Results of the meeting will be presented at the retreat on Tuesday (not Monday)

== Board Meeting Review ==
 * Mike gave status report; Illia presented proposal; Trey promoted workflows.
 * Pre-retreat meeting should produce a prioritized shopping list within the constraints above to facilitate board decisions.
== Retreat Questions ==
 * All developers need to register; when asked to pay, simply choose "invoice" and you will *not* be billed.
 * How to indicate room details with Doelen?  We assume the retreat organizers will rearrange rooms efficienlty, just indicate roommate preferences in your email to cytoretreat@cytoscape.org
 * Check your passports!

== Cytoscape 2.6 ==
 * Themes: RFC 48 ready for comment
 * Filters: progress
 * Network Manager: Mike
 * Web service client types defined, e.g., attribute, network.
 * Modal Label: just needs a little dedicated time
 * Bugs: Mike will prioritize
 * Session saving: everyone should TEST
 * Properties: Sarah will begin work on it soon
 * Workflow Panel: Allan has started work. Trouble with CytoPanel 3 (East)
 * xGMML: rename "network URL loading improvements".  Estimate 60% complete. Use of Abstract classes with better handling of null.
 * Load Networks: Ben is refactoring; Ethan and Kei should work together on Web Services with Pathway Commons.

Thursday September 13, 2007
Alex, Scooter, John, Mike, Kei, Peng, Sarah, Ben
Notes: Alex

== Retreat Questions ==
 * Conference Hotel = Doelen?  Is there a conference rate?
 * Scooter's travel funds?
 * Use the site to register, but DON'T pay :)
 * Demos and Tutorials: Unilever will be giving tutorials to general audience.  Demos are for plugins.  We should develop a process for signing up.
  * post sign-up opportunity on cyto-announce + discuss. Alex will post.
  * tutorials for developers? Topics: plugins, layout, group viewer, vizmapper, web services. Present at retreat, then refine presentation for posting on wiki page. Mike will present this idea to board.

== Board Meeting ==
 * Next Wed morning
 * Contact Mike with any questions/issues for the board

== Retreat Pre-meeting ==
 * Seattle, Oct 11-12th
 * Sarah will coordinate agenda. Send her ideas. Scope will be better defined after board meeting.  Major goal is to get everyone on the same page talking about the same thing.
 * Note: Cytoscape comparison to other apps published in Bioinformatics

== 2.6 ==
 * cPath plugin is targetted for 2.6. Ben will coordinate with Kei.
 * Scooter will work with Mike on the xGMML part of in-memory session saving.
 * Kei and Web Services:  class loader issue with plugins installed after startup (i.e., via Plugin Manager)
 * Peng and Filters: something ready next week
 * Themes: RFC will be posted today
 * Bugs will be prioritized and posted on 2.6 list by Mike
 * Follow through with deprecations. Giny will be an exception.
 * Goal: beta (or a good alpha) for retreat

Thursday September 6, 2007
Notes: Sarah
Mike, Kei, Peng, Allan, John, Ben, Ghislain, Sarah

== 2.5.1 ==
  * Released by Mike yesterday
  * If 2.5.2 needed let Mike know

== 2.6 ==
  * Themes: Sarah & Alex - basic use case can be supported.  Don’t use the word ''bundle'' (conflicts with the OSGi concept of bundles)
  * Filter UI design: Kei has design and mockup together est 3-4weeks, then work on algorithms
  * Attribute namespaces: punted
  * Refactor Network Manager: Mike working on this
  * Web Service client Mgr: Kei put together prototype in csplugins directory.  API to communicate with core not finalized.  Sarah & Alex will work with Kei to finalize.
  * Mobile Label Position: Mike - make small change to label position dialog to make it simpler to use and update dynamically on view.  ~1 week
  * In Memory Session Saving: Mike has figured out a way to do this, may be fairly easy
  * Properties: Mike/Sarah/Scooter will work on major refactor but not for 2.6.  For 2.6 we will tweak bookmarks to work a little nicer (Sarah).
  * Load Networks: punted
  * XGMML improvements: Scooter has already checked them in and no one has complained so far, needs testing
 *  Clean up old bugs EVERYONE ongoing

== Pre-Meeting ==
  * Alex, Scooter, Mike, Allan, Ben, Sarah, John
  * Need to work out when/where.  Early Oct? San Francisco/Seattle/San Diego?

== Network Import ==
  * Mike sent an email out last week regarding this
  * Kei/Sarah working on web service for id mapping and we may want to do something similar for network import (Mint, Reactome, Dip, etc)
  * Somehow use ''Tunables'' to allow user interaction with the type of data we can get back

== Expression Data ==
  * Agilent doing a plugin for heat-map visualization, should tool require data be in specific format (exp/sig)?
  * Tool needs metadata about attributes
  * Current exp format is kind of a hack and can’t really be relied on
  * No formal substitute to id p-values, either check the attribute or ask the user

== Plugin Website ==
  * Soon to be released, need to handle issues with plugins not having correct props/manifest files first


Thursday, August 30, 2007
Scooter, Mike, Kei, Peng, Kristina, Ben, Allan
Notes: Mike

-- Retreat Questions --
 Where to stay?
 Who registers? Do we all pay 40E for the symposium?
   Not sure...
 Who is doing the demos/workshops?
   Not sure... Alex will write email.

-- Release 2.5.1 --
 Image export bug is fixed
 New session file for galFiltered sample data

-- Pre-meeting for 3.0 --
 Significant changes on the table for 3.0, requiring serious discussion to hash out detials.  This is probably best done in person.  The day before the retreat is probably too late.  We are all west coast (except Ben). We might pick UCSF and patch in Ben via iChat.  Tentative dates: Oct 18-19? (Ben might be able to come via Marathon trip, and Gary may be able to stay in town after BioPAX). Mike will send email.

-- 2.6 Development --
 * Cytoscape Themes: Basic idea for 2.6 is to introduce the concept of 'bundle' to Plugin Manager to allow the installation of multiple, functionally related plugins.  Scooter suggests including a vizmap.props and other session file features along with the plugin bundle. Alex will write up RFC soon.
 * Filters: Combination of boolean is done. Now focused on dynamic controls. 
 * Attribute Namespace: pushed to 3.0
 * Refactor Network Manager: Allow selection of more than one network for application of layouts, for example.  getCurrentNetwork() will, of course, still work as is.  
 * Web Service Client Manager: (1)Web start manager. Integrate with ISB's plans. (2)UI. First UI is being developed for BioMart. Will upload prototype next week to csplugins for us to play with.
 * Modal Node Label Positioning: Allow users to drag labels around. Mike is considering a mode versus a keyboard control. Introducing a mode may be problematic. Alternatives include keeping the current override mechanism and just make it more intuitive (easier), or to look into an Editor solution (harder).  Let's try easier solution first: provide visual feedback for node label changes and alter gravity for selection.
 * Bugs: lots of 'em!
 * In-Memory Session Saving: should take just a week or two.
 * Properties: make get punted.  Mike will follow-up with Sarah.
 * Pathway Commons Plugin Update: work will start after MSKCC grant due Sept 25th. Therefore, may not be 2.6. Kei is looking at general solution for loading networks from multiple sources. This work could extend the same pattern used for Layout Broker and Web Service Client Manager.
 * xGMML: Essentially done. Let's bang on it and keep your eyes open for oddities.

Thursday, August 23, 2007
Participants: Mike, Allan, Scooter, Gary, Trey, Ben, Sarah
Notes: Ben

Retreat funding:

Scooter to check w/Annette & Guy (retreat organizer board) if funding exists.  Possible money freed by Ethan

Editor Bug:

Allan to try and fix over the weekend, then 2.5.1 can be released on Monday.


Scooter doing lots of work on XGMML reader/writer.  New one uses about 1/3 less memory and about 25% faster.  Speed improvements achieved by incrementing the document format and making changes in the XGMML file that is written.  However, 2.6 would not be read on a 2.5 cytoscape (some vismap changes would be lost: node: translucency, label font, line type....edge: source/target arrow, line type, source/target arrow color.  Scooter added Cytoscape namespace.  Now using SAX parser, not JAXB.  No intermediate objects saved.

Scooter to checkin code, less complex attribute code for testing.  He will then continue to work on adding complex attribute support.


People to add task time estimates to 2.6 wiki page.
Scooter:  Is adding attribute namespace support feasible to do in 10 weeks ?  Mike to rethink task and return with thoughts next week.

Please continuing making comments on Cytoscape 3.0 RFC's on wiki.  Maybe turn render study group into 3.0 architecture group for a couple weeks prior to retreat.

Thursday, August 16, 2007
Participants: Ben, Gary, Alex, Sarah, John Boyle, Mike, Kei, Peng, Allan, Kristina, Ghislain
Notes: Gary

2.5.1 – Mike is still waiting to do this.  Hoping to put this together shortly.
  A number of bugs have been fixed.  Plugin manager webstart bug that Mike Creech reported is not yet fixed.
Cytoscape 2.6
-Follow up on email by Mike after discussion with Trey – make Cytoscape easier to use by removing micro-barriers. Seems to be general support for this.

MSKCC will likely focus on pathway commons connectivity to Cytoscape
How would this affect the priorities that we came up with before?  People need to reevaluate their priorities listed on the 2.6 page.

Goal with 2.6 would be almost all bugs closed, unit tests, additional testing. We would need more user and tester involvement

RFCs – John Boyle discusses re-architecting for 3.0.  ISB is producing 4 RFCs 1. Relayering 2. Plugins 3. Integration and 4. Componentizing
These will be out in the next few days.

Should we have a pre-meeting to discuss architecture?  Yes, but not sure about the date.  One idea was early or mid Oct and another was the Monday before the retreat – Nov.5, but it is not clear that everyone can make the latter. We should coordinate to find an appropriate date.  Some people could conference call in.

Google summer of code – It ends Aug.20. Students were very productive and we should do this again next time.  All of our students passed, which is unusual compared to other projects.

Thursday, August 9 2007
Mike, Kei, Peng, Scooter, John Boyle, Sarah, Ghislain
Notes: Sarah

        - Can’t read large networks into Cytoscape with xgmml, problem for the session file too
        - Scooter put together couple of approaches to deal with the slow loading
                1. Rewrite xgmml writer to not use JAX, no benefit from JAX and it’s slow
                2. Switch reader to use SAX instead of JAXB - Kei has a different approach that is more incremental and improves memory use, but may not improve performance.  Maybe try Kei’s work first then try for better performance with Scooter’s approach
        - Think about how xgmml is read in over a network, currently entire file is read in and written to a temp file and no processing is done.  Could this be done while reading the stream instead?
        - Currently not handling graphics data/layout data as we’re reading the xgmml, we could instead do it as we read instead of keeping the large argument around
        - writing some elements out to xgmml poorly, not using namespaces can fix this and keep backword compatibility
        - Mike suggests spending a day or two (Kei and Scooter) looking at current code for performance improvements.  If there is nothing further to be had then switch over to Scooter’s approach with the SAX parser

Cytoscape Dev Meeting (John)
        - Hold a special session regarding architecture document
        - John has talked to Annette, Lee, Ilya and Gary, will be talking to Benno and Guy soon 
        - Would like to have a session at the beginning and a short one at the end to discuss the architecture
                - Good idea, lets also talk lots about this beforehand and put RFC’s up
                - Need to know about how long things will take, what sort of deliverables, what groups can/will be involved etc in the RFC’s
                - Answer the question ''where do we want to go with Cytoscape?'' 

        - Need to look more seriously at RFC’s in terms of  the costs, the time involved, resources
        - Everyone read/comment to start the discussions before we go to Amsterdam to be sure we have enough time to discuss everything
       - Should we try to get together somewhere else for a day or two ahead of time to hash things out?

        - Need to pare down the features to go into this release, may be easier to do if we are sure the next release is 3.0
        - Keep this small so we can release in January (on time), maybe mostly polishing
        - Punt spreadsheet capability, layered graphics(?) 
        - Discuss namespace further, Mike suggests making them hierarchical.  Implementation may be too big for 2.6??
        - By next week we need to be able to decide what we will work on, keep in mind it will be small (we want to narrow the list) and that we will also be doing some work on 3.0 stuff

Thursday, August 2, 2007
Participants: Mike, Allan, Gary, Alex, Sarah, Christina, Ethan
Notes: Gary

2.5.1 – Mike would like to put this release out next week (e.g. Wed) to cover a Mac graphics export bug which Samad has fixed. Some other details, menu enabling, vizmapper.  If you have other bugs you want entered, you need to make sure you check them into the 2.5.x release branch.

MIM – Allan is taking the lead, MSKCC is interested in being involved. Ideally NCI would get involved.  Allan added this and listed features in increasing order e.g. snap to grid.  Some of these will be 3.0 issues, but at least they are up on the wiki.

Support for layered graphics – Ben is taking the lead, Agilent, Gladstone

Cytoscape themes – Sarah and Alex will work together.  using the plugin manager with theme files. E.g. expression analysis and time course data themes. Nature Protocols theme. Biology theme vs. network analysis theme (e.g. network analyzer). These could be defined by props files, which could be distributed.

Dynamic filters – should be doable in the 2.6 time frame. Peng will take the lead.

Consolidated graph analysis plugin – ideally will get the network analyzer folks involved. Kei is taking the lead.  Could be a graph algorithm library and a separate UI.

Spreadsheet capability for attribute browser – may be better for 3.0. Allan: Robert Kincaid built a tool called VistaClara, which is a nice visualization system with spreadsheet functionality.  Not developed in a product ever, so it may be made into a Cytoscape plugin.  Mike Creech will take the lead.  Waiting for it to become official before any further specification.

Scripting – Kei will take the lead – Scooter interested. Need some discussion on vision for this feature, full scripting interface (Kei’s prototype in ruby) or simple commands (Scooter’s prototype). Some concern about allowing scripters to access to everything. Ideally would have a simple scripting API with a few actions (e.g. link directly to Cytoscape actions – this should be explored more). This connects to workflow, which could be included in a theme. This could be like Microsoft Office, where you have UIs, macros, scripting and programming. E.g. bean scripting framework, with different scripting language plugins (part of Java 1.6). Mike ''It sounds like this opens up a big can of worms. But, a very powerful bionic worm.''

Attribute namespace – we need to collect use cases – been started on the RFC. No lead yet (probably Mike).  Scooter, Karl, Daniel Abel are interested.

Properties - 

Graphics export – actually done for 2.5 by Samad before release.

Network manager to support operation on multiple networks

Refactor event handling, GINY and others – should be moved to 3.0

Undirected edges – Daniel from Hungary is interested.  We need to support this. Mike will take the lead on this.

In memory session saving – avoid problems with temp files

Better headless mode

3.0 – more next time.

Eccentric label feature RFC is posted by Ethan, will send around a prototype next week.

Cytoscape book chapter – Natalie has worked on it for ~1 week and wrote quite a bit – Gary will send this out to the other authors.


Alex, Sarah, Scooter, Mike, Kei, Peng, Ethan, Ben, Allan

Thursday July 26, 2007
Notes: Alex

== Cytoscape 2.5.0 Release ==
 * Congrats and great job, everyone!
 * No major bugs reported yet; some minor bugs
   - menus, vizMapper, image export (mac)
 * 2.5.1 timeline?
   - Minor bugs
   - Hyperedge plugin
   - Plugin Manager: new class loader per plugin issue
   - next couple weeks; then 2.5.2
 * Need for a helpdesk position?
 * ISB/John Boyle's document: send to mailing list

== Plugin Website ==
 * Ready to go?
 * Finalize, test, and announce

== Next Release: 2.6 Planning == 
 * Plan for smaller release right after Retreat
 * Then Retreat can focus on major 3.0 release
 * To branch or not to branch: for major changes to the tree for 3.0
 * We should keep 3.0 plans in mind when prioritizing 2.6 features
   - e.g., attribute namespace, scripting, etc
   - these may be lower priority with the major API and event handling changes planned for 3.0
 * Theme release via plugin manager?
 * Everyone should be picking features they can dedicate time to, for 2.6 and 3.0 planning pages
 * Goal: get a prioritized feature list together before the board meeting in Sept for their feedback

Mike, Kei, Peng, Alex, Scooter, Ben, Ethan, Gary, Trey, Allan

Thursday July 19, 2007
Notes: Sarah

== Cytsocape 2.5 MONDAY JULY 23 ==
  * Low priority bugs for 2.5.1?
  * Most current bugs are for the new functionality (vizmap, plugin loader, filters)
  * Everyone will go through their bugs, decide if they can be fixed quickly or are high priority to fix for this release       
  * Ready to release?
  * Everyone needs to glance at documentation, make sure all sections are there  
  * Mike will create release files, everyone will test
  * Alex will update webstart and release notes
  * Release will occur on noon Monday
== Image Exports ==
  * Samad using iText to export to PDF, jpeg, bmp, png
  * Get SVG working from Batik?
  * Warn users that Freehep is going to be removed for 2.6 via cytoscape-announce and README file in lib/
== Plugin Website ==
  * Roll out what we have with 2.5
  * Talk next week about how to tell plugin developers about this
  * How to handle plugins that get submitted and break Cytoscape

Sarah, Mike, Peng, Kei, Alex, Allan, Gary, Ben
Thursday July 12, 2007
Notes: Ben

== Nature Protocols Paper ==
Paper went out last week, only outstanding issue is webstart 
 - Mike: no problem if plugins/prop files is put in correct place, problems appeared to be caused by old props files
 - All four plugins mentioned in paper will be included in webstart (including BINGO, Mike S. reduced its size from ~60MB to 9MB)

== Cytoscape 2.5 Beta Release ==
Outstanding Bugs
 - 110 bugs not resolved, 1 high priority, about 50 updated or reported in last 3 weeks
 - high priority bug (1441) relates to graphics exporting.  Solution, replace freehep with batik or java/itext.
 - beta 4 released tomorrow afternoon (UCSD to address bug 1441 before this release)
 - release will probably be pushed back one week (7/23)
 - People should continue updating the manual when appropriate
 - Natalie (student in UToronto) will continue working on manual for the rest of the day then goes away for two weeks

== Misc ==
ID or Canonical Name Attributes for Edges
 - "Canonical Name" attribute for edge should be created and will be mutable.

Strategic Plan / Future directions - ISB (John Boyle)
 - Proposal from Lee Hood to take Cytoscape to next level, rearchitect, refactor

Mike S. - conference in Switzerland
 - Workbench, network visualization platform/workbench (Indiana U)
 - based on OSGI platform (eclipse)
 - clean way of enforcing modularity
 - potential use w/Cytoscape

Ethan, Alex, Sarah, Ghislain, Kei, Peng, Allan, Gary
Thursday July 5, 2007
Notes: Alex

== Pathway Commons ==
Ethan: New Release! pathwaycommons.org
 - more accessible query methods via full web API
 - vizANT folks might try to use API
 - Ben put together a webstart version of Cytoscape that starts from within PC
 - can pull in network neighborhoods and merge networks
 -> try it out and give feedback

== Cytoscape Future Visions ==
Allan: Wants to put together a few bulletpoints of future directions
 - Biological Content (PathwayCommons)
 - Network Analysis (Trey and Gary)
 - Enhance Representation (GenMAPP)
 -> Can generalize to ~"biologically relevant views of the model for cellular representations"
 -> Allan will send out email for additional feedback

== Nature Protocols Paper ==
Allan: Paper Post-Mortem
 - was resubmitted (we pressume)
 - Bingo was removed from webstart, to be loaded as plugin from website: not working?
 -> Peng is working on some aspect of this
 -> we need to send a message to the Bingo folks to get their help 
 -> go through protocols to check working status: Allan (pc) and Alex (mac)

== Cytscape 2.5 Release ==
Buggy Issues
 - Webstart Fix (above)
 - Plugin Manager: License agreement encoding into XML has a minor bug
 - Plugin Proxy Caching bug
 - Proxy Support bug (URL Utils)
 - Revision versions of coreplugins from Ant builds? Mike?

 - Hyperedges: new jar uploaded and documentation in progress
 - vizMapper UI: 2-3 more major bugs, but should be fixed soon
 - HelpDesk: need to add new FAQ
 - Filters: works, but has a nasty bug related to data model state of sliders prior to view
 - Library Reduction: finished
 - Release Date: July 16th
 -> Need more testers!
    - Filters
    - VizMapper UI
    - Plugin Manager


Ghislain, Mike, Sarah, Melissa, Scooter, Allen, Kei, Peng
Thursday June 28, 2007
Notes: Sarah

== Paper ==
-Melissa has addressed a lot of the feedback still missing
        - sample data
        - description of jAM/MCODE interfaces Trey & Gary will look at this
- Software, Allen has new version of plugin ready he will upload it to the website and Melissa will test the webstart
- Will provide reviewers with a link to install 2.5 in case webstart doesn’t work
- Allen will copyedit

== Plugin Stuff ==
- Will switch the getPluginInfoObject() method to a plugin.props file that describes the same information
- Core plugins will need to know what their unique id is from the database and add that to their props file, all others can just switch to a props file instead of a method
- Cytoscape database can then use the props file to get the information about the plugin instead of asking a user to input it all again

== Beta Status ==
- beta 1 was sent out this week not offered publically yet
- one bug in quickfind, exception is thrown but not handled
- beta 2 will be announced publically on Friday 

Mike, Peng, Kei, Alex, Allan, Sarah, Ben, Ghislain, Trey (9:37)
Thursday June 21, 2007
Notes: Alex

== SecondLife ==
- fun opportunity for social gathering
- not necessarily the best medium for a working meeting

== Canonical_Name ==
- deprecated for over a year, so Mike yanked it
- issue: function to copy identifier to canonical_name
- now there is no atribute linked to identifier
- solution: keep it, rollback changes and undepricate canonical_name
- follow-up with Gary and Trey

== Nature Protocols Paper ==
- submission deadline: end of the month
- key plugins don't yet work with 2.5
- we only need to be generate figures for the paper, but we need to fix the plugins for 2.5 release anyways so let's work towards that goal
- mike will assess a reasonable timeframe for getting plugins to work
- protocol steps seem to be the same in 2.5
- red-green mapper is still in vizmapper, but it will be out by 2.5
- aim for next beta to get screenshots: next week?
- be prepared for editors or reviewers to be testing
- point-by-point response
- issues with the litsearch tool: organism display (fixed), non-yeast citations (Pubmed issue)
  - this can be avoided by adding context terms; or by manually removing false hits
  - lexicon name give false impression that search is organism specific
  - could add checkbox to include organism as context, or just add organism name to context area by default
- melissa would like steps to set node color using new vizmapper
- should distribute manuscript to all authors to confirm inclusion

== Cytoscape 2.5 Release ==
- beta will be built Friday and announced Monday
- test, Test, TEST!

Allan, Mike, Peng, Kei, Scooter, Kristina, Ben
Thursday June 14, 2007
Notes: Ben

- Attributes
- 2.5 Status
- Deprecation
- Proxy

How do we maintain the hidden property of attributes ?
- adding child attributes are redundant, can we do it as network attributes ?  If an attribute is hidden for a node, its hidden for all nodes (Scooter)
- we are pushing the boundaries of how nodes/edge/network attributes are used.  how do we prevent attribute name conflicts ?  we should adopt namespace model.  scooter to start an rfc on a attribute/namespace proposal.

2.5 Status
- Peng to deliver filter code by end of the week.  After that, Mike will make a beta release and put it out.
- There are still some outstanding bugs assigned to people.
- Documentation needs to be updated for 2.5 (screenshots & updated text).  For post 2.5, we will look into automated screenshots.

- Mike still looking at what to remove and what to deprecate.

- How do plugins handle proxy server settings ?  Should we be using cytoscape.util.ProxyHandler.getProxyServer() to get the proper url prefix ?


Allan, Mike, Peng, Kei, Ghislain, Sarah, Gary, Ben, Scooter
Thursday May 31, 2007
Notes: Allan

- yFiles
- wiki reorganization
- board meeting update
- 2.5
- CurrentNetworkView issue

- there is an unobfuscated yfiles.jar in the SVN repository.  Mike needs to take the repository down in order to completely remove the jar.  He will send out an announcement beforehand.  
- It is recommended that people to a fresh checkout of Cytoscape afterwards

wiki reorganization
- Natalie Yeung at Toronto is doing a reorganization of the wiki pages.  Among other things, inconsistent and/or obsolete links are being cleaned up, for example links at the bottom of the wiki home page.

Board meeting update
- a board meeting was held yesterday (30th May).  
- Mike gave an excellent update on 2.5 status which was very well received.  He will circulate his slides.
- retreat news: there is a high-calibre lineup of speakers for the public symposium.  Three additional speakers are being invited to complete the lineup.  
- Cytoscape 'competitive analysis' discussion postponed to the next board meeting due to lack of time.  Allan has written some preliminary notes and started a chart on the NetworkAnalysisLinks wiki page.

- Groups: Alex, Christina, Allen have been using Groups and have found some issues, have updated the API and will work with Scooter regarding these.  Needs some UI consistency work.  BubbleRouter works, layout regions are groups and show up in NameSelection view, there is now round-trip support for layout regions via XGMML read/write.  A problem has come up, possibly in relation to the PluginManager, wherein a NoClassDefFoundError is generated when a plugin looks for one of its internal classes.  Sarah is looking into this.
- VizMapUI Redesign: working on backward compatibility, many bug fixes, integration with legend.
- Plugin Website: almost complete.  checking that links all work.  Sarah has hooked this up with plugin manager.
- Filters UI Redesign: almost done, working on making use of QuickFind widget
- Testing: Still lots of testing needed.  Mike will send out a link to the testing news group.
- Release date: still tentatively set for July 1st, but likely to be pushed out to July 16th, in order to do a more thorough job of testing.

CurrentNetworkView issue
- There is an issue related to where the Cytoscape CurrentNetworkView is being set.  Problem is that this setting is currently made upon a focus change event, whereas readers, while adding nodes and edges to the network view in progress, generate callbacks, such as groupCreated().  Implementors of these callbacks cannot correctly make references to the current network view, since it hasn't yet been set.  We will look into whether the current network view can be set earlier on in the process of creating a network view.

Allen, Mike, Peng, Kei, Ghislain, Sarah, Gary, Ben
Thursday May 17, 2007
Notes: Sarah

Current 2.5 Release date July 1st

- 2.5
- Bug 1266
- Tutorials/Workshops

- Groups: Alex, Christina, Allen have been using Groups and have found some issues, will work with Scooter regarding these.  Needs some UI consistency work.  BubbleRouter works, layout regions are groups and show up in NameSelection view
- HyperEdges: Mike Creech has checked in a new version for the HE editor and the CE to support the vizmapper API changes.  Documentation needs finalization.
- Document Event Handling: ongoing, need to work out events like mouse clicks etc at the retreat?
- VizMapUI Redesign: Most functions ready for testing, still working on it’s use in Mac.  Some backend changes still need to be made.
- Plugin Website: Working out a couple of bugs, then will set up test website for Cytoscape to connect to
- Auto Plugin Download: Working out a few bugs from changes made in installation process
- Helpdesk: No progress
- Performance Profiling: Same, will run these again when everything is stable again
- Pathway Commson Connectivity: Plugin finished
- Filters UI Redesign: Long to-do list, may have it done by the end of May
- Library Cleanup: Done
- Testing: skipped
- Undo Manager: Done, needs more testing
- Interactive Layout: Released to core dev’s, will be released as plugin for 2.5
- Layers/Annotation/UI: 2.6
- Papers: ongoing
- Bug Fixing: ongoing
- Remove Deprecation Warnings: ongoing
- Test List: Start getting volunteers for testing now (Everyone)

Bug 1266
- Issue importing xgmml, complex attributes not restored correctly, ask Ben?
- Has to do with embedded attributes that get saved in the session file, Ben/Kei don’t know about these.  Scooter may know more about this.
- Assign bug to Scooter, Ben will add information to the bug

- cytoscape-discuss list user was asking for workshops on how to use Cytoscape, tutorials aren’t helping enought
- Should start putting workshops together, Trey suggested doing it at conferences
- Put together a workshop package, post it on the wiki with a list of conferences where they will occur
- Gary will get someone in his lab to create an RFC for ''ideal state'': user meetings, conferences, etc.  Work on plans when we have resources.

Thursday, May 10, 2007
Sarah, Ghislain, Alex, Mike, Kei, Peng, Trey, Gary, Melissa, Ben, Ethan, Allan

 - Welcome Ghislain from Benno's group in Pasteur
 - Protocols Paper
 - Cytoscape 2.5 Development

=== Protocols Paper ===
Currently in review. A few questions remain:
  1. Shoot for webstart with 2.4 or 2.5?  Version 2.5 should be out (or very close) by the publication date. Many changes are to VizMapper and Filters, including screenshots.
  2. Are there already written sections (e.g. manual) that should be used for tutorials?  Mike has used Tutorial #4 in the past.
  3. Got yeast dataset?  Gary has used the Rosetta Compendium dataset which is quick large. Perhaps we can extract out a subset.
  4. Criteria for 'good' datasets for the protocols should include the timing, i.e., choose datasets that will work quickly and smoothly.
  5. Should certain plugins be migrated into the core? Or should focus be only on core features?
     - Import/Export
     - Filters
     - QuickFind

=== 2.5 Development ===
 - Layout and Groups are in good shape via Mike and Scooter
 - Hyperedges are comming along, a couple of weeks off
 - Document Event Handling: Allan, Mike and Sarah.  Some work done, but it is shifting to an ongoing task.  May not be completely complete by release.
 - VizMap aiming for next week, with some follow-up refactoring.
 - Plugin Website is done and ready for testing. Tied to automatic plugin download, which needs to be integrated.  In the hands of Sarah and Peng. All core plugins should be updated to implement the manager. See BioPAX as an example and updated How To page:
 - Linkout: no update
 - Helpdesk: ongoing
 - Performance: no update
 - Pathway Commons: ongoing. Update will be released on website next week.
 - Filter UI Redesign: Peng foresees performance issues. Getting real-time feedback via text or sliders is challenging. Can 'level of detail' be utilized?  Will try, but real-time may not be in place for 2.5 and moved to 2.6 in order to keep release schedule.  Using an Apply button greatly simplifies the task.
 - Library Cleanup: done.
 - Web Services / Databases: for 2.6
 - Usability: ongoing.  Sarah has a survey out at ISB, but no response yet.
 - Testing: Piet will update
 - Undo: waiting to be tested
 - Interactive Layout: new name = CellArranger.  Trying to add new Groups and Layout features
 - Layers/Annotations: 2-pass strategy, aiming for 2.6. Performance will be key issue. Some changes might be needed in order to render certain annotations.  Looking into JLabels. Caution about 1000's of these being added?  Main use case is for manual curation of pathways and thus should be few in number.
 - Deprecation: Giny has been moved into corelibs and is working on pruning, conservatively.


Thursday, April 26, 2007
Cytoscape conference call

Mike, Kei, Peng, Sarah, Scooter, Kristina, Trey, Gary, Ben, Ethan

Feedback is needed on many new Cytoscape RFCs. Two specific requests:
        Peng RFCs
        Daniel Abel’s new RFCs on rich line types, local network attributes and undirected edges

2.4.1 release – ready for testing, will be made public in the next day or so

2.5 scheduling
        -Need everyone to update timelines for their tasks so we can estimate when we will be able to release Cytoscape.
        -Lots of new features which will need more testing effort than usual.
        -Scooter: it may be worth making a pre-release without filters so testing can get started.
        -Cytoscape testing mailing list will be created to help communicate with testers.  E.g. Shoshana Wodak, Marian Walhout, Babbit group

Layout manager:
-Layout threading/tasks issues were discussed, based on recent list discussion.

-new API is now checked in – looking for more feedback, also with 2 group plugins

VizMapUI design
-Code is now checked in.  Biggest remaining task: continuous mapping editor (event handling) + some backend refactoring.

Plugin website:
-Needs to be part of testing as well (before the testing release)
-Mike will look into hosting plan for this.

Automatic plugin download
-Some discussion about versioning scheme
-Chose a simple versioning scheme – decision: use two integer digits for versions

-framework in place, just need to add more events
-Apple has a free Java profiler available in a toolkit called Shark as part of the CHUD http://developer.apple.com/tools/sharkoptimize.html
tool at http://developer.apple.com/tools/performance/

Filters UI redesign
-Waiting for feedback – will begin coding next week

Library reduction – done

Web services DB connectivity guideline – RFC is up and discussion is ongoing

Usability – ongoing

Testing – adding more unit tests and swing unit tests

Undo manager – checked in and waiting for testing – let Mike know if you uncover problems

Interactive layout: still a few things to implement, but basically done. More work on this next week.

Layers / Annotation / UI for custom nodes – Allan will visit MSKCC in NYC (week of May.7) – hope to make progress on this during this time. Deliverable: prototype. Will not be a public part of the release

Papers: protocol paper was submitted

Tutorials: Need to be updated, but we need to wait until UIs for filters and vizmap are complete.
-Can we automate screenshot taking e.g. take all screenshots

Bug fixing – encourage everyone to continue to do this.

Deprecation warnings:
Mike turned on option to show all warnings and we have almost 2000.
We should undeprecate some methods that are widely used.  Some of these are in giny – if we move this into corelibs, it will be easier to deal with this.


Thurs April 19, 2007
Mike, Kei, Sarah, Ethan, Ben, Scooter, Alex, Gary, Melissa
Notes: Alex

-- Summer of Code --
Keep an eye on student involvement and performance.  We can and should drop dead weight early.

-- 2.4.1 Release --
Should we do a point-release with bug fixes?  Turn in bugs to Mike in the next week and it will happen.

-- Protocols Paper --
Web Start still needs a bit of work, but it doesn't necessarily have to hold up the paper. The fixes to LitSearch, etc should be done well before reviewers actually look at it, i.e. within a month. Let's go ahead and submit the paper. The updated version of cPath will be checked in promptly. Remaining issues:
  * cPath update
  * Lit Search tool
  * Tab-delimited text export (but MIME type is still xls): Mike will update paper accordingly
Once text changes are complete, Trey will send it out! w00t!

-- Layout --
Scooter proposes a mod of createNetworkView to add a new signature to allow the layout algorithm to be explicitly passed (including 'null'):  createNetworkView(network, layout).  The passed layout goes to doLayout and checks for a TaskManager.  Mike is concerned about the proliferation of redundant method calls.  With the 2-3 concepts intertwined as they are, it is a challenge to implement cleanly.  Scooter and Mike will examine offline.

-- 2.5 Status --
* Viz Mapper UI: Kei did something about unhiding... - on track
* Plugin Website: Peng - on track
* Plugin Manager: Sarah - on track
* PathwayCommons: Ben - will check in to csplugins or coreplugins (overlapping but distinct from cPath)
* Filters: Peng - will take some time and some features may have to be postponed

-> Should 2.5 be postponed?  We want a buffer of a full month for testing, etc, after code freeze.  Draw up a 2.5 release timeline that includes completing Filters and allowing enough time for testing.

Thurs April 12, 2007
Trey, Mike, Sarah, Allan, Ben, Alex, Kei, Peng
Notes: Ben

-- Summer of Code --

Four positions have been filled.  The following projects will be worked on: layouts & enhanced search.

-- Web Start --

Allan/Mike C. have been having problems with web start read/write disk access.  Most likely problem with JNLP file setup.  If problem still exists when paper gets reviewed, a self-contained demo only version of the lit search plugin will be created.

-- 2.5 Status (highlights) --

* Event Handling: build a map of which classes are sending events and which are listening (start at canvas and editor).  possible publish-subscribe model applied to a new event manager.  goal of next meeting next week is to produce an rfc. [Mike S, Allan K]
* Viz Mapper UI: some discussion about checking in viz mapper code that is not 100% working.  Code will be checked in but tag will be created prior. [Kei]
* Plugin Website: website code checked in...needs to be integrated with Plugin Manager. Host on Cytoscape.org unless it cost more money, otherwise Chianti. [Peng]
* Plugin Manager: Checked in & working. Add support for license agreement is next. [Sarah]
* Performance/speed/memory: Same as last week, framework in place, needs to add swingunit tests, flesh out some events. [Mike, Piet]
* Giny Refactor: punted
* CyAttributes Name Clashes: punted
* Pathway Commons Connectivity: communication between pathwaycommons.org and Cytoscape complete. [Ben]
* Filters: no change. [Peng]
* Library Reduction: all accounted for but piccolo and phoebe. [Sarah]
* Web service/db connectivity guidelines: Ethan, Alex and Sarah to start discussion tomorrow. [Ethan, Alex, Sarah]
* Undo Manager: Progress made this week inside the editor. Not able to restore edges yet.  Next up will be attribute browser. [Mike S.]
* Interactive Layout: Implemented some of Mike S. suggestions.  Next thing is to use CyUndo & JavaDoc [Allan, Alex, Kristina]
* Layers/Annotation: Ben & Allan to possibly meet next week to discuss some new use cases proposed by Scooter during rendering code session. [Ben, Allan]
* Bugs: Everyone needs to check/fix bugs!

Thurs April 5, 2007
Kei, Sarah, Peng, Mike, Allan, Piet, Gary, Melissa, Ben
Notes: Sarah

-- 2007 Retreat --
Assembling list of speakers.  Lee Hood keynote.  Chris Sander, Benno, Trey, waiting on a few others to respond.  Will make announcement in a couple of weeks.  Applying for funding currently – Dutch Bioinformatics, Unilever, others.

-- VizMapper --
Kei uploaded executables to ucsd website to play with VizMapper UI.  Sent out an email describing the ui.  Would like more feedback before finalizing.

-- Webstart/Paper --
Issue with lit search running on webstart due to config files.  Allan has been trying to get Mike Creech back early to get his help with lit search file handling.  Hoping to hand it over to him on Monday.

Have two bullet points to deal with for paper 1. Equipment setup  2. Lit search setup
Webstart page on site referenced by paper will be for reviewers only.  Book chapter is still an option as copyright material shouldn’t be an issue once reformatted for the book.
Melissa, Mike, Allan currently authors for the book chapter.  Melissa will send out email to see if anyone else is interested.

-- Layout --
Mike got email from Roland Weisse (?) CEO of yWorks (yFiles) thinks that calling yFiles layouts in the manager would violate the license agreement so yFiles will not be part of the api.  Motivation to replace yFiles with open source?  Perhaps layouts could be part of Google Summer of Code as a few students were interested.  Gary has some documents regarding refining hierarchical layout.

-- 2.5 --
* LayoutManager – Scooter not on call.  Allan has played with it thinks it works well
* Groups – Scooter/Alex not on call.  Alex has been using groups with interactive layout tool, has found issues relating to selection handling (even handling propagation?)
* Hyperedges – Tool is there as a plugin, needs documentation will be done before 2.5 (Allan)
* Event Handling Doc – Allan/Mike dealing with within the next week
* Plugin Website - Set up test site on his development machine, cleaning code and bug fix.  Hoping to send out tomorrow for testing. (Peng)
* Plugin Manager – Needs to be tested with the website and get more feedback from plugin developers (Sarah)
* Linkout Attribute Browser – No work yet.
* Helpdesk – Not started yet, after plugin website finished
* Performance/speed/memory – Framework in place, needs to add swingunit tests, flesh out some events (Mike/Piet)
* Giny Refactor – Punted
* Properties/XML Config – Scooter not on call.
* CyAttributes Name Clashes – Punted
* Pathway Commons Connectivity – Working on a plugin to connect to Pathway Commons.  First version driven from the website rather than a gui in the plugin.  Neat  way to create a local server in the plugin (Ben)
* Filters – Had a teleconference, approach will be to redesign UI for filters leveraging quickfind package.  Simple filters should be straightforward, issues with topology filters, compositing, naming and saving filters.  Composite filters will not be a full Boolean logic for 2.5, approach will be similar to Spotfire.  Topological filters will use network attributes.  Saving filters ''not rocket science'' according to Allan.  Peng will write RFC.
* Library Reduction – Jdom updated from 0.9 to 1.0, Freehep updated to 2.0: would Batik svg be better (Gary/Ben)?  Going through libraries for anything unused
* Web service/db connectivity guidelines – not started (Sarah)
* Undo Manager – Pretty ready to go
* Interactive Layout – suggestions from Mike, Alex is implementing.  Available for download if anyone wants to play with it.  Will be released as a plugin, eventually port to groups. (Allan)
* Layers/Annotation – No work in the last week (Allan)  Fixed exporting with multiple canvasses, will add support for more layers within the next week (Ben)
* Bugs – Everyone needs to check/fix bugs!
* Remove Deprecation – If it’s dated April 2007 and has an alternative use mentioned go ahead and remove it.  Gary/Mike will set up FishEye to help.


Alex, Melissa, Mike, Peng, Kei, Trey, Sarah, Kristina, Allan, Ethan
Thurs, March 29, 2007
Notes: Alex

-- Nature Protocols Paper --
We should add more specific biological examples/use cases. Right now it reads more like a Manual than a Tutorial... we want Tutorial.  This involves more step-by-step examples.  One concern is that we lose generality, but that may be OK. Example: describe specific search term for cPath.  Current draft assumes that the reader has their own dataset; let's also include sample datasets, references to public datasets, and/or specific example terms, etc.

LitSearch fixes/mods discussion will be taken offline. If taken off webstart, then how would the user add/install LitSearch? We should consider the WebStart as a proper client option for Cytoscape users, rather than just a demo tool. This will be solved with the v2.5 plugin loader.  Also consider, however, that the protocol paper won't be published until near or after the v2.5 release!

Should we start a v2.5 branch of the paper?  We will have to update the protocols/screenshots after peer-review (which would overlap with v2.4), but before final publication (which would overlap with v2.5). Trey will contact editor.

Invited book chapter in "Current Protocols in ..." by Lincoln Stein. Opportunity to reuse 50% of the text from the paper? Copyright issues may be side-stepped by making new examples.  We haven't formally agreed to doing this yet, nor asked directly about overlap with published papers or online tutorials. Need focused group of authors: Mike Smoot and Allan volunteered.

-- Patches Submitted by Other Developers --
How to prioritize and balance the community interest? Current example includes patches from Abel which seem intune with our architecture but are not part of the 2.5 schedule. The integration of these patches could take a full week to check for breaks.  How do we integrate these contributions into our RFC and implementation cycles?  We should encourage these external developers to participate on phone calls and run RFCs to help merge their contributions.

-- Cytoscape 2.5 --
- Undo Manager -
ViewChangeEdit objects are created in a couple places in Ding; they need to be created in manual layouts and other places where undo is needed.  ViewPortChangeEdit might be abstracted out of current ViewChangeEdit. We need a few more methods for other data types, e.g., changes to attributes. Please review the code in cytoscape.util.
Menu state handling might need to change. Cytoscape.action is a menuListener so that each action is responsible for knowing the states of menus.  Please review and provide feedback.
Example: AbstractLayout now calls Undo Manager at the begining, before layout, and the end; two lines of code in AbstractLayout pass all management to Undo Manager. And Undo only tracks actual changes, i.e., when end-state is different from begin-state.

- Interactive Layout Plugin -
Collecting feedback on beta; ready for release in parallel with v2.5

- Annotations -
We will have a couple annotation supported by the model and the editor, but not for primetime use for v2.5

- Bug Tracking -
Everyone should take a look at Mantis and try to start early with bug fixes.

Sarah, Allan, Alex, Scooter, Peng, Kei, Mike, Christina, Ben, Ethan, Melissa, Piet
Thurs. 3/22/2007
Notes: Sarah

-- Nature Protocols Paper –
Nearly done, see webstart section.
Action item: Should look at submitting to webservices issue of NAR

-- 2.5 --
- LayoutManager (Scooter): Working out headless mode stuff as well.  Trying to work out tasks.  Mostly done.
- Groups (Scooter): API finished, metanodes/name selection set up.  Ready for stress testing
- Event Handling: Allan and Mike will talk
- VizmapUI (Kei): Run into Mac/Win incompatibility issues, need to write some controller code.  UI design nearly done.
- Plugin Website (Peng): Nearly done, working out submission page and loading into database
- Plugin Manager (Sarah): Needs better error handling, and Mac/Win incompatibility issues to be worked out.
- Linkout: not yet
- Help Desk: not yet
- Performance Profiling (Mike): Close to done
- Giny refactor: punting past 2.5
- XML Properties config: Haven’t talked about it yet, need RFC
- Cytsocape Class cleanup (Ethan): postponed
- Name clashes (Ethan): low priority
- Attributes/Formulas: push to 2.6, talk about it during filters discussion
- Library reduction/cleanup (Sarah): putting together lists for updates/cleanup
- Usability (Sarah): looking at Melissa’s work, have emailed Kathrine
- Webservices (Sarah): not started

-- Filters --
Settled on time for discussion 3/27 10:30 PST - Peng, Mike, Allan, Ethan, Gary
Read the section on the wiki and RFC 14 to prepare.  Will have an RFC for filters after discussion.

-- Webstart --
Melissa can’t run lit search tool because it expect certain files to exist.  Fix is to embed the files into the jar file.  Test to be sure that getResource will retrieve the files.

-- Headless Mode –
Ben has been working to get current Cytoscape to run headless.  Has required a lot of core code be commented out due to references to the desktop.  Need to look at how these parts could be decoupled from the core to support headless mode.  Some things (like layout) are referred to only through the desktop.

- Desktop may need to be refactored to segregate model/view correctly
- CyInitParams has method that lets you know if you’re in gui/headless mode.

Action items: Document modes in CyInitParams

-- Pathway Commons Plugin –
Website up called pathwaycommons.org
cPath is engine behind pathwaycommons
4 data sources available, working to add KEGG, Biocarta
Working on RFC:
- pathwaycommons plugin for next version of Cytoscape
- site will offer web service functionality that plugin will use to offer similar
  functionality within cytoscape
- offer Cytoscape webstart on pathwaycommons

Gary, Alex, Mike, Peng, Kei, Trey, Kristina, Allan
Thursday, March 15, 2007
Notes: Alex

Google Summer of Code
 - GenMAPP was accepted as a Mentor Organization; Cytoscape was not. However, half of the development plan for GenMAPP is Cytoscape related and we should be able to migrate additional Cytoscape development ideas to the GenMAPP page.
 - Alex will check with Google, review ideas and then coordinate with mentors to migrate them over.
 - While the applications were very similar, the critical difference was probably the time of application, unfortunately.  GenMAPP applied 2-3 days before the deadline.

 - Update provided by Piet via email:
 * The retreat committee, consisting of Annette, Guy and me, will have a weekly conference call on Wednesday 1500 GMT
 * In the coming two weeks a keynote speaker should be arranged; Guy is writing letters, we're still hoping for Lee Hood to come.
 * We already have preliminary promises of (amongst others) Chris Sander and Guri Giaever (thanks a lot to the people asking them) so this might win over other potential speakers
 * When the keynote speaker is known a first announcement will be mailed
 * Next week more...

 - Plan meeting for focus group.
 - Interested: Allan, Peng, Mike, Gary, Alex
 - Come up with proposals to present to board, a clear Plan A or B.
 - Critical decision regarding release deadlines may need feedback from the Board;  the Board found it difficult to pass down development plans.

2.5 Development
 - Undo Management (Mike)
   * abstract common code
   * "when to record a state" is difficult to automate and will stil require developer implementation, but can be modularized to make it simple
   * create an undoable edit
   * do CyNetwork and CyAttribute and CyNetworkViews require different implementations?
     - Layout Undo (local: separate stack per view)
     - Attribute Undo (global: across multiple networks and views)
   * can you have a reference stored with each action to the view (local) or global frame?
     - you would want the current view to follow the undo references -> a critical useability issue
   * Use Cases
     - correct a mistake, last event (most common)
     - track a history of changes (less common)
   * mouse down = record state
   * mouse up = record edit
   * a stack per view?
   * still a fair amount of work to do
   * refer to Undo Manager wiki RFC

 - Testing (Mike)
   * found somethings in swing unit that make it easier
   * Gary knows software engineer he will
   * wait to hear from Piet and Tero for update

 - Release Timeline (Allan)
   * more times for bugs before a "real" code freeze
   * clarify how to branch for early 2.6
   * a lot is already done. let's organize and set dates

 - Layout Manager:
   * Test and give feeback!

 - Groups (Scooter)
   * API is ready
   * Plus 2 implementations: named selection, basic metanode function (collapse, expand)
   * Test and give feeback!

 - Hyperedges (Allan)
   * need to update documentation
   * it'll be ready

 - Document Event Handling: a planning step
   * what events are being fired?
   * plan refactoring
   * awaiting Mike Creech (Agilent contractor)
   * Allan and Mike will follow-up on documentation in the meantime

 - VizMap Redesign (Kei)
   * will upload screenshots of new interfaces
   * something by next week
   * Give feedback!
   * Gary's undergrad (5 hrs/wk) will work on VizMapper

 - Plugin website (Peng)
   * Dynamic, database-driven, Java tree for navigation is working locally
   * Also working on submission page for plugin developers
   * Cytostaff needs to approve submissions
   * Sarah is working on cytoscape interface? Will get update later. See cytoscape/plugin/ package.

Agilent Literature Search tool
  - FYI there is a 'silent release' available for the Agilent Literature Search tool on the cytoscape plugins page.
  - Allan needs to update documentation, e.g. many figures need to be updated
  - Allan requests that people download the plugin and kick it around

Sarah, Kristina, Kei, Peng, Gary, Allan, Piet, Ben, Ethan
Thursday, March 8, 2007
Notes: Gary

Organizing committee has been formed (Guy, Annette, Piet) – They are working on the speaker proposal. Members of the board are asking around for more speakers.

Board meeting
        -financials – Cytoscape has a bank account, currently with ~$11,500, mostly from a grant from Pfizer that Trey facilitated. This will be used for ongoing operations, which cost <$1,000 per year (e.g. taxes, trademark applications)
        -trademark – Louis Coffman is trying to register the Cytoscape trademark
        -development status – filters – they board is now aware that we need a plan

Cytoscape 2.5
Combining attributes/Formulas – along the lines with what’s in GenMAPP. SQL like statements ability to combine attributes.  E.g. if the expression value is X and the p-value is Y, then do this. – Should be included in the filters discussion – we should have a conference call to discuss the Filters API. Action item: Allan will set up the conference call.

Library reduction and cleanup. Evaluate library updates, remove old libraries – sarah will start in the next 2-3 weeks.

Web Services / Database Connectivity Guidelines – not yet started

Usability Assessment – Sarah has had some correspondence with Melissa about this and is gathering a user group. Sarah will work with Melissa to follow up on Catherine Letondal’s involvement.
Trey and Annette talked after the board meeting around users in a pharma company – if we know of pharma e.g. AstraZeneca.  People could go to help the pharma using Cytoscape. Allan is available to do this.  When people talk to pharma, we can ask if they are interested in having Allan visit them to help them use Cytoscape and help determine their needs. (should be in a nice place, not Iowa :)

Filters – try to do API design initially. What quickfind does is almost everything you want in a filter. Filters are just another way to query.  It may make a lot of sense to fold filters into what is currently quickfind. In particular, the advanced quickfind features are what the interface to filters should be anyway.  E.g. combine filters using Booleans could be designed as an API initially, which would enable plugin writers to use it.

Is filters the right word?  Yes, it seems like an intuitive concept.

It would be nice for someone to work with Ethan to define the API and someone else can do the user interface.

Interactive layout (Alex, Allan, Christina) – a beta version will be sent out soon for comment – it will be called the ‘interactive layout’ plugin.

Annotation – Mike Creech will be back in April and may be able to help out with this. Ben will check the layer API changes out over the next few weeks.

Finish testing/undo manager next time, then start over.

Thursday, March 1, 2007
Participants: Mike, Kei, Peng, Trey, Allan, Melissa, Gary, Alex, Nathan (?), Christina

= Protocol paper status =
- Status is good!
- Backed away from a mammalian network since we couldn't an example that included everthing we needed.  Therefore, we're back to using yeast.
- There is still an interaction isssue between cPath Uniprot IDs and BiNGO's inability to use them.  Melissa will email the group with details.  One of us may fix the BiNGO code to help move things along.

= Release 2.5 =
- Layouts are in good shape.  A grad student is working with Scooter to help improve things.
- The groups API and a sample plugin have been checked in.  Scooter would like feedback on both the code and the plugin.  When working with this, consider the problem of a default viewer.  What should happen if an xgmml file specifies a group but not a viewer?  Should we have a default viewer?
- Hyperedges has been checked in to csplugins.  The functionality is all there, only documentation and a few clean-up details remain.
- VizMapUI.  Kei has created all of the components needed and has been working on backend refactoring.  He should have working mockups available next week.
- The website side of the Automated plugin loading should be complete in 1-2 weeks. Peng is actively working on this.
- Performance evaluation is nearly complete, but faces a few more hurdles.  Mike will complete when he's not doing other things.
- There was a request to move a copy of GINY into corelibs so that it is more easily accessible to us.
- There was a request to update the API docs on Cytoscape.org to include pointers to GINY.  Mike will do this.
- Filtering.  YELLOW FLAG!!!  This is low on all developer priority lists but high on user needs list.  We should bring this up at the board meeting to see if there's a way to fix the disconnect.  At the minimum, we should do a design/RFC for this release.  This may be important enough to bump the release date.


Thursday, February 22, 2007
Participants: Alex, Mike, Kei, Ben, Piet, Allan, Gary

= Google Summer of Code =

 * Google to fund student to work on project over the summer to work on open source project of their choosing
 * One person per/project, mentor assigned for each student
 * Application submission March 5-12
 * Project adminstrator required
 * Possible project(s): web interface to Cytoscape (ajax or applet)

= Retreat =

 * Piet put up proposal page on wiki, see wiki page for more details
 * November 6-9, 2007
 * Still looking from speakers from SAB

= 2.5 Release =

 * Not ready to go down feature list yet
 * Think about code freeze around May 1

= Performance Evaluation =

 * Mike checked in semi-function performance evaluation tool
 * Basic idea: written an aspect that keeps track of a few key method calls, run against test suite
 * Interested in having other people get the test code to work

Thursday, February 15, 2007
Participants: Alex, Scooter, Sarah, Chris, Piet, Ethan, Ben, Allan, Peng, Kei, Mike, Melissa

= Renderer Study Group =
 * Friday at 10:30, possibly regular time
 * First topic: R-tree

= Retreat in Europe =
 * Dates: 6-9 November, large room available on the 8th
 * Wiki page will be set up by next week
 * Unilever on board
 * Collecting names for speakers, see the wiki

= VizMapper Refactoring =
 * New features: arrow type, color mapped to viz properties
 * GUI project
 * Chris: decision on the separation of discrete mappable?
  * General goal: go for the most flexible solution
  * Separate dashed/solid line from line width
  * Be aware of creating too many options -> need for good UI

= Update on the Paper =
 * Melissa: features all described in one place
 * ID mapping from Bader's wiki is great resource
 * Webstart still challenging; Mike will help
 * Mike: do we need a new release?  -> Will assess at submission time
 * Submission est: end of next week
 * Latest version will be posted tomorrow

= Cytoscape 2.5 =
 * Scooter: Checking in Group Model and working on API plus View implementation, includes changes to xGMML read/writer
 * Any exceptions? -> silence

Thursday, February 8, 2007
Participants: Gary, Mike, Kei, Peng, Alex, Allan, Ben, Piet, Sarah, Scooter

Possible Retreat in Europe:

NBIC, Dutch bioinformatics organization, interested in funding retreat in Holland.
Piet to draft proposal based on last year's retreat, present at next conference call.

Potential dates: week of Nov 5, Nov 12, or Oct 22; held at Academic Medical Center (University of Amsterdam).

Rendering Study Group:

Weekly or Bi-weekly call to discuss in-depth how the rendering works.  Next Weds, Feb 14, 3pm PST.  RTree stuff.  Allan to setup webex and lead discussion.  Mike to format code through Jalopy.

Release 2.5:

Most people have updated 2.5 task schedule.
Groups - Scooter proposes to modify CyNode (model) and add group membership list.

Thursday, February 1, 2007
Participants: Trey, Benno, Mike, Melissa, Gary, Alex, Ben, Ethan, Kei, Scooter, Sarah, Peng
Notes: Gary

Scooter has been in contact with George Robertson from Microsoft research about visualization collaborations.

Ben is looking into an Xgmml bug – will work with Kei on the issue.

Paper – Melissa still having some trouble loading ontologies in 2.4 – she will talk to Kei about this after the call.
She would like to put up a webstart version of the software somewhere. There is an issue about users accepting the licensing terms of the litsearch plugin for this webstart. Melissa will chat to Allan about this.
2.4 version of jactive modules? – yes, it is on the website.
Melissa will send out the latest version of the paper for comments, Gary will provide comments by this weekend.

2.5 time estimates.
MSKCC will focus on pathway commons connectivity.  Other things currently tagged with MSKCC will be lower priority. Ethan will hope to have some time to work on the Filter API, but not the GUI.

Gary asked if anyone is interested in ID mapping/synonym systems. This may be something that he can contribute with new software developer resources.  Alex and Sarah are interested and are working on similar systems. Gary wrote a page about this at http://baderlab.org/IdentifierMapping which could be turned into a Cytoscape RFC in the future. Alex and Sarah will edit the page in the meantime on Gary’s site.  Ideally, we would have and API, a GUI, import from various sources and be able to update the merge plugin to work with the API.

Layout manager is done – Scooter will update the wiki.  The layout manager allows layouts to register themselves and code to call these layouts.  He also cleaned up all layouts, fixing ones that almost work and removing ones that will never work. All layouts will partition the graph and layouts that can work on selected parts of the network now do. The interface allows layouts to inform Cytoscape of their capabilities and allows users to change parameter settings.  yFiles is not part of this, since Scooter doesn’t have the source code to wrap the functionality.

Everyone should flesh out 2.5 timelines as much as they can.


Thursday, January 25, 2007
Participants: Mike, Kei, Peng, Trey, Gary, Alex, Kristina, Sarah
Notes: Mike

* Mike brought up the notion of a rendering study group to get a better understanding of how to change things.

* We agreed to have time estimates for our projects for 2.5.

* Alex agreed to talk to Piet and Benno about their roles in 2.5.

* Trey reiterated his desire for performance testing.

Thursday, January 18, 2007
Participants: Mike, Kei, Peng, Trey, Gary, Allan, Kristina, Alex, Sarah, Ethan, Ben
Notes: Alex

Bug Reports

 * Allan: Mike Smoot identified a bug (Mantis:1266) with Import and Attribute Names; Ben will follow-up; 2.4.1 fix.
 * Allan: Alex Ade has drag&drop issues.

Recap 2.4 Release

 * Went smoothly; let's hope 2.5 goes the same
 * Number of 2.4 downloads so far?

2.5 and Beyond

 * Metanode Groups: Scooter
  - Being implemented by Scooter
  - UCSF + Agilent groups will be working heavily on Groups for 2.5

 * Annotation Layers: 3, 4 or user-defined number?
  - Need to get the API nailed down
  - Interactive Layout (a.k.a. Bubble Router Plugin)
  - Background images
  - Print issues
  - Come up with new name to avoid confusion with GO annotations
    - Markups
    - Notes
    - Annotations
    - Paint
    - Decorations
    - Pizazz!

 * Vizmapper UI Redesign: Kei
  - Consider work on Filters

 * Plugin loading/Import: Peng

 * Linkout: UCSD

 * Filters: Ethan
  - Consider Vizmapper redesign
  - Create API?
  - Rename to "Selection"

 * Organize and Schedule
  - Everybody should assess time committments
  - http://www.cytoscape.org/cgi-bin/moin.cgi/RoadMap2006
  - http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_2.5

Gary: 2 new people

 * Mike Mitan(sp): software developer starting in a couple weeks
 * Volunteer interested in tutorial work, updating and making new ones; other task ideas, e.g.,testing?

Thursday, January 11, 2007
Participants: Mike, Kei, Peng, Trey, Allan, Kristina, Alex, Sarah, Ethan
Notes: Mike

2.4 Release

- There don't seem to be any showstopper bugs.
- Most existing bugs should be fixed at the discretion of the developer.
- Allan found a bug in the browser combo box.  When a hidden attribute is first added it is seen in the browser combo box, however after the first look at the combo box, the hidden attributes are appropriately hidden.

- There is a problem with the cytoscape.props file in the .cytoscape directory, specifically with the plugins property.  This property stores old plugins that may or may not work in new versions of cytoscape.  Since there are several other ways of specifying plugins, we've decided to remove this feature.  Specifically:
  * No longer store plugin locations in cytoscape.props.  Ignore them if they exist from previous versions.
  * Print a message to STDOUT describing where we looked for plugins.
  * Revisit plugin loading in version 2.5.  Consider whether or not to specify default locations for plugins.

- The manual seems to be in pretty good shape.  Everyone is encouraged to continuing editing as they see fit.

- Trey brought up the issue of performance testing.  He is concerned that we don't have a performance test suite in place to ensure that we're not losing performance between releases.  We've decided to:
  * Compare node/edge selection to previous versions of Cytoscape because some have noticed slowing when lots of nodes/edges are selected.  This may be related to select event handling.
  * Immediately after the 2.4 release, UCSD will develop a performance test suite to compare the speed of operations between versions of Cytoscape.  If performance issues are found, this may necessitate a 2.4.1 release.

- Since Jan 15 is a holiday we're bumping the release date to Jan 16.

Thursday, January 4, 2007
Participants: Sarah, Alex, Mike, Kei, Peng, Aditya, Ethan, Scooter
Notes: Alex

2.4 release

-- Assessing Remaining Bugs

- Possible conflict with bundling process (Ethan):
Will check this with next beta release.

- Installation Problem (Mike):
Having an old .cytoscape directory is interferring with new installations. Should we create a user option for using/replacing the old directory?  Or should we create a new directory per version, e.g., .cytoscape_2.4.

-- Next Beta Release?
In the next day or two (Mike).

-- Branching?
Branch at release.
Scooter is maintaining his own branch for layout code and needs another branch for other development.  What is the best way to procede?
Branch again and perform two, two-way merges upon release.  Not ideal.

-- 2.4 Release: scheduled for Jan 15th
On schedule.

Cytostaff_Development/Conference_call_notes/2007 (last edited 2009-02-12 01:03:08 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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