Thursday, Dec.17, 2009

Participants: Sarah, Mike, Allan, Brian, Noel, Scooter, Johannes, Samad, Maital


use of google wave for conference calls

board meeting


possibly U Michigan will host in July

will maybe be close in time to ISMB

    * next two conference calls 12/24, 12/31 cancelled
    * next call we will have will be Thursday, 1/7/2010 

Thursday, Dec.10, 2009

Participants: Sarah, Mike, Allan, Brian, Noel, Scooter, Johannes, Samad, Maital


use of google wave for conference calls

board meeting


possibly U Michigan will host in July

will maybe be close in time to ISMB

    * next two conference calls 12/24, 12/31 cancelled
    * next call we will have will be Thursday, 1/7/2010 

Thursday, Dec.10, 2009

Participants: Gary, Allan, Mike, Noel, Brian, Sarah, Peng-Liang, Kei, Scooter, Johannes

-Etherpad is moving, move to Google wave? - test next week.

-Project updates from different groups for report for Cytoscape Board meeting
--give the board a short presentation ~Dec.22.  Can each group/person send Mike a quick update of what you're working on related to public Cytoscape,  -a few sentences is fine.  Ideally by next Thursday (Dec.17)

-Allan announcement
Samad Lotia is now working with our group at Agilent for a one-year period to work on Cytoscape things.

-Google grants

-Holiday schedule for calls 
-Meet Dec.17, then next Jan.7.2010

What people are working?
-Gary: 1. Cytoscape web, 2. test plan for 2.6, 3.0, 3. enrichment map plugin for 2.6 (http://baderlab.org/Software/EnrichmentMap/Description), 4. BioPAX import plugin update (Level 3 support)
-Allan: Cytoscape extensions for Agilent products.  Cytoscape is a plugin to the project. 1) probe design (Agilent eArray), 2) metabolomics and proteomics - controlling 2nd run of mass spec based on a network neighborhood
Mike/UCSD - 3.0 until summer, working on nested networks now for 2.7, new edge types, bug fixing, updated visualizer/renderer to view nested networks, nested networks file format, editing, two new methods - setNested, getNested.
Noel - fixing many bugs
Brian -1. New plugin for 2.6/7. Display dual PPI/gene networks from 2 different speices and highlight related (sub)networks. 2. Hosting of various cytoscape resources.
Peng - nested networks
Kei - PSIQUIC plugin to access standard PSI-MI compliant web services - will be part of 2.7. 3D renderer prototype
Scooter - CyAnimator, clustermaker (4 new clustering methods and visualizations), CyCommands (inter-plugin communication), phylogenetic tree plugin, ChemViz (depends on 1.6), plugin updates (metanodes), making many plugins available via CyCommands
Johannes - covered under UCSD

Sarah - integrating Cytoscpae and an old version of Cyto-Web (Gary's project) with a number of our data viz/integration projects here.  Also looking into using it with a protein-protein interaction application we have

Alex - GenMAPP/CS - working on the alpha version, network importer, integrating with CyThesaurus, web service capability - non-redundant gene expression enrichment analysis (Go-elite)

Thursday December 3 2009

Attendees: Mike, Sarah, Noel, Gary, Kei, Peng, Johannes, Allan, Brian

-Wiki - aplus hosting is bad.  Should we move to Sourceforge - at least SVN and the website.
Importing from other SCMs http://sourceforge.net/apps/trac/sourceforge/wiki/SVN%20adminrepo#ImportingfromotherreposincludingotherSCMs
-Decision: investigate use of sourceforge to host SVN, website.  Maybe bug tracker and wiki in the future. Maybe the wiki should be the website.
-Would be a good opportunity to clean up the website.
-Cytoscape.org redirect instructions:

- There was a request for onsite training.  Should we have a procedure for sending people out?  Should we outsource this?
--Procedure: ad hoc open call to cytostaff list.
--Open Helix may be an option for outsourcing, but we need to find out more about it.
-- Advantage of giving it ourselves is 1. we know Cytoscape best and 2. we get valuable user feedback. If we outsource, we will need to be involved e.g. to supervise and gather feedback.
-Mike will ping OpenHelix to see what they offer
-Mike will email Peter Hornbeck to keep him aprised and Allan will email cytostaff

- Retreat status update
--Trey is investigating hosting in Michigan
--Targeting late spring
--Maybe some discussion at board level - Dec.22 is next call.

- Deprecated code removal
--Code deprecated for more than 1 year. Should we pull it out?
--Yes, let's remove it.  If people start complaining, then we can revisit.

-Cytoscape lite
--Maybe name it Cytoscape Web

- Cytoscape 2.7 and 3.0 status


Thursday November 26 2009

No call due to Thanksgiving

Thursday November 19 2009

November 19th
Attendees:Noel, Brian, Mike, Sarah, Piet, Allan, 
Agenda Items:
Website migration
Wiki is now working again, thanks to Brian.
Changes since Oct 22nd will need to be recreated.
Mike will email details for accessing alternative web site server.

Ideker lab work
Network Search algorithms, will work on adding support in Cytoscape for these.
CyNode will get new methods to permit nesting of Networks.
New file format will be defined to support this.
Editing and view will be modified

New Edge types are being added.

Trey is thinking about where it will be held, no decision so far, board meeting in Dec. may provide one.

Thursday November 12 2009

November 12th
Attendees:Noel, Mike, Allan, Sarah, Brian, 
Agenda Items:
No change to date.
Brian will take a look at hosting
Will try to use wiki.cytoscape.org to point to new host

no estimated release date
UCSD has new requirements that they want to get into 2.7
earliest is around Xmas
realistically January or so

a bit awkward for the remote people (mostly due to video conferencing software/quality)
Still good to have time to focus on portring work
Lead into discussion on how to proceed with 3.0 and other 3.0 topics

we need to start getting this set up
U Michigan has offered to host but need lead time
MIke will talk to Trey about approaching them

Advanced notice of no conf. call Nov 26th (Thanksgiving in US)

Thursday November 5 2009

November 5th
Attendees: Noel, Sarah, Alex, Mike, Maital, Daniel, Jeremy
Agenda Items :
New Programmer

Aplus (Cytoscape hosting) :
Site migrated to new server.
Wiki is broken due to no Python.
Trouble ticket opened, not resolved.
Need to think about hosting by one of core groups.
Contract with Aplus ends early next year, need to decide by then what's going to happen.


Thursday October 29 2009

No call due to Hackathon.

Thursday October 22 2009

Notes AWOL

Thursday October 15 2009

Thursday October 15 2009
Participants:  Mike, Peng, Sarah, Samad, Gary, Piet, Daniel, Maital, Allan

Agenda Items:

Samad found an issue with Cyto3 on the mac - Mike will check it out.

Everyone organized travel and hotel?
some discussion about people's travel plans.
If people are coming early, Allan was going to organize a tour of San Francisco. If you will be there earlier, contact Allan about it if you're interested.

Integrated Search Bundle (Maital):
see slides Maital sent to the cytostaff mailing list. Allan also mentioned Gang Su's recent post about searching. The gsoc code works, but is not finished - needs bug-fixing. Hoping the student will have time to work on it after December. Maybe Gang Su would be interested in continuing work on searching in Cyto3?
Mike: we should decide which plugin to use based on the architecture underlying it.

round robin discussion:
- Cyto3: Samad's question about accessing all rows - may need to add some methods to the API
- Cyto3: event model - some discussion about batch events, micro/macro
- Cyto3: command tool that Scooter is working on - Mike and Scooter are discussing how to best set this up in 2.7 recognizing that CyTask is in Cyto3.
- http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/DevelopmentModules
- SubNetwork API being worked on by UCSD, but no updates to the group yet.
- Allan will be working on editor
- Samad working on update IO, including SIF. May get time to finish XGMML.
- Peng: build scripts for cyto3 release
- Gary: BioPAX Level 3 is done and will be released in mid-November. A Cytoscape 2.6 plugin is being written and then will be ported to Cytoscape 3.
- Maital: working on bug fixes for EnhancedSearch, which will be a core plugin in 2.7. Will enhanced search replace quicksearch? We probably only want one to appear at the same time - maybe a toggle button. Filters depend on quickfind, so it needs to be there.  2.7 release expected towards December / January
- Allan: working on extensions to Agilent products such as GeneSpring using Cytoscape. Mass spec representation to search compounds. Design custom array probes based on gene interactions. Also working on GoLayout tool.

Thursday October 8 2009

Thursday October 8 2009
Participants: Noel, Allan, Maital, Scooter, Mike, Piet, Gary, Sarah, Peng

Agenda Items:
Selection of bugs I need guidence on:
Bug 1960 fix or not ?
Make sure behaviour is conistant between network and attribute import.

Bug 1932 apply Daniel's patch ?
Include this fix.

Bug 1891, have modifications to commons-cli that make required change in arg parsing semantics, commit or hold ?
Check for any other code besides CyMain and BatchTool for use, then document and commit.

Expected behaviour when importing attributes using case insensitive mapping (ref. bug 1961)
My understanding of behaviour confirmed.
Will commit changes when tested.

URL handling/parsing (ref. bug 1936)
Centralise URl sanitisation, and fixup file: URLs
Defer decision on what to do about other URLs

Table Import behaviour
Scooter will open bug report on annoying option reseting behaviour

Cytoscape 3.0 developers retreat:
List of tasks to tackle, is it right ?
Answer: Pretty much
Need to use time for programming, hence anything needing a design decision during a porting attempt must be parked and we move on to something else

Should try to talk over problem areas / subjects at TCs leading up to Hackathon
Maital to present on integrated search bundle at a TC prior to th
I/O API needs some discussion
How to do certain things with OSGI bundles, e.g. providing abstract base classes
Session serialisation format

Point to guide from Hackathon page

Thursday October 1 2009

Thursday October 1 2009
Participants: Noel, Maital, Mike, Daniel, Sarah, Samad, Kei, Alex

Wont be on call: Allan, Gary

Agenda Items:
Next 2.x release
Will it be 2.6.4 (so as to include recent bug fixes) or 2.7 (so as to include core changes to 
support inter-plugin communication) ?
Want input from those with any major changes to make
Next release will be 2.7 unless anything urgent comes up
Provisional target date December 2009 / January 2010

Two days (October Thur 29 - Friday 30, 2009)

Bug report placed by E. Stepanova on Etherpad will be posted to user mailing list with instructions on how to sign up.


Thursday September 24 2009

Participants: Noel, AllanK, Piet, Sarah, Maital, Alex, Kei, Peng

Mike, Gary not on call, submitting Cytoscape grant application
Scooter not on call, traveling.

Agenda Items:
CruiseControl: Main page is OK, but project detail pages are coming up with class file version errors (mismatched JDK 5 and 6)

dates are 29-31 October, with some arrival time on 29th and leaving time on 31st
location San Francisco
we should try to optimize the schedule so that people in Europe can participate in the earlier hours
we need to have the development environment setup: http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/Eclipse/CoreDevelopment
should we break into pairwise programing teams?
goal: port the core plugins to 3.0
action item: identify nearby hotel
   one was the Queen Anne: http://www.queenanne.com/
action item: setup a wiki page for the hackathon

Google summer code 
all plugins that came out of this summer's GSoC are up on the plugin manager

2.6.4 release
there are a lot of bugs to be fixed
some changes to core to support inter-plugin communication (that may be for 2.7)
we should bring this up at next weeks TC

Thursday September 17 2009

Participants: Mike, Daniel, Sarah, Brian, Scooter, Noel, Maital, Allan

Agenda Items:
 - getting presentation dimensions for "export as graphics":
   put in viewmodel or add no-arg RenderingEngine.getImage() method? (Or meaning of TwoDVisualLexicon.NETWORK_SCALE_FACTOR?)
   ->  agreement on needing to have a feature for this, no decision yet on how exactly to do it.

CruiseControl, is it possible to force build from front page ?
For me it refreshes before the request completes.
Mike will look into 

If there is only one global filter it isn't removed from filters.props when deleted (Bug 2076), am I right in assuming this isn't intentional ?
Not intentional.
Peng will look at Noel's fix.

Some files in the Filters plugin are missing license headers, should these be added (if so what year to use for copyright) ?
What about other core and core plugin files.
License headers should be added, using 2009 for the year.

Dates for Hackathon
Google Summer of Code Mentor Summit: October 24-25 - Saturday and Sunday

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

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

Prioritize your own bugs
Snow leopard is going to be tested


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

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.

-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/ )

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.


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

Cytoscape retreat update - Trey is contacting David States
-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

3.0 build infrastructure (Hudson, sonar, maven repository). is being updated, might be down during the weekend.
-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,


plugin website:


Thursday July 2 2009

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

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.


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.

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 ?

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

 * 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/

 * Bug 1990 : discussion of proposed changes (Noel)

 * 2.6.3 (Scooter)
 * Cytoscape 3 module page (Gary)
 - Module leaders: please update relevant table with more information
 - Next Tuesday: board meeting to discuss development modules

 - 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


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
-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





Testplan update


Thursday May 28th 2009

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

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


Thursday May 21th 2009

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

Agenda: 3.0, XGMML bug, ISMB - BOSC





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:


Boardmeeting tomorrow;



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,



core plugins:


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)



Thursday April.9th 2009

Agenda: GSoC, 3.0

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



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




ISMB 29nd June



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


...modify viewmodel state...



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



EBI Intact Training

Thursday March.5 2009

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

-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.


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


Mini retreat


Web site


Thursday, Feb. 19th

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






Thursday, Feb. 12th

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

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





3.0 stuff

Thursday, Feb. 5th

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

agenda: 2.6.2, mini-retreat, helpdesk


mini retreat #3

helpdesk/discuss list questions


Thursday, Jan. 29

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

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




cytoscape.org down:

Thursday, Jan. 22

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

agenda: 2.6.2, release protocol,


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


web app framework:


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


next mini-retreat:

event handling:

Cytostaff_Development/Conference_call_notes/2009 (last edited 2010-02-04 18:29:05 by GaryBader)

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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