2009

December

Thursday, Dec.17, 2009

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

Agenda

use of google wave for conference calls

board meeting

retreat

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

Agenda

use of google wave for conference calls

board meeting

retreat

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

Agenda
-Wiki - aplus hosting is bad.  Should we move to Sourceforge - at least SVN and the website.
https://sourceforge.net/apps/trac/sourceforge/wiki/Hosted%20Apps
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:
https://sourceforge.net/apps/trac/sourceforge/wiki/Custom%20VHOSTs

- 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

November

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.

Retreat
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:
wiki
No change to date.
Brian will take a look at hosting
Will try to use wiki.cytoscape.org to point to new host

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

hackathon
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

retreat
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.

October

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.

hackathon:
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

Hackathon
http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/Hackathon
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.

September

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)

Hackathon
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:
3.0:
 - 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.

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

2.x
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.

2.x
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
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:

• hierarchical layout is very crufty (old and kinda undocumented)
• Scooter wants to replace it with a prefuse tree layout (since that seems to be simpler than fixing it)

• Decision: keep the current one, add the prefuse tree layout (by wrapping prefuse the same way ForceDirectedLayout is done)

plugin website:

• currently cytoscape and plugins are built on java 1.5; Cytoscape's plugin website only handles java 1.6; (the issue is with supporting 32 bit mac users)
• should the plugin website extended to handle either version of plugins?
• Mike suggests rebuilding this single plugin on java 1.5 instead (which would involve some porting since it uses 1.6 features)

ISMB:

• Alan gave cytoscape 3.0 talk at satellite conference; will write up some notes

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

• Piet's going to EBI to talk on 3.0, just talk about directions, plugin demo not yet feasible
• Course materials partly based on stuff from Scooter, Tero, assembled that (thanks!)
• Allan talks end of the month shares materials (will contact Piet)
• Scooter is giving a talk in September also; hands on. Piet shares ppt etc on wiki
• Allan, has arranged an internship (Ana Kuchinsky (!)) the existing documentation in mediawiki over this summer as a repository for assembling presentations
• Mike, Kei might have some information/PPT on Cy3 available also

SVN

• Should be fixed
• Everyone is now a full user; Mike wants to offload usermanagement. So set up a dedicated SVN server someplace. Will use https. Would solve problems, will happen in a few months time

2.6

• Everybody: remember quite a few bugs; there are enough justifying a next release.
• Mike is going to assign bugs

3.0

• Development modules haven't been updated. Gary is going to do that.
• May 15 board meeting: organizing development
• Approaches: Modular division of cytoscape with respective leaders assigning tasks, Gary's going to provide info on that; one of these modules is IO; Status: interfaces and basic parsing; visualization is tedious. Noel might take responsibility, will be informed by Mike. Rest of the modules should be assigned
• More distributed process == more robust, so a bunch of people rotating chairing the call. Gary's going to assemble a list, we'll have a separate conference call on that

Testplan update

• 100% done with coreplugins
• 80% done for UI
• Continu with bugtickets
• Now in a schedule of creating testcases and running them in the same time
• There are still microbarriers... something not really working, workarounds work, how do we find these?
• Mike has the feeling that 2.5 is better appreciated than 2.6
• What works is get the programmers working with new users
• There seem to be a host of problems with the Mac, is a prime platform though. In between jdk versions (latte?) are no solution, probably approach Apple directly.Osprey did contact apple and got support. Try identify specific mac bugs, write them down and sent to apple, they're hard to reproduce though
• Can be introduced systemspecific in the bugsystem
• We're going for a new day of bugs for 2.6, than release 2.6.3
• Ask the discuss list: what bothers you? We're on a mission to fix that!

May

Thursday May 28th 2009

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

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

2.6.x

• bunch of new bugs in bugtracker, sign up for those you are interested in / are important for you
• maybe have a 2.6.3 as a bugfix release when those bugs are fixed.

Thursday May 21th 2009

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

Agenda: 3.0, XGMML bug, ISMB - BOSC

BOSC

• Allan will be representing Cytoscape at BOSC. He will speak about porting plugins to 3.0.

XGMML bug

• Scooter will try to fix it.
• More 2.6 bugs out there, none is a show stopper.

3.0

• Plugable renderers: Kei is working on vizmap-gui refactor, which is needed for pluggable renderers.
• Getting pluggable renderers in the ding presentation (once vizmap-gui refactor is done) should be pretty easy according to Daniel

• Groups or Modules are used by ActiveModule, clusterMaker, and other plugins.

• We have two levels of selection, implemented through ding - primary and secondary selection. Currently there is no clean API allowing access to these two levels of selection.

• Since no code that depends on primary & secondary selection is ported yet to 3.0, Mike wants to punt on implementing 'selection' until the code that uses it is in 3.0

• yFiles - the most used layout in 2.6. If we wish to exclude it, we will need to offer our own version in Cy3.

GSoC

• Coding period starts on May 23rd.
• By now students should know their mentors and be acquainted with the code base. Communication ways should be clear (weekly meetings / reports, discussion lists, etc.).

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:

• Cellar crashed, issues; restored from backup, some dataloss: one svn version, fileownership info
• An extra copy of svn on another server would be nice; there is something like an hotcopy service in svn. Scooter might be able to do something like that.
• There are tools available according to Daniel; he'll send a mail to Mike

SONAR:

• Basically a code quality website. Ties in with website; Mike sends out links.
• Runs some 420 checks on code. Everybody is encouraged to explore the site. Use it to improve your code!

Boardmeeting tomorrow;

• Evaluation of dev modules plan, distributing responsibility; talk with your board member about which preferences you have

Testplan

• Toronto group started putting together a testplan, it's on wiki. Started with 3.0; 2.6 will follow. Now at high level but will be branched out. Separate testplan for GUI testing. Results will be logged and ticketed. Feel free to provide suggestions etc.
• There are quite a few wiki-type of apps that tie testcases and bugtracking together. It would be useful to explore these tools. These enable systematic testing of resolved bugs etc; Mike will send his suggestions to the cytostaff list; Farzana will be added.
• The type of bugtracker has to be taken into account, Scooter has experience setting up Track, to their satisfaction. People at Toronto (Jason), and Alex having experience setting this up also.
• The more testcases can be tied in in normal development the better it is.

EBI;

• Samad was there, lot of pharmaceuticals; lot of interest from industry, everybody heard from Cytoscape. Samad will write the specifics down in a report.
• Scooter also needs info from recent plugin developers.
• Allan is waiting for this type of info to justify Cytoscape involvement with Agilent.
• Contacts with people from Genentech

Cytoscape Lite code request:

• Email lead developer Christian Tannus Lopes <chrtannus@gmail.com>.

• Will be opensource in the near future, it's written in Flex(?); xml files, javascript api

Thursday May 7th 2009

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

Agenda: NodeViewTaskFactory, GSoC, core plugins,

GSoC:

• This is community bonding period. Students get to know mailing lists and other communacation methods, and the code base.
• Students are expected to contact mentors at least once a week.

NodeViewTaskFactory:

• TaskFactory: a simple interface with just a getTask method

• NodeViewTaskFactory / EdgeViewTaskFactory - special case of TaskFactory. Used for context-menus: (right click on a node/edge). Lets you set a particular node view /edge view.

• Why do we need the duplication of NodeViewTaskFactory and EdgeViewTaskFactory? Because the Type <T> gets lost later.

• No particular use case for a general ViewTaskFactory

• similar TaskFactories for model are not yet added, will not be added if they are not needed; similarly for CyNetworkViewTaskFactory

core plugins:

• Cytoscape-IDE (Eclipse plugin) will be updated. Alternatively, Eclipse developers can manually install the needed plugins.

April

Thursday April 30th 2009

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

Agenda: Cytoscape 3.0 development modules, Porting core plugins

• Cytoscape 3.0 development modules
  • Development modules wiki page - extremely useful for planning
  • Development modules vs. core plugins status wiki page?
  • Modules are general areas and plugins are specific code segments
  • Relationship between core plugins and modules? -strategy is getting 3.0 to work, so port plugin first with same features and then redesign if necessary.
  • list developers names rather then institutions
  • list core plugins next to modules, to make the relationships more clear
• Porting core plugins
  • We may want to orginize a hackathon to port core plugins and work on tips for plugin developers

Thursday April 23th 2009

Agenda: Hudson, 3.0,

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

• Hudson: we are done with configuration for Hudson.
  • Is this triggering off commits of subversion repository?
  • Hudson checks once/hr for subversion commits, does a build if respository changed.
  • Also does a check once/day, does a build once/day.
  • Email will be sent to cytostaff only on failure, and when a build succeeds after previously failing
• 3.0:
  • update on code development: code is now in a shape were people can now start porting core plugins this is separate from the development of 3.0 modules
  • all plugins should be private impls, e.g. linkout-impl some plugins may want to expose a public API, should be in API bundle
  • a lot of this is mechanical, but not the event handling.
  • go into cytoscape 3 and look at top-level POM. coreplugins are now commented out. some are tricky like manual layout, has some wierd internal structure some things should be consolidated: e.g. quickfind, filters
• 3.0 modules: consortium members commit to owning one or more modules wiki page has list of modules and who has been working on them add entries for size of module and its impact communicate with your board member about what your organization will commit issues: what happens when someone moves on?
  • UCSD (Mike, Kei, Peng) will have to dial back involvement in a few weeks to get stuff done with 2.6. 3.0 should be in a good enough shape now that others can take over.

• CytoscapeCommons: see http://www.cytoscape.org/cgi-bin/moin.cgi/CytoscapeCommons

  • critical resource for getting plugins up and running on 3.0
  • consensus appears to be to use outside hosting (google code or similar), but no decision yet.

Thursday April 16th 2009

Agenda: 3.0 and GSoC

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

GSoC:

• we appear to be all set, we are waiting for official announcement from Google

3.0:

• how to ask 'does presentation support foo' question? (is it 3d/2d)
  • concern is that users will come to the helpdesk mailling list if a plugin doesn't work because analytical plugin is too heavily tied to visualization.
  • capabilities Scooter would like to query about:
    • 2d/3d

    • what kind of TableRenderers are available

    • multiple selection (do we want to have presentations that don't support this?)

  • warn users if VisualProperties are ignored because although they are defined, the current Presentation doesn't use them?

• Mike considers core bundles finished enough that core plugins can be ported
  • there might be minor things still missing, but those will come to light only if porting of plugin begins.
  • we need to ensure that most popular plugins are ported, (even of their authors don't have time)
  • 'community site/etc for plugins': possibly use google code; tie in with plugin system; make autobuilds which rebuild plugins if core changes
• Gary has a programmer who will work on making a detailed testplan for 2.6/3.0; not sure when to start
• Brian and Sarah worked on getting automatic bulds (with Hudson) running; not yet finished
• Mike actually managed to open (load and render) large (~100.000 nodes) networks and it was only 2 (maybe 4) times slower than 2.6. This would appear to suggest that firing an event for every node might not be that catastrophic as originally feared. Since this used old presentation code, which needs to be cleaned up and optimized, further speedup is expected.

Thursday April.9th 2009

Agenda: GSoC, 3.0

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

GSoC:

• first round of student allocations will be published today
• currently we have 11 projects we would like to do

• 2.x vs. 3.0 projects: GO layout is specifically 2.6 by design (would need CyDecoratedNetwork and that might not be ready in time); most others are planned for 3.0

3.0:

• Mike got presentation and application working to the point that network can be imported and rendered
• event efficiency still not fully decided, Daniel will try to make prototype of 'edit views' idea

• CyDataTable: have seperate schema class?

• should aim for relational database-like or more like simplified like Amazon simpleDB or google BigTable?

  • current API is more on the simple side; in the future, do we want to add more features, like joins, which would make it more complex than BigTable, for example?

• would need someone to cleanup the current presentation: many methods and interfaces are not used any more.

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

• Student deadline is tomorrow; after that 2 weeks evaluation till the 15th of April.
• Mentors should read the applications right now and communicate back to students. Make sure applications are submitted ASAP.
• We have to prioritize the applications, probably in combination with priority of the idea. Not multiple people for one app. There will be a meeting at UCSF to discuss the apps.

• All info here http://socghop.appspot.com/program/home/google/gsoc2009 ; you have to create a mentor-profile first

• Alex has marked a few ineligible:
  • submitted twice (left a note)
  • apparent spam
• Alex keeps track of mentors

EBI/Intact

• Piet was invited there to give a talk. Also extra day for interaction with dev-team with focus on 3.0.
• Piet prepares documentation and gives feedback. Is a good dry-run for dev-docs.

3.0

• Cytoscape now running with new model and presentation code (repackaged ding code). No viewmodel communication with presentation though.
• Relates to eventmodel decisions. An idea: two tiers of events: white board (main events) and lowlevel (between tightly coupled classes), basically optimizes event firing overhead; no real event creation (i.e. no seperate Event object); would still mean firing one event for each 'add node' (i.e. for each node). Would keep .updateView() method to signify "stuff has been set, redraw network".
• Presentation is now really decoupled, so it will be straight-forward to change it if needed.

ISMB 29nd June

• Is anybody going: Trey is there, gets an award. Allan may actually go, budget dependency though. Maital plans to attend.
• Presence at the Bioinformatics Open Source Conference (27th-28th) would be nice. Will be followed up off-line

Other

• Wiki was down again since last night, some issue with CGI rights keeps troubling us, probably a CRON-job would help? Up again now...

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

• 17th of April; issues should be discussed with respective board members; important issue: who does what. (this division of labor should be decided by the board with hints from us.)
• Everybody should sit down and specify what is being done in respective institutes. Will be transferred via mail; not meant to be public. (so as to not influence board too much.)

Server debacle

• File server crashed; Mike's busy with that, notify him if you note any hiccups (it should be fixed now.)
• Wiki was briefly down due to .cgi permission issues, but it is fixed now.

3.0

• Mike has been working on getting new viewmodel to work with rest of cytoscape code
  • may have to reconsider "use bulk methods" decision.
  • many parts of the code currently do:

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

• i.e. current structure of client code uses a 'set state then fire event' structure, with the 'fire event' part being 'network.redrawGraph();' It might be better to stick to this structure to avoid forcing plugin writers to rewrite everything.

• Mike will send out an example code to show three different ways of using the current viewmodel api; he would like to have feedback
• cancel() method in IO: Samad has an implementation of it; no objections yet.

GSOC

• quick start guide is needed, becomes an issue in a couple of weeks
• put up javadocs of 3.0 someplace public for new students

• Alex sent word: student applications are starting to come in (2 so far). Another week until the deadline, then we'll start reviewing and choosing. http://socghop.appspot.com/ There's still time to recruit good students to apply!

EBI/Intact

• Kei's still in Japan, Gary received feedback; they will contact people directly; Scooter, Piet, Yeyeide. If information earlier needed, mail Gary

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

• We got in again, good news. Students applications will come in from Monday. Google funds approx 1000 students. We might get in the order of 6-8.
• Now's the time to update ideas.
• Starting next week evaluating students. Might be an idea to include a little test. Probably former mentors can comment on this. Especially given the fact that some (but not all) projects should focus on 3.0. It adds a whole cycle to the evaluating process though. Writing down a proposal is enough as indication. It is probably instructive for us also, how easy it will be developing in Cy3

3.0

• Daniel's view code will be introduced into the current trunk. It's expected that a lot of things will break; this will be a signal for what's needed and what's not.

• View model will be independent of Swing, the relation of Swing to Presentation layer is not yet clear. DragAndDrop, Events etc will be an issue.

• Samad is rewriting the Task part using Java concurrency
• Kei's document on Cy3 plugin development is being improved
• There might be a hackathon at some point: once viewmodel and presentation are roughly working. Will be useful for documentation also

EBI Intact Training

• 2 days in June 15th -18th.
• Have to wait till Kei gets back from their meeting with update. Gary mails Kei.
• Scooter, Piet are interested, Yeyede hasn't responded yet.
• It depends on the type of training needed who; either user or developer oriented.

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

• Alex finished build. Doodle poll is up again. 8 People tested it means ok (on different platforms). Hopefully released in the next couple of days.
• Scooter added a change in the manual layout, but is no showstopper.
• There was a request for specific layouts through Trey; Scooter suggests recruiting graph drawing experts of some sort; current implementation is sufficient though

Mini retreat

• Mike added first version of agenda; feel free to modify and please add issues.
• Mike gives overview of goals reached. Things seem to come together really clean and well.
• Other than mentioned points: Scooter suggests discussing a documentation base.
• There will be a conf call next week.
• Is there a possibility of organizing car pooling to the Watertown hotel from the airport. There are ISB shuttles at the airport, Watertown might have shuttle opportunities. Taxi is another opportunity. In case of emergency Allan can come to the rescue. Email exchange to arrange rendez-vouz.

BOSC

• Basically a special interest group of ISMB, coincident with that. Relative informal, includes tutorials, descriptions of projects. Topics; design, data management, etc. Chair Ken Dalguish (founder of GenMAPP). Seems like a good venue for Cytoscape. Feedback from other groups is of importance given our current shift to 3.0.
• Who's going in these tough times. Mike is interested, Scooter might go if paper is accepted. Allan same story.
• Other participants are encouraged! Deadline april 13th.

Web site

• Aplus complained: is consuming loads of CPU? APlus doesn't have access to log files though!!! Mike checked but did not find anything. We should migrate some place else. (Possible migration to Trac mentioned)

3.0

• Mike contacts Daniel off-line.
• Loads of bundles have been replaced and sorted into implementation and api bundles.
• Tunable/Task implementation example is in core3. Now loads automatically. This refers to the mail sent by Mike. Mike will come back to this on the retreat.

Thursday, Feb. 19th

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

Agenda:

2.6.2

• Mike had a hard time with Cytoscape lately. Very slow loading of quite regular session file. Problem is in list-attribute implementation, combined with XGMML importer. Noel wrote a workaround fix. Sends it to Mike. Scooter has to be consulted also (Mike).
• Another point is panning on Mac, and right-click in some situations. CTRL is sometimes consumed. There are some specific multi-touchpad techniques on Mac that have to be checked. It might be related to more general issues with Swing on Mac.
• Webservices: some plugins weren't found in a theme. This can be fixed according to Peng. Sarah states that the breakage was caused on the server level, plugins were removed from db. Cytoscape did not fail gracefully though. Updates of plugins within themes leads to confusion.
• So how about the 2.6.2; several people tested regular features. Mike got frustrated, will this release frustrate users also? We get this release out of the door, tag it as a beta of some sort; including known bugs, and work on next version 2.6.3; maybe even before next mini-retreat. Are new features to be included? If so than increase the version number, but in general we should be working on bug fixes only.
• We actually need a comprehensive testplan. Test coverage is not good. This will be extensive but can be distributed. No bug should be considered fixed unless it's addressed as unit and functional test. There should be some type of software package/website to assess these QA issues. In due time a QA person will be working on Cytoscape in Gary's group. They might be able to design a simple first QA-capturing tool. Another approach would be to integrate this in Cytoscape code; where counters keep track of functionality tested.
• Mike sends a mail on his ideas on QA

MiniRetreat

• 6-7 March; all day Friday, all day Saturday
• Hotels, mention ISB gives discount at the Waterfront
• Wiki will be filled; be aware of some markup changes
• Mini retreat has focus on 3.0

Cytoscape.org

• Cytoscape announce postings are missing; this is a problem related to google-groups. Probable fix is through a proxy-server. Mike lacks time to do this, any volunteers?
• Maillist: Sarah didn't receive anything on sysbiol account. Allan knows how to do things. People can be added directly by Admin.
• The deploy script can be used; you have to upload your key though; Mike can help.

GOSC

• Is now on Wiki

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

• Alex holds new release till bugfixes of Sarah have been tested. Mike C. is testing this. Allan checks. If Allan and Mike are ok, release will be done; we have to get it out the door.
• 2.6.3 is almost guaranteed.

Webserver

• Migrated to Aplus, dns should switch to new sit soon. Migrating moinmoin is absurd. Expect some problems, links might be broken. Don't edit wiki till Mike gives the green light.
• Cytostaff is now on googlegroups. Invitations have been sent, not everybody has gotten them, seems like only gmail accounts received them so far, rest must be checked by gmail. Temporary url: treyideker.web.aplus.net Managing will be the same as always; through svn; scripts will be updated.

Mini-retreat

• Wiki pages wait till wiki is up and running.
• Sarah checks for block of rooms, will mail end of day.

GSOC

• Google summer of code has been announced; Applications are due March 9th; end of March the students start.
• Start thinking about projects, put it on the wiki. Mike assembles a startup guide for student/developers. Expect more mails on the subject

3.0 stuff

• Mike has been cleaning up application code.
• Next big thing is View code and Pluggable renderers.
• Daniel is working on making vizmap's gui play nicely with pluggable renderers and making it work with the 3.0 viewmodel and vizmap bundles. vizmap-gui will hopefully be usable late next week, definately by next mini-retreat. A simplistic prototype Presentation might be ready by the next mini-retreat.

Thursday, Feb. 5th

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

agenda: 2.6.2, mini-retreat, helpdesk

2.6.2

• Doodle poll worked rather well; 10 are in favour. 2.6.2 will be released.
• Platforms tested as comment would be a good addition. Leave that as a comment by convention; might be an option as radiobutton.
• There probably will be 2.6.3. People who care about bugs will drive the coming releases
• Mike C, Sarah are working on plugin manager problems; there is a problem between 2.6.1 and 2.6.2. There is a workaround that will be mailed by Sarah

mini retreat #3

• March 6-7th, hotel info has been mailed. Now put up a wiki for further details. Watertown was nicest, Sarah might arrange some discount, cheaper is better. Next week everybody has to let know.
• Main topics haven't been decided upon. Some topics: events, io, application layer.
• What is our target for webservice? This has huge impact on application layer, so needs to be fleshed out. Sarah puts some ideas together. Gary looks for something like middle-layer. The result of the retreat should be some requirements wrt web. Are we heading in the ingenuity (totally web-based) direction? ISB, Toronto, UCSF and Agilent have a drive to the web and flesh that out for the mini-retreat. 3.0 scaffold should allow for scaling towards the web

helpdesk/discuss list questions

• some questions don't get answered on the mailling lists; Piet volunteering for 'first-level user support', i.e. answering questions first or bugging someone else who knows the answer. (Not indefinately, this task should be rotated among developers.)

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:

• Next step of integration; Daniel is needed for that, for integrating vizmap changes etc into main trunk. Mike will contact Daniel about that separately.
• Mike etc work on tunables
• Task is being worked on
• Events still have to be decided, while integrating view and model several approaches (as on wiki) will be tested

2.6.2:

• Question is whether it is ready. Status of plugin is ok according to Kei. New release bundels will be created and we'll go from there. E.t.a. next week

mini-retreat:

• March 6-7 or 13-14. Kei can't on the last so will be settled on March 6th and 7th in Seattle. Mike sends a announcement mail, Sarah sends hotel information. Allan might not be able to come, but can check in remotely. Either skype or yogma.

cytoscape.org down:

• The provider Cedant hasn't reacted yet, Mike is calling (site up again now, obviously

• This moment can be used to update some stuff on the site; the developers pictures(Maital, Matthieu, Samad, Noel, Piet (and ?) have to be added; please send picture to Allan); Allan arranges that photo's will be checked in, Mike handles deploy

Thursday, Jan. 22

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

agenda: 2.6.2, release protocol,

2.6.2:

• Pathwaycommons problem -- considered show-stopper for 2.6.2, so release is delay until it is fixed

release protocol:

• establish voting procedure to give feedback for bigger decisions (like whether is a release candidate ready for release)
• each core developer would have a single vote
• possibilities:
  • use doodle polls or similar
  • use +1 / -1 reply on cyto-staff
• would not in itself fix problem if people don't vote (and don't test the release candidates)
• should release candidates be publicized on cytoscape-discuss to involve community in beta-testing?
  • big question is: at what stage would a release candidate be good enough for such public beta-testing
• Mike will setup a doodle poll to vote on 2.6.2

mini-retreat 3:

• will pick a date during next week's conference call

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:

• distribution rebuilt due to bug on linux
• release notes needed
• will start thread on cy-staff
• (would be much easier if everyone would write descriptive svn checkin comments)
• build will be released tomorrow

web app framework:

• Sarah plans to pick and choose framework; cytoscape should be independent enough to be 'compatible with everything'.
• many people plan to use Flex
• JSON will be connecting server part to the client code running on browser
• something like Tunables could be used, but not planning such for now (would be too much a task)
• cytoscape code on the server would be somewhat parallel to the framework used by the rest of the app
• web frameworks ususally assume db behind, supporting multithreaded, concurrent access -- cytoscape is not ready for that yet.
• does the web ui talks to a stateful cytoscape backend
• Gary: planning Flex framework which is a mini-cytoscape, and server is stateless, serving individual requests.
• Sarah: couple of different applications communicating with databases; some state is stored on server; basically everyone uses databases for the model layer
• do we need a cytoscape web ui, or is what people will want to use simply a headless interface? -- this would cover Gary's usecases;
  • - this might mean that only cytoscape-on-desktop needs to use events - it also means that forcing plugins to use swing ui would be acceptable, i.e. they wouldn't have to be ui-agnostic - this is a pretty big decision and should not be made lightly
• three web based modes of interaction:
  • - simplest: just use headless version of cytoscape (Gary's group will do stuff like this) -- this imposes no additional requirements on cytoscape's design apart from supporting batched mode (i.e. like calling headless from command line) - statefull cytoscape running on backend, but not exposing any UI directly; somebody else (i.e. not cytoscape) would write components that uses cytoscape libs, but this is seperate from cytoscape. - full-feature UI on web: have as much functionality as possible, statefull server, (this will most likely be postponed, it is too big for 3.0; but we will most likely be forced to do that due to "move everything to the web" tendency)
• how we do web uis will impact the design of the event framework

events:

• we also talked about events

• Daniel will merge the discussion-thread on cytoscape-staff to the EventHandling wiki-page, and try to summarize it

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:

• Mike found some bugs:
  • - double-click to open session file on mac -- user will have to set file-association by hand when installing cytoscape
• will create 'final' bundles tomorrow, then see if known bugs are serious enough to delay release

next mini-retreat:

• most likely Seattle
• topics for mini-retreat:
  • io
  • application
  • event handling (most likely won't have a solution till then)
• will look into some shared desktop tools for tele-conferencing
• etherpad for taking notes will be useful
• maybe in first half of february
• in the meantime:
  • would need a few weeks to integrate current modules being worked on into 3.0 trunk
  • work progressing on vizmap, viewmodel, tunables and work/task modules

event handling:

• EMF used eclipse: too complicated, would provide undo/redo using transactions, etc. and it is not planned to use the event framework for that.
• traditional listener patter not designed for event batching
• implementing batching is really really hard:
  • - consistency depends on event being fired

    - biggest example is deletion due to the AboutToDelete events:

    • during a batch / transaction, the model is in an in-between state: some nodes are already marked for deletion, but are not yet deleted, but will be soon. All client code would have to be aware that they are running in an in-complete transaction
• accumulating the events in eventHelper instead of actually firing them.
• two ways: using annotations or method calls
  • - ie. annotate a method as a batch
• one possibility is to make the client code responsible for firing the event
  • obvious problems with ensuring that the event is fired
  • bulk methods (like .deleteNodes() instead of .deleteNode()) is a way to make sure events are fired correctly, with similar burden on the client code
• plan: work on other parts of 3.0, and try to gauge how serious a problem this is
• look at code! usage of generics, how events look like, etc. are fleshed out in some detail (will post link and summary to list)

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