Contents

  1. 2009
    1. September
      1. Thursday September 10 2009
      2. Thursday September 3 2009
    2. August
      1. Thursday August 27 2009
      2. Thursday August 13 2009
      3. Thursday Aug 6 2009
    3. July
      1. Thursday July 30 2009
      2. Thursday July 23 2009
      3. Thursday July 16 2009
      4. Thursday July 9 2009
      5. Thursday July 2 2009
    4. June
      1. Thursday June 25th 2009
      2. Thursday June 18th 2009
      3. Thursday June 11th 2009
      4. Thursday June 4th 2009
    5. May
      1. Thursday May 28th 2009
      2. Thursday May 21th 2009
      3. Thursday May 14th 2009
      4. Thursday May 7th 2009
    6. April
      1. Thursday April 30th 2009
      2. Thursday April 23th 2009
      3. Thursday April 16th 2009
      4. Thursday April.9th 2009
      5. Thursday April.2nd 2009
    7. March
      1. Thursday March.26th 2009
      2. Thursday March.19th 2009
      3. Thursday March.5 2009
    8. February
      1. Thursday, Feb. 26th
      2. Thursday, Feb. 19th
      3. Thursday, Feb. 12th
      4. Thursday, Feb. 5th
    9. January
      1. Thursday, Jan. 29
      2. Thursday, Jan. 22
      3. Thurs, Jan 15
      4. Thurs, Jan 8
  2. 2008
    1. December
      1. Thurs, Dec 18
      2. Thurs, Dec 11
      3. Thurs, Dec 4
    2. November
      1. Thurs, Nov 20
      2. Thurs, Nov 13
      3. Thurs, Nov 6
    3. October
    4. September
        1. Cytoscape 3.0
        2. mini-retreat dates
    5. July
    6. June
    7. May
    8. April
    9. 2.6 Release
    10. 2.6.1 Release
    11. 3.0 Planning Overview
    12. Google Summer of Code
    13. March
    14. February
    15. January

During conference calls, etherpad is used to take notes (since it updates instantly compared to the delay when editing the wiki). The etherpad url is: http://etherpad.com/hb7mF9KAXt

In between conference calls, the same etherpad is used to collect agenda items for the next conference call.

2009

September

Thursday September 10 2009

Participants: Noel, Mike, Sarah, Brian, Daniel, Samad, Maital, Piet, Allan

Agenda Items:
Sarah: New grant
Trey and Illia discussing new grant (R1) complementary to P41, board members will start work on it immediately.
Will build on 3.0 architecture to include data, instrumentation etc. integration
Looking to get letters of support (likely to be from same sources as for P41)

Mike: P41 grant update
Actively writing application
Letters of support have been requested from list 100 gathered from various sources
Working out budget that makes sense
LoS from NIH sources particularly welcome

Retreat confirmed as officially postponed until Spring 2010
One option is Michigan
Another is quebec, but this is unlikely due to lack of local representation

Would like there to be a Hackathon in November or thereabouts.
Very likely to be held in San Franciso
Mike will send out email to get the ball rolling (collect dates etc).
There will be several remote attendees
Goal will be to port as many core plugins as possible or at least teach people how to port plugins
Will probably be over two days

Thursday September 3 2009

Attendees: Noel, Allan, Mike, Scooter, Piet, Maital, Brian, Sarah, Samad

(Gary won't be able to make the call)
(Daniel won't be able to make the call)

Agenda Items:
Letters of support for P41 grant
Cytoretreat

Letters of support for P41 grant
Mike wants names of people (anything helps, but PI's have higher impact) for a mass email; send this to Mike the next few days.
Contact people directly, automated scripts, or preferably contact people you know personally informally before any automated mail is sent
Plugin writers should be targeted specifically
Focus on NIH funded researchers; P41 supports providing other NIH funded projects with resources

Cytoscape retreat
Trey got in contact with David States; David said not to worry, november still ok. Time is pressing however (2 months is hardly feasible!), we need an announcement to start preparations. Mike volunteers to keep in touch with David. Lots of issues (grants, sitevisit P41) though, so postponing might be the best option. When the site visit is there however everybody has to show up. The development team proposes to postpone the retreat after the site visit. Why not combine retreat and site-visit, after the site-visit. Both events require a lot of effort however so might be hard to combine. Mike contacts Trey and Gary first about postponing. This also means that the 3.0 hackathon won't happen in november. Current consensus: Spring, there's a Keystone meeting in Quebec on networks around that time...(http://www.keystonesymposia.org/meetings/ViewMeetings.cfm?MeetingID=1068#utm_source=newsletter1&utm_medium=email&utm_campaign=Aug09Newsletter) No core team members localized there however. Would be an opportunity for extra hackathon

Bugs
Prioritize your own bugs
Snow leopard is going to be tested

August

Thursday August 27 2009

Attendees: Noel, Daniel, Mike, Scooter, Gary, Allan, Piet, Brian

Agenda Items:
Mike announcement
P41 grant
Cytoscape 2.6.x, 2.7, 3.0
ICSB/SBGN meetings next week
Cytoscape retreat

Mike: Daniel has been nominated and approved  as a core developer!  Everyone thinks this is great and welcomes Daniel.  Mike will update the list of developer names on the website.

ICSB in Palo Alto next week. also an SBGN meeting as a workshop (systems biology graphical notation).  Alex will be at the SBGN workshop.

P41 grant - grant to NCRR branch of NIH -- a research resource grant.
Large grant, requires huge amount of work, letters and support from the community of users, etc.
structure => technology, research, and associated driving biology problems
each section assigned to teams
everyone needs to help in gathering letters of support
list collaborations with biomedical researchers that use cytoscape, their publications, possible relations to other grants
Stephanie Mirkin <smirkin@bioeng.ucsd.edu>

Cytoscape retreat
still need to hear back from David States

Cytoscape 2.7 release -- do we have a timeline?  what should go in it?
polished released that will be demoed during site visit.
November time frame, to be shown at retreat

3.0 is up and ready to have core plugins ported to it
people should play with code, figure out how it works

Thursday August 13 2009

Attendees: Noel, Gary, Maital, Allan, Alex, Samad, Sarah, Kei, Peng, Scooter

Agenda Items:
-Bug 2055 : Thoughts on changing regexp used to match JAR filenames to allow characters other than [a-zA-Z0-9_]
If no change, need to better document restriction on naming.
Decision : Will remove regexp and match any jar contained in zip file, bug reassigned to Noel for fixing.
-SBGN, Bioinform (Allan) - will we support SBGN?  Ideally, but no plans right now. We're keeping an eye on it in the meantime.
-GSoC - ending officially next week, code can still be worked on, but Google wouldn't track it
--CyAnimator update - should be released soon. Would like to be accessible programmatically.
---The idea is to add a new interface into 2.7 (if there is one) that mimics the 3.0 Command mechanism.  The plugin would have to register itself similar to the way Layouts register themselves, but once registered, other plugins could find the Command interface to the registered plugin and use it.   I'll post a more detailed description after I get back from vacation.
-Cytoscape 3 update
--search plugin - hoping to get search functionality by next week, student hit some roadblocks.
--Processing update - Sample images for Processing renderer: http://twitpic.com/d50sj/full http://twitpic.com/doymx/full http://twitpic.com/dp1jn/full
Schedule note: Scooter, Allan, Gary, Sarah not on call. Cancel the call for next week, so next call would be Aug.27

Thursday Aug 6 2009

Attendees: Noel, Gary, Sarah, Scooter, Samad, Maital, Peng, Kei

Agenda Items:
Cytoscape Retreat:
Trey has contacted David States.
David has confirmed commitment to hold retreat on previously mentioned/agreed dates/location.

What are people doing:
Noel: fixing IO bugs - files not being properly closed - 40-50 places that needed fixing, 4-5 difficult ones. Next: SBML import module, IO discussions for after August.

Gary: Working on Cytoscape Lite.
Those interested can try it out ( http://beta.genemania.org )
Adding filtering capability using JQuery
Visualisation done via Flash, rest is JavaScript and there is a JS API
Follows design of Cytoscape
Supports XGMML import/export (designed to work with 2.6)
V1.0 when released will be embeddable in other sites (contact Gary if you want to try before release)

Sarah: Did new tutorial for SysBio course. First airing went well
Will be working on assigned bugs
Planning on finishing Google DataSource for CytoscapeLite

Scooter:
New release of clustermaker, include much better MCL, community clustering from Gang Su, added a histogram to tune the edges to use for clustering, fixed interactions with heatmap (paper with Krogan)
-Babbit lab - 3500 node, 2M edges network - Cytoscape worked fine
-Dendogram work that ChinMoy is doing combined with chemiinformatics plugin - 2D molecule structure visualization
-GSOC: CyAnimator - works reasonably well. Record cytoscape animations for movie making.
-Brian Shoichet group - protein sequence similarity vs. ligand similarity
-Meeting Robin Haw - chemiinformatics data into Reactome

Samad:Still working on logging. Some details of startup and configuration are still being defined.

Maital:
-GSoC: Search functionality added. Trying to combine all aspects. Nearing completion (estimated next two weeks)
Search API will be available to other plugins

Peng: Working on plugin manager.
Looking at Cytoscape release bundle building process
GSOC working on formats for Phylogenetic visualisation :-
Phylip ( http://evolution.genetics.washington.edu/phylip.html )
PhyloXML ( http://www.phyloxml.org/ )

Kei:
Cytoscape 3 - mainly working on vizmap GUI, trying to make it work, but there are still some problems. Refactoring CyDataTable to fire the correct events.
GSOC: New rendering engine with processing and openGL.
Cytoscape 2.6, some of the web service clients are no longer working, possibly an issue with the service provider. Updated jaxb library. Please try the latest 2.6 with the new library.

Q: does clustermaker use group API? Increasingly. Kei and Peng's new module viewer can browse any set of groups, and connects with BubbleRouter. Segue to metanode discussion. Q: can you add a node to multiple metanodes? Yes.

July

Thursday July 30 2009

Attendees: Noel, Brian, Maital, Sarah, Samad, Mike, Alex, Gary, Scooter, Allan

Agenda Items:
Cytoscape 3.0
-clean-up of application code - reasonable API is almost defined, so it is almost ready to move into the core3 version.
--Everyone should look at http://cytoscape.wodaklab.org/javadoc/ to comment on the cytoscape.* pacakges, which is the application layer.
-command line is mostly running.
General status of Cytoscape 3.0 vs. 2.6 - application runs, but missing io, session, node browser, some vizmap functionality and a few others.
search/filters for 3.0 is going well as a GSOC project
Target date for 2.6.4?
-no target date yet.
-plan? need to improve the software in preparation for the P41 submission at the end of the summer.
--need to prioritize which bugs to fix - find the most annoying bugs. Go through the discussion list to find specific things that are confusing people and deal with them - then we have specific example, which may be good for the grant.
e.g. support for old expression formats vs. attribute based expression is very confusing to lots of people. We need to make it clearer that people should not use the old formats any more and should instead use the new table importer, which is a lot easier (but the checkbox for loading of all attributes may not be clear right away). Fix: Make the expression data load button on the attribute browser link to the table importer. Update expression correllation plugin to use attributes in general (other plugins using the old code?). Update the manual to say that the old expression data formats are deprecated and everyone should now use the table importer.
e.g. review all defaults to ensure they are reasonable
e.g. Tooltip in filter stays forever bug 0002038
e.g. some things saved to properties file that maybe should be somewhere else e.g. cytoscape version - immutable property list would be great
e.g. menu disappears bug 0002048

Thursday July 23 2009

Participants: Daniel, Gary, Sarah, Brian, Mike, Kei, Peng, Samad, Mathieu, Noel, Allan, Alex

Agenda:
Cytoscape retreat update - Trey is contacting David States
3.0
-logging (samad)
  - only one logger will be used, messages above a certain level will be reported to the user
  - tie in with automatic bugreporting system
  - internationalization of logged messages (storingmessage strings in a seperate file to allow translations, etc.) will be dealt with later.
  - Decision, we will use SLF4J and log4j going forward.
-general status update (Gary)
  - updating DevelopmentModules page on wiki.

Workflow work offer from Anna-Lena Lamprecht from Biojeti group - she is contacting Benno to see if she can work on implementing a workflow tool on top of the task layer.

Thursday July 16 2009

Thursday July 16 2009

Participants: Noel, Daniel, Brian, UCSD, Sarah, Gary, Allan,  Alex, Scooter, 
Matthieu , Samad

Agenda: 
3.0 build infrastructure (Hudson, sonar, maven repository). is being updated, might be down during the weekend.
3.0
-Session format (Noel)
 - How are groups serialized, and how is the state of groups stored?
 - need session api so that modules can add things during serialization
   to avoid clashes between modules, use classname or java package name to prefix key used to store things.
 - will an xgmml-like format for CyDataTable be needed?
 - how to handle inter-dependency between modules? -- loading networks and DataTables first might help, is it enough?
  - using graphml instead of xgmml? -- graphml supports mixed networks better, for example.
    native format for 3.0 might be graphml.
    Noel to prepare wiki page
-Reading sessions saved in 2.x (Noel)
- rendering (presentation) api
  discussion on cytostaff -- current main question: do we want to have seperate top-level objects like CyNetworkView, or have a scenegraph where any View<> can have arbitrary children?
  will continue discussion on list, and Kei will summarize to wiki
- task API (allan)
 TaskFactories added which take Network, Edge, Node arguments and Task will operate on given object.
 provide seperation between UI and Tasks
-Logging (Samad)
Samad will send out questions - discussion postponed until next week
ICSB/SBGN workshop (AllanK)
 Anyone going? should cytoscape be represented? Trey is going

Retreat - Nov.6-9 - Trey is looking into it.
Nature PID primer? (Gary) - anyone interested?  Yes - Arman Aksoy and potentially Samad. Gary will wait for more answers and people seem to be open to working together.
3.0 status - new modules? (gary) - postponed until next week

Conference call quality (Gary, Allan) - a number of people were dropped on this call. Hopefully it was a temporary glitch, but we'll try freebridge for a few more weeks. If it continues to be an issue, then we can try freeconference.com. Skype is not ideal because not everyone can use it a work.

NOTE: Nexus, Hudson, and Sonar will be unavailable intermittently Sat. July 18.

Thursday July 9 2009

Participants: Noel, Mike, Daniel, Kei, Brian, Maital, Scooter, Alan

Agenda: layouts, plugin website, ISMB,

layouts:

plugin website:

ISMB:

Thursday July 2 2009

Brian, Noel, Gary, Daniel, Mike, Kei, Peng, Sarah, Samad and Matthieu

Agenda:
Question about Benno's article - Sarah. Announcement related to a grant with Trey and the Broad to use Cytoscape and the Cleo system.
2.6.3 - Mike - seems to have gone well, but we need to focus on another release for more bug fixing.
2.6.4 - fix bugs and microbarriers.
3.0 - increased external pressure to get it done - academic and industry requests are increasing.
-Daniel is porting layouts which are really important. Brings up issues with tunables - porting core plugins 
-io is the next big thing.
-events may change once enough parts of cytoscape are implemented to find issues with them.

June

Thursday June 25th 2009

Participants:Sarah, UCSD (Mike), Noel, Maital, Gary

*Cy3: Estimated time of arrival? Did board mention anything? (Piet) 
Not discussed at board meeting
Board not anticipated to be setting one.

Mac:
Basically solved
Two main problems :-
1) Windows running over each other
Solved by updating swinglayout
2) Menus
Cause dialogs need parent
More or less fixed in core
What to do about plugins ?

2.6.3
Release ASAP 26/6, 29/6, or 30/6
Mike will build release bundles 25/6

Developers should set bugs to resolved.
Testers will confirm fix and set to closed.

Biopax plugin update
Being updated to BioPax 3.0

cpath2 plugin update

Thursday June 18th 2009

Participants: Daniel, Scooter, Sarah, Noel, Maital, Alex, Gary, Mike, Peng, Kei, Allan, Brian

Agenda:
 * mac issues (Mike)
 - Recent security update to Java broke a lot of Cytoscape functionality.  Java 1.5  32-bit .
 - Among broken functionality: any code that uses the swing-layout library, such as plugin manager dialog or import table.
 - Piet ran into problems during a demo at EBI. Anyone using apple is expected to encounter these problems.
 - Mac users will try to characterize and fix these bugs during next week
 - A quick release of 2.6.3 to fix these bugs next week?  Later on, a 2.6.4 version to fix other bugs.

Ref -> http://www.theregister.co.uk/2009/06/16/apple_java_patches/
http://db.tidbits.com/article/10352

 * Bug 1990 : discussion of proposed changes (Noel)

 * 2.6.3 (Scooter)
 * Cytoscape 3 module page (Gary)
http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/DevelopmentModules
 - Module leaders: please update relevant table with more information
 - Next Tuesday: board meeting to discuss development modules

 * ISMB
 - We will hold a Birds of a Feather meeting, probably on Tuesday
 - Opening remarks by Trey or Allan
 - Plugin demo by Jim: MiMI and MetScape
 - Informal users discussion
 - We will be handing softballs and markers with Cytoscape logo

Thursday June 11th 2009

Participants: Brian, Noel, Gary, Maital, Mike, Peng, Kei,  Allan, Daniel, Samad, Piet, Sarah

Agenda: 

ISMB (Allan)
-Talks at the bioinformatics open source conference before the start of ISMB, in coop with Trey, Kei and Mike; in spirit of 3.0; why switch; trying to obtain feedback from other opensource software projects
-A birds of a feather session might a possibility also; basically only a room available and people present to chat with; Allan will try to apply
-Jim, Maital, couple of people from Toronto are there also, might help out Allan, especially at the BOF session
-Daniele Merico, Magali Michaut from Gary's group are familiar.
-TODO: send BOF announcement to Allan (Gary)

2.6.3 status (Mike)
-Bugs have been assigned by Mike, please
-Piet is trying to get feedback during hands on session at EBI/EMBL (17th of June)
-2.6.3 release is something to work on but not that imminent; not before August
-Microbarriers might be something to discuss at BOF at ISMB; ask users what they find annoying
-Last time we also discussed to send a mail to discuss list asking specifically for annoyances, Mike sends this mail, asap

Review of Cytoscape 3.0 module wiki page
-http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/DevelopmentModules
-Gary updated the module page
-Trying to flesh out this page; to enter it as discussion item for the boardmeeting
-Every module has a leader and interested people; if none assigned than that's something to take to the board
-Lead is not necessarily lead developer; more manager, and has knowledge about the module
-Interested people are mentioned
-Assign yourself when you start working on a bundle in the wiki; inform the lead also
-Keeps track of progress

Thursday June 4th 2009

Participants: Mike, Piet, Maital, Sarah, Brian,Scooter,Allan,Rosanna, Gary, and others

Agenda: EBI, SVN, 2.6, 3.0, Testplan

EBI

SVN

2.6

3.0

Testplan update

May

Thursday May 28th 2009

(was pretty short, somewhat due to lack of quorum)

Participants: Alan, Daniel, Noel, Kei, Samad, Alex,

2.6.x

Thursday May 21th 2009

Participants: Scooter, Sarah, Daniel, Noel, Maital, Brian, Mike, Peng, Kei, Allan, Alex

Agenda: 3.0, XGMML bug, ISMB - BOSC

BOSC

XGMML bug

3.0

GSoC

Thursday May 14th 2009

Participants:Alex, Maital, Mike, Peng, Kei, Piet, Scooter, Daniel, Noel, Sarah, Gary, George and Farzana from Gary's group, Brian, Samad, Allan

Agenda: SVN status, Sonar set by Brian, Boardmeeting, Testplan, EBI

SVN status:

SONAR:

Boardmeeting tomorrow;

Testplan

EBI;

Cytoscape Lite code request:

Thursday May 7th 2009

Participants:Daniel, Piet, Maital, Alex, Scooter, Mike, Sarah, Noel, Peng, Kei, Allan

Agenda: NodeViewTaskFactory, GSoC, core plugins,

GSoC:

NodeViewTaskFactory:

core plugins:

April

Thursday April 30th 2009

Participants: Sarah, Mike, Kei, Peng, Noel, Gary, Allan, Maital

Agenda: Cytoscape 3.0 development modules, Porting core plugins

Thursday April 23th 2009

Agenda: Hudson, 3.0,

Participants: Piet, Allan, Alex, Brian, Noel, Mike, Kei, Peng, Daniel, Samad, Sarah, Maital

Thursday April 16th 2009

Agenda: 3.0 and GSoC

Participants: Mike, Scooter, Daniel (bit late), Gary, Kei, (maybe others, as well)

GSoC:

3.0:

Thursday April.9th 2009

Agenda: GSoC, 3.0

Participants: Daniel (a bit late), Kei, Mike, Alex, Sarah, Noel

GSoC:

3.0:

Thursday April.2nd 2009

Participants: Allan, Gary, Sarah, Piet, Noel, Mike, Peng, Daniel (was a bit late), Alex, Maital

Agenda: GSoC, EBI-Intact training, 3.0, ISMB

GSOC

EBI/Intact

3.0

ISMB 29nd June

Other

March

Thursday March.26th 2009

Participants: Daniel, Noel, Piet, Mike, Sarah, Samad, Gary, Allan

Agenda: Board meeting, Server debacle, 3.0, GSoC, EBI-Intact training

Board meeting

Server debacle

3.0 

...modify viewmodel state...
 network.redrawGraph();

GSOC

EBI/Intact

And a reminder: next week Europe is switching to daylight saving time; so will be at 18:00 (Amsterdam, Paris, Budapest)

Thursday March.19th 2009

Participants: Scooter, Piet, Sarah, Mike, Kei, Peng, Gary, Allan, Matthieu, Samad

Agenda: GSoC, 3.0, EBI-Intact training

GSOC

3.0

EBI Intact Training

Thursday March.5 2009

Participants: Allan, Mike, Scooter, Noel, Gary, Daniel + others

Agenda: 
Mini-retreat
-Will online access be available by Skype?  Should be possible.
-View and view model implementation is a big missing piece that is being worked on. API is generally agreed upon.
-Full update on status of Cyto3
-Event model, batching of events
-Web interface - how detailed is it going to be
-Finishing layout API porting
-Project management
Virtual Cell (http://vcell.org/)
-Scooter talking to Virtual Cell at NCRR annual meeting. VC is migrating to OSGI. Goal would be to write plugins to use graph visualization, not integrate simulation capability in Cytoscape. Read in BioPAX, add modeling information and model it in a plugin.
Web site - went down, but now it's back up. Considering moving to a new hosting provider. Share credentials at mini-retreat.
Google Summer of Code - a little short on Cytoscape ideas vs. previous years.  A couple more coming up.  Please send your ideas to Alex.

February

Thursday, Feb. 26th

Participants: Sarah, Allan, Gary, Noel, Scooter, Piet, Daniel, Brian, Mike, Kei, Peng

Agenda: 2.6.2, Mini retreat, BOSC (Bioinformatics Open Source Conference), Website, 3.0

2.6.2

Mini retreat

BOSC

Web site

3.0

Thursday, Feb. 19th

Participants: Noel, Sarah, Mike, Piet, Alex, Daniel, Gary, Allan, Maital, Samad and others

Agenda:

2.6.2

MiniRetreat

Cytoscape.org

GOSC

Thursday, Feb. 12th

Participants: Brian, Noel, Sarah, Mike, Piet, Daniel, Alex, Allan

Agenda: 2.6.2, mini-retreat, webserver migration, 3.0 stuff

2.6.2

Webserver

Mini-retreat

GSOC

3.0 stuff

Thursday, Feb. 5th

Participants: Gary, Mike, Piet, Sarah, Scooter, Daniel, Trey, and others

agenda: 2.6.2, mini-retreat, helpdesk

2.6.2

mini retreat #3

helpdesk/discuss list questions

January

Thursday, Jan. 29

Participants: Sarah, Mike, Kei, Matthieu, Brian, Piet, Allan, Noel

agenda: 3.0, 2.6.2, mini-retreat, cytoscape.org

3.0:

2.6.2:

mini-retreat:

cytoscape.org down:

Thursday, Jan. 22

Participants: Alex, Gary, Brian, Noel, Mike, Allan, Sarah,

agenda: 2.6.2, release protocol,

2.6.2:

release protocol:

mini-retreat 3:

Thurs, Jan 15

Participants: Daniel, Sarah, Alex, Mike, Allan, Scooter, Piet (and many others)

Agenda: (any web framework plans?), 2.6.2, events

2.6.2:

web app framework:

events:

Thurs, Jan 8

Participants: Daniel, Mike, AllanK, Alex, Sarah, Brian (and some others)

agenda: event handling framework, 2.6.2, next mini-retreat,

Google Summer of Code is funded this year, with similar funding, maybe bit fewer students; timeline expected to be similar to last years

2.6.2:

next mini-retreat:

event handling:

2008

December

Thurs, Dec 18

participants: Allan, Daniel, Mike, Noel, (others?) agenda: events, 2.6.2, 3.0, plan schedule for holidays,

events:

2.6.2:

schedule:

3.0:

Thurs, Dec 11

conf. call notes for dec. 11

participants: Mike, Daniel, Scooter, Sarah, Allan, Piet (and maybe others)

agenda: 2.6.2, ISMB,

ISMB: attendance of Allan, Scooter, Piet depends on paper submission next meeting more info

2.6.2:

Thurs, Dec 4

conf call notes for dec. 4

participants: Sarah, Alex, Daniel, Alan, Kei, Noel, Gary, Brian

agenda: 2.6.2, events, ISMB 2009,

2.6.2:

event handling:

ISMB 2009:

November

Thurs, Nov 20

participants: Mike, Sarah, Noel, Daniel, Gary, Scooter, Alan, Piet, Trey, Mathieu

agenda: 2.6.2, webstart bug, mini-retreat, (vizmap api)

2.6.2:

No conference call next week (Thanksgiving), Mike won't be able to attend week after that (but there will be a conf. call then).

vizmap api:

3.0:

Thurs, Nov 13

conf call notes nov. 13

participants: Scooter, Sarah, Daniel, AllanK, Noel, (and some others)

agenda: mini-retreat, "undefined column CyDataTable issue"

mini-retreat:

"undefined column CyDataTable issue":

Thurs, Nov 6

2008.nov.6 conference call notes

participants: Alex, Maital, Piet, Allan, Gary, Scooter, Daniel, Noel, Mike, Trey, Brian

agenda: mini-retreat,

mini-retreat:

NCRR grant application possibility:

Metanodes:

2.6.2:

3.0:

developer awareness tool:

October

=== Thurs, Oct 23 ===

participants: Daniel, Sarah, Noel, Mike, Alex, Scooter, Gary (I think I missed some people -- Daniel)

agenda: Matlab, mini-retreat, metanodes

mini-retreat:

 * additional hotel recommendations added to wiki (http://cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/MiniRetreatTwo)
    (Queen Anne  most recommended, but bit out-of-way thus maybe organize shuttles if  everyone stays there)
 * mini-retreat agenda: added some items to wiki-page
 * Daniel will refresh writeup about pluggable renderers and link it from mini-retreat page

Matlab:

 * make Matlab script engine?
 * large body of Matlab code that people would want to use
 * possibilities:
   * javabuilder http://www.mathworks.com/products/javabuilder/ (although that would not be a fully solution)
   * connecting octave to cytoscape instead (with octave being somewhat compatible with matlab)
     might work, but since octave is not used much by the target audience (who have the existing Matlab codebase) most likely octave is too incompatible with Matlab.

     links about octave-matlab (in)compatibility:
     http://www.gnu.org/software/octave/FAQ.html#MATLAB-compatibility
     http://users.powernet.co.uk/kienzle/octave/matcompat/
     http://users.powernet.co.uk/kienzle/octave/matcompat/HTML/summary.html
    
   * maybe use Matlab distributed computing server (If the API of that makes it easier to interface to Matlab)

Metanodes:
 * Scooter tried writing testcases from current usecases
    issues: (list of questions in post to cy-staff)
    * what should a plugin see? (when some metanodes are collapsed, some are not): what the user sees, or all metanodes?
    * 'current network' no longer exsist, since if it contains metanodes, it is not unambigous: expandedness of metanode is a view-related property


Software development paper invite from Greg Wilson (Gary)
Deadline is April 2009.  Still interested? - delay until next week


=== Thurs, Oct 16 ===

participants: Benno, Mattew, Mike, Kei, Peng, Piet, Sarah, Noel, Alex, Allan
Notes: Sarah

== New core developers ==
* Piet has been nominated as and been made a core developer
* Benno has a new core developer as well Mattew (spelled that wrong)

Please see mini-retreat 2 page on wiki.

Extreme echo on the call line, if anyone really needs to discuss please send an email.

=== Thursday, October 9, 2008 ===

2008. Oct. 9. Conference call notes

participants: Daniel, Brian, Scooter, Sarah, Noel, Mike, Alex, AllanK, Gary, Piet(had to leave earlier)

agenda: confirm mini-retreat scheduling, 3.0: subnetworks, book

==== mini-retreat ====

 * final decision: nov. 14-15 (Fri-Sat) at UCSF
 * Alex will create [:Cytoscape 3.0/MiniRetreatTwo] page on wiki, with hotel information
 * Arrival on Thursday evening, so full Friday can be scheduled
 * possibility for teleconferencing via skype, etc: didn't really work last time
 * UCSF has video-conferencing room (uses standard polycon, so a video-conferencing room on other end is needed; will post requirements to cyto-staff)
 * want to focus on viewmodel and view

==== calls about OSGi book ====
 
 * Manning (competitor of O'Reilly), AllanK, Mike and Kei talked with them about a book on Cytoscape (and general network visualization)
 * arguments for and against writing book didn't really change since discussion in Toronto
 * Maybe book now, between 2.6 and 3.0 is too early
 * consensus: too early now, tell Manning that it should be revisited after 3.0

==== 3.0 ====

 * Mike has been writing implementation of model layer, subnetworks, etc.
 * need unittests, to tests API, too (i.e. for "typical usage")
 * Scooter will write unittests from some of the usecases
 * CyNetwork interface is considered finished, Scooter will add javadocs
 * model layer is (apart from subnetworks) pretty much finished. (events, CyNetwork, etc.)
 * events: list of viewmodel (and view) related events is not defined yet, but for model-related events is done.
 * CyDataTable: having different backends was discussed, but the mechanism for getting them was not yet considered. It depends on where CyDataTable objects came from (injected by spring, etc.)
   * big question: is CyDataTable API complete enough or will it be problematic that other backends will be limited by it? (like having an SQL-backed implementation without join-capability in CyDataTable)
   * one possibility is to push the issue to plugins: the plugin that brings the SQL-backed implementation could expose a richer API. This means that those plugins that use that richer API will depend on that plugin
   * or add richer metadata to CyDataTable to make it possible to query capabilities


Greg Wilson invited us to contribute to a special issue of "Computing in Science and Engineering" next year on the theme "Software Engineering and Scientific Computing". Some general interest from Mike, Sarah, Scooter and Allan.  So Gary will get the relevant deadlines from Greg and if compatible with people's schedules, say yes.

=== Thursday, October 2, 2008 ===

participants: Daniel, Noel, Mike, Sarah, Piet, AllanK (sorry, I came late), Gary

agenda: OSGi book, 3.0, mini-retreat

==== 3.0 ====
 * performance tests work for Mike, not for Sarah (runs out of memory when running all tests, but tests individually work)
 * will split performance tests into seperate project, so that they won't run at every build
 * will set cruisecontrol to run after every checkin (and at least nightly) so that performance-tests will be run after every checkin; and to run performance tests after API bundle changes

==== mini-retreat ====
 * nov. in Seattle would be bad for  AllanK,
 * possibly move mini-retreat to San Francisco, or have travel funds from cytoscape consortium

==== OSGi book ====
 * as mentioned on cyto-staff
 * skype conference tomorrow at 10, ask for invitation from Kei
 
==== Gary's group working on a Cytoscape-lite ====
 * Ajax, web-based
 * required for GeneMania project

September

=== Thursday, September 25, 2008 ===
present: Daniel, Mike, Scooter, Noel, Sarah, Allan

==== Cytoscape 2.6.1 ====
 * Only reported issue is OpenJDK issue
  * Need to change the toolkit from MToolkit to XToolkit in the installer:
  * {{{ sed "s/MToolkit/XToolkit/" Cytoscape_2_6_1_unix.sh > Cytoscape.sh

Cytoscape 3.0

mini-retreat dates

}}} 

Thursday, September 18, 2008
present: ?
Notes: DanielAbel (but feel free to edit -- I hope I dont mis-represent anyones opinions)

== cy 2.6.1 ==
- considered finished, javadoc-generation problem fixed (shouldn't cause problems next release)

== mini-retreat ==
- some discussion on CyDataTable etc. (i.e. mini-retreat results)
  conclusion: api not yet described well enough, no consensus yet on what naming to use. (like RootGraph or ParentGraph )
  API should be easy to to understand, although metanodes part might be inherently complicated with no way to make it simple
 
- further development: two alternatives were discussed:
 -- merge api plan in current cy3.0 (more of a refactor)
    pro: less chance of re-inventing old bugs and of total rewrite; how api changes affect plugin developers would be more understood.
    cons: lots of code to fix, would destabilize code when lower layers are refactored; would have to re-fix the same code several times (first when model is fixed, then when viewmodel, when view, etc.)

 -- create seperate branch, implement model layer there, then pull code over from cy3.0 (this would be closer to rewrite)
    pro: it would be easier to enforce the cleanness of the new branch
    cons: too much incentive to rewrite too much from scratch
 -- opinions differed on severity on pro/cons for each (like how much re-fixing first alternative would mean, how much bug regression would be in second). Someone commented that either way it would end up to be a circular process, with code moving both ways.
- organization of project layout:
  -- currently 3.0 branch: one maven project with many modules (easy to compile everything, but a bit less modular)
  -- Mike will break it apart into separate projects
- HyperEdges / HyperGraph
  -- current consensus: hypergraph semantics should be stored as Attributes (like "this is a connectornode, so don't count it as real node")
  -- no competitor "hypergraph system" identified (although many wanted to have one to steal ideas from)
- mini-retreat considered success, next mini-retreat plan: mid-october, early november (before US thanksgiving) maybe in Seattle (to coincide with some other meeting?)
- 'private' maven repository for cytoscape: will be one in future, but not yet in short term (although a public one might be used instead of a cytoscape-specific one)

July

Thursday, July 31, 2008
AlexP, AlexA, Sarah, Brian, Noel, Gary, Mike, Kei, Peng, Trey, Allan
Notes: Alex

== Post Retreat Questions ==
- Keep an eye out for retreat wiki notes and materials: feel free to add or edit
- Next year: University of Michigan by David States

== 2.6.1 ==
- Scooter's last commits?
- Mike will update release bundle instructions
- Anyone volunteering to handle release while Mike is OOT

== 3.0 ==
- Kei is working on clean build in Eclipse
- Everyone should test and provide feedback
- Follow up on Daniel's work
- Mike will start it and then distribute tasks
- First CyWest Meeting in San Diego (beach house!) Sept 12-13

June

Thursday, June 19, 2008
Sarah, Maital, Noel, Brian, Scooter, Mike, Kei, Peng, Allan, Gary
Notes: Alex

== 2.6.1 ==
 - Scooter is going to squeeze in a couple key features for tunables and then give Mike the green light when ready to package and ship.

== 3.0 ==
 - Everyone should have reviewed the view portion of the API: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/mes/api/src/main/java/org/cytoscape/view/
 - Terminology: ViewModel and Presentation
 - X,Y,Z,T in VisualProperty may not be ideal for continuous updating, e.g., in animated layout; may lead to performance hit.  Keep for now.
 - Should the VisualProperty enum implement an interface to "keep the door open" for plugin developers, e.g.,  to add their own Node_Shape?
  -- Does this control belong in the ViewModel or Presentation? ViewModel, if you expect to store your Node_Shape.
  -- The advantage of using an enum is the ability to simply get at all possible values.
  -- Alternatively, we could use an osgi registry to support a new Node_Shape. 
  -- Or, add User_Defined in the enum. This allows it to be serialized and keeps it simple. This mechanism could use Attributes to support multiple shapes.
  -- Of course, if the plugin is not loaded when the file is reopened, then Node_Shape would default back to "circle" or something.
  -- Ideally, we can "leave the door open" with having to "have it open", meaning keeping for 99% of the cases. This could potentially be done by extending enum.
  -- Within the "1%" we'll want to make sure we are taking care of power users/developers who need custom shapes e.g., mims group?
  -- Perhaps we need to think top-down here, to balance the design and consider the Presentation concerns/needs.
  -- Important to distinguish _custom shapes_ (size and color controlled by vizMapper) and _custom graphics_ (a *substitute* node that has a fixed shape, size, color, but behaves fully as a node, rather than as a sticker on top of a node). There are use cases that blur these, however, and thus suggest having a single system that can have overrides per parameter. E.g., a custom graphic like a photo that you still want to have vizMapper controlling size; or a donut node with vizMapper-controled node in the center and a custom color on the outer rim.
  -- Fill color and opacity -or- Paint? Breakdown -or- lump?
 - Next week we will continue the discussion of ViewModel and Attributes

== Retreat ==
 - Detailed schedule is up on wiki. Please sign-up to lead sessions with Gary.
 - http://cytoscape.org/cgi-bin/moin.cgi/CytoscapeRetreat2008

May

Thursday June 12. 2008
Allan, Peng, Kei, Mike, Sarah, Noel, Brian, Kristina, Trey, Gary, Scooter
Notes: Sarah

== Retreat Update ==
  - Some issues with sign up/paying via credit card
  - Big dinner Thursday evening
  - Need to know who is interested in a dinner for the cyto staff group on Sat. night?
  - Let Gary know about specific requests or presenting on application showcase day.
  - Funding, Trey and Gary working it out

== 2.6.1 ==
  - Bugs have been assigned, everyone needs to triage and get back to Mike ASAP
  - Mike will put together release and get it out to group to test

== Mike 3.0 API ==
  - Everyone needs to look through the API emailed
  - Some concern about the distinction between global/local attributes
  - Need to make sure we can still use them through things like VizMapper etc
  - There is some concern about the memory management in regards to the attributes
  - Open issues: 
    - Are we happy with Attributes?
    - Are we punting groups, splitting the concept, etc?
  - Ignore groups in the model for now.
  - Keep the use case of metanodes/named-selection for later and if we need it we can iterate back over the model API later
  - Start thinking view model, read the 3.0 discussion.  Iterate over based on interface discussed for graph model/attributes

Thursday May 22, 2008
Notes: Alex
Alex, Brian, Sarah, Mike, Peng, Kei, David, Scooter, Allan

== Maven Builds ==
* Brian raised some issues with bundling during build
* Mike will continue to assess build/package options beyond Felix; we can work around current issues in the meantime

== Model Issues ==
http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/ModelDiscussions

=== Event Model ===
* Here, "events" refer to events that travel up the hierarchy, e.g., node added to graph; events communicated between layers
* Our modules form a directed acyclic graph and event listening should "listen up the graph"
  - for example, the View module should listen for events in CyNetwork (CyNetwork is higher up in the hierarchy)
  - VizMapper changes CyNetwork; CyNetwork fires event; View detects event and controls layout, etc.
  - This is "event driven" and more consistent with MVC
* Synchronous or Asynchronous?  Currently, we have synchronous, but asynchronous would clearly be advantageous for clean operation and external application integration
* Two approaches: (1) an Event Type Model, (2) an Inheritance Model (see advantages and disadvantages on wiki page)
* Mike is currently leaning towards Inheritance; consensus agreement. 
* Single broad listener or multiple type-specific listener?  Both? Or, a "specific" listeners can be more general?
* User interface events will be handled within layers and then rely on the event hierarchy to pass between layers
* OSGi advocates a "whiteboard model": register yourself as a listening service; handler checks registry
* Network Loading use case: "add node" events should be ignored until done
  - listen for "start load", ignore "add node" for *that* network, until "end load"... this would require processing each "add node" to determine whether it can be ignored
  - alternatively, wait to register for "add node" events until *after* loading is complete
* We should investigate additional patterns, since we are not likely to be the only ones facing these issues.

== Next Week ==
* Gary's attributes use cases

Thursday May 15, 2008
Notes: Sarah
Mike, Kei, Peng, Scooter, Allan, Sarah, Brian, Maital

== 3.0 Summary ==
* Mike put together a diagram of steps required to get to 3.0, not yet posted.  Graphical view of project plan currently on the 3.0 page.
* Note it will be an iterative process, not a straight line.  

== Build Stuff ==
* Issue with assembly not packaging libs the way we need?
* pax tool that creates osgi packages
* Brian & Mike will work out how to clean up the build

== Attributes ==
* Mike has proposed two possible solutions
* New use case: a global pool of unmapped attributes
* Look back at Gary’s SUID proposal which would handle both local and global attributes.  Provides a database abstraction for attributes and their mapping to networks.
* Need to address various use cases at the application layer and plugin writer layer
* Need the idea of foreign keys in order to establish a basic relationship that is accessible to users and plugin writers
* Make sure we handle user mapping (users won’t see the SUID’s) where nodes may have duplicate “names” (which are not necessarily guaranteed to be unique), this may be a tool by tool basis?
* Gary has captured use cases and will add these.
* Everyone ADD COMMENTS!

Thursday May 8, 2008
Gary, Allan, Scooter, Brian, Noel, Alex, Peng, Kei, Mike
Notes: Alex

== Cytoscape: The Book ==
 * Wiki page established: http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_Book
 * Lots of information there
 * Review the outline and modify to get a solid plan together

== Open Helix ==
 * CEO emailed Mike asking if it was legal for them to use Cytoscape in their training material
 * Apparently they have been getting requests for Cytoscape (and GenMAPP) training!
 * Folks pay them to put together free tutorials

== The Merge ==
 * Done!
 * Remember, if you have a bug fix, you have to make it in both 2.6 and 3.0
 * Maven: we still have a few things to sort out (e.g., Felix) and we want to keep it simple for the plugin developer

== 3.0 Development ==
 * Updated wiki page on model discussion: http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/ModelDiscussions
 * Review new content regarding network model and model API proposals
 * There are remaining open issues that need to be addressed (preferably, one at a time):
   - fundamental issue: node, edge and network relationship/coupling 
   - need for speed/performance, need for simplicity for plugin developers 
   - alternative proposal illustrates the type of simplicity a plugin writer needs, not necessarily a specific impl
   - degree of coupling at various "layers" of the hierarchy is at issue
   - some simple examples like "traversing" or "getting node name" need to be very easy
   - how should attributes be modeled and accessed
   - separate core and plugin APIs?
   - the concern for impl and javadoc view are separable
   - the javadoc necessarily follows the impl, but we should all have the same javadoc goal in mind before settling the impl plan
   - need for overview vision of modules to settle higher-level issues and contextualize impl work, including
     * attribute
     * groups
     * hyperedges

April

Thursday April 24, 2008
Allan, Gary, Alex, Mike, Peng, Scooter, Sarah
Notes: Allan



== Presentations, Book chapter ==
 * invitation for a Cytoscape book chapter, picking up on Nature Protocols work
   - Humana Press, book on systems biology of yeast
   - analysis of gene expression with Cytoscape -- can mention SGD as source of yeast
   - leverage from Nature Protocols package
   - draft due March 2009 
   - Allan and Scooter may co-author?
  * invitation for tutorials
   - with BigCat group at Maastricht , all travel expenses paid, June 23-27th, actual talk is June 26th
   - European Molecular Biology Organization: 26-30th September, 2 hour lecture, assume travel expenses paid but doesn't say in email, Mike will look into this.

== GSoC 2008 ==
 * between now and May 21st is community bonding period, get people prepared
 * mentors should let Mike know when to add students to Cytostaff
 * should they code to 2.6 or 3.0?  
   - probably 2.6 for people building plugins, possibly 3.0 for people working more closely in areas related to 3.0

== Retreat Update ==
 * have local organizing committee
 * still raising money
 * do we need a registration deadline?
   - currently booked room is for 100, which should be sufficient, but may want larger room for showcase
 * Wednesday (possibly Tuesday) for hackathon, Thursday application showcase, Friday tutorials / decision making, Saturday decision making
 * possible conflicting sessions with ISMB saturday morning tutorials, BioPathways meeting


== 3.0 ==
 * merging: we need to fork off 3.0 version for future development
   - merge of 2.6 with 3.0 is organizational, not re-coding.
   - should we merge before we first re-start the discussions? 
   - merge will be week of April 28th - May 2nd
   - Mike will make assignments and send email
   - look at Mike's email 1-4 for instructions for merging.

== 2.6.1 Release ==
 * what bugs need to be fixed?
 * critical bugs should be fixed, but non-critical features should be added to 3.0
 * get 2.6.1 out in the next couple of weeks
 * Scooter and Sarah working on a logging prototype for 2.6.1, this can be post-merge
 * bug fixes are post-merge

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

2.6.1 Release

3.0 Planning Overview

Google Summer of Code

}}}

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

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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