Cytoscape WikiContents
During conference calls, wave is used to take notes (since it updates instantly compared to the delay when editing the wiki). The url is: https://wave.google.com/wave/#restored:wave:googlewave.com!w%252BYcpSNqUuA
In between conference calls, the same wave is used to collect agenda items for the next conference call.
2010
April 15, 2010
Participants
Justin (Sage), Sarah, Gary, Brian, Ryan (ISB), Mike, Kei, Peng, Johannes, Samad, Noel, Allan, David Henderson (Sage)
Agenda
* Cy3 builds - error messages from the build system, probably a server configuration issue. Do we want to continue emailing to cytostaff? Would be better if messages will be sent to cytoscape-build@googlegroups.com. There is also an RSS feed.
* Summer of Code
* Please remember to rate the proposals you're interested in and speak up if you think a project should be chosen that is not currently chosen, before Apr.21.
* Digital Biology Foundation
* Brian Bramlett - Interested in providing support structure for open source projects.
* Merging branches into trunk
* Integrating custom graphics in the vizmapper, plugin manager (adding search and refactoring main panel), equation editor in the attribute browser.
* 2.8?
* UCSD has 3 new features and would like to release sooner than 6 months from now, especially because a paper is in preparation that uses the features. Scooter also wants to include new CyCommand features and Allan is writing plugins that will use 2.8 features.
* ISMB
* 25 minute technology track. Should we do a 50 minute version? Yes, let's try.
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April 8, 2010
Participants
Allan, Brian, Noel, Ryan, Alex, Sarah, Justin, Andrew, Mike, Peng, Kei
Agenda
* Google Summer of Code
* now is the time to review, comment and score student applications
* student proposals due by the 9th, we should score by the 12th, ranks and scores due on the 21st
* 2.7
* new release is out
* dev branch will be started for 2.7; trunk will be for 2.8 dev
* ISMB 2010 technology track
* 25 min ($400) or 50 min ($2,000) demo sessions; apps due 23rd.
* we should be able to give an overview demo in 25 minutes
* Allan, Alex and Scooter will put together a 1-page outline of the demo. We'll send a draft on Monday for your edits and additions.
* Round Robin: go around and talk about what each of us is work
* Sage Bionetworks
* interest in network tools; interest in our dev roadmap
* Sage Congress April 23rd in San Francisco
* Cytoscape Retreat: request for a wiki page has been made
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April 1, 2010
Participants
Noel, Samad, Brian, Mike, Kei, Peng, Johannes, Sarah, Ryan, Alex, Scooter, Allan
Agenda
* p41 site visit post-mortem
* score was good, cautiously optimistic
* 2.7
* ready to go, alex will do web site deployment and release announcement
* Google summer of code
* student applications now coming in, due by April 9
* we will have one week to score and respond
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March 25, 2010
Site visit at UCSD today, conference call cancelled
What coincidence: Site visit at AMC also! Piet
March 22, 2010
2.7 release call
* Ontology loading broken - GO files had errors. Code now logs a warning in the logger if can't parse. Well tested against a broken file.
* Fixed and tested
* Plugin manager broken - http://cytoscape.org/plugins/plugins.xml needs to redirect to chianti
* Email sent to Benno about DNS
* Save images is broken - network was not being rendered
* Now fixed
* GO human annotations ontology is too large, thus always fails to load. It is 400MB uncompressed.
* Works if file is downloaded locally
* NCBI webservice exceptions
* Scooter will confirm if this can be reproduced - can't reproduce in current build
* Bug: 2208 - selected nodes not refreshed in the control panel
* Kei will look at this - should be easy to fix. Listener isn't firing in a reproducible way.
* Bug: session file won't open - throws an exception - error about node height being too small
* Need to study the bug
* Release plan - looking at 2 new bugs today and will aim for a release bundle tonight.
March 18, 2010
Participants
Brian, Samad, Allan, Alex, Scooter, Kei, Peng, Johannes, Sarah, Noel, Gary
Agenda
* 2.7 Release
* Issues
* Ontology loading broken - Scooter is taking care of this one and testing.
* Plugin manager broken - Peng will look at this today
* Save images is broken - Scooter will try to track this down
* GO human annotations ontology is too large, thus always fails to load. It is 400MB uncompressed.
* Kei will look at this today
* NCBI webservice exceptions
* Kei will look at this today
* Do another round of formal testing - TODO: Farzana
* Need a 2.7 release conference call early next week - Mar.22
* 09:30 PDT (12:30 EDT, 16:30 GMT, 17:30 CET)
* Release notes
* site visit
* Presentation discussion/brainstorming
March 11, 2010
Participants:
Brian (Wodak Lab), Gary, Noel, Mike, Scooter, Samad, Piet, Sarah, Kei, Peng, Johannes, Allan, Daniel
Agenda:
* new addition to core plugins (proposed by Scooter) - corecommands
* Decision: yes, it should be a core plugin. We should put it in 2.7.1
* Cytoscape 2.7 status
* testing
* bug 2199 is major, but we can't figure out how to resolve it in a good way, thus it will be listed as a known issue.
* manual updates
* BioPAX import - supports Level 3
* Noel - system properties
* release schedule
* Finalize manual Mar.12
* Package deadline: End of day, pacific time, Fri.Mar.12
* release notes
* Gary to draft release notes on wiki by this weekend
* known issue - 2199
* Cytoscape 3.0
* Will likely have a concrete plan forming after the site visit (so in April) - idea would be to review 3.0 with all core developers and plan a development roadmap. A more concrete plan will likely be available after the retreat
* Board meeting update
* Presentations for site visit Mar.25 are under development
* Editorial committee nominations and vote will be held soon
Note: Day light savings time this Sunday - Europe participants will be on the call 1 hour earlier until Mar.28
* Email notification for Google Waves are now possible
February
February 25, 2010
Participants: Sarah, Ryan, Mike, Kei, Peng, Johannes, Noel, Brian, Allan, Samad, Gary Agenda Cytoscape 2.7 -bug status --Bug 1922: authenticating proxy server ---May be a Java issue, need to --Network View windows disappearing in Java 1.6 in Windows and Linux when dragged (bug no. 2199) ---We need to figure out which JDK6 versions this affects. --make Semantics.INTERACTION attribute non-user-editable?. ---Yes, let's make this immutable and see what happens. -testing status Branching 2.7 vs. trunk? - once 2.7 is released, it will be tagged as 2.7.0 and no new features should be added to that, just bug fixes.
February 18, 2010
Participants: Gary, Samad, Mike, Kei, Johannes, Noel, Allan, Brian, Daniel, Sarah, Piet, Scooter Agenda Cytoscape 2.7 -testing status Planning on bug fixing: UCSD, Allan, Noel, Scooter at least -UCSD planning to help test and fix all their bugs by next Wed, then release another beta. -TODO: update manual for biopax level 3 -Maybe test with reduced memory settings ISMB 2010 participation? - Boston in July. -BoF -Technology track demo - April.23 submission deadline. -Scooter, Alex, Allan submit an abstract. demo new 2.7 features: edge types, kegg loader, layouts, nested networks -ISMB: Allan?, Gary, Piet?, Scooter?, Sarah? (? = contingent on having work accepted for presentation) GSoC -Please post your project ideas at http://genmapp.cgl.ucsf.edu//wiki/Google_Summer_of_Code_2010 Request for speaker at Pasteur - Scooter Retreat: still thinking Michigan in July, but still looking for a date. Preference for being near ISMB to make it easier for travel
February 11, 2010
Participants: Noel, Mike, Johannes, Scooter, Samad, Sarah, Gary, Alex, Allan, Piet (somewhat later) Agenda Google GSoC 2010 http://genmapp.cgl.ucsf.edu/wiki/Google_Summer_of_Code_2010 Mar.8 mentor applications due - start posting ideas on the wiki. Alex will send a note around. Cytoscape 2.7 -New feature review --Guidelines writing a 2.x plugin in preparation for 3.0 --Decision: -Testing status --Farzana --New beta releases as required Training at CST done by Scooter - went really well. About 18 people attended -Lots of mass spec work and phosphorylation mapping. They have the phosphosite database/website and want to use Cytoscape to analyze it. E.g. they were interested in the STRING plugin. Additional utility code - can it be migrated into the core? A new method in CyAttributeUtils to convert attribute type strings. Yes, everyone is ok with this.
February 4, 2010
February 4, 2010 Participants: Sarah, Allan, Noel, Gary, Daniel, Brian, Samad, Mike, Kei, Peng, Johannes Agenda Many people reporting the following bug on the mailing list - any resolution? java.lang.NullPointerException at cytoscape.plugin.DownloadableInfo.isCytoscapeVersionCurrent (DownloadableInfo.java:390 SBML reader 2 from matthias? Not included in core in 2.7 - problem is integration in a clean way. Cytoscape development process -How do we know what needs to be reviewed. The facilitators will need to sort this out. -Tests should be reviewed - e.g. tests should be present. Cytoscape 2.7 status Reviews -CyCommandHandlers: needs a response to Mike's points and additional reviewers (Gary to email Scooter today) -Nested Networks: 2 reviews, Samad will review today. --Gary to send more general data structures to Mike (e.g. INOH) -Testing: Farzana will be ready to test next week sometime. At that point, Mike will create a test release and publicly post it as a baseline. She will then run through the 2.6 test plan and additional tests postedat http://cytoscape.wodaklab.org/wiki/Cytoscape_2.7/Test%20Plan%20-%202.7 Then we can prioritize the resulting bugs and get a better idea about how long bug fixing will take. Other 2.7 things of note: -Install web services button - PC is installed by default - but there are a lot of errors with the install web services button, so include NCBI and Biomart plugins as core. The only other one not included is intact, but they keep changing their webservice. UCSD still working on allocate memory at startup problem - will be done in a few days and will report. Installer will generate the right memory options for the user automatically + a dialog in Cytoscape that allows you to change those options. Planning on bug fixing soon: UCSD, Allan, Noel at least Manual for 2.7 - automatic export from wiki as docbook is broken on the current wiki. Mike will email Brian about this.
January
January 28, 2010
Participants: Samad, Noel, Brian, Mike, Gary, Sarah, Alex, Kei, Peng, Johannes, Allan, Daniel Agenda -Talk about revised Cytoscape Launcher (Mike) -Current development environment question. --grenache is still the main SVN repository, but we should move to sourceforge once code is stabilized after 2.7 release. -Cytoscape 2.7 status update --Code review - feature vs. code review - how do I review, what am I reviewing? Timeline - how long is the review open for? How many reviewers are necessary? What if no one wants to review the code? ---Communication/planning is really important - need to announce that the RFC is coming well in advance (how long?) ---Nested networks will be reviewed by Samad and Allan ---Goal to have reviews done by next week. --Feature freeze ---http://cytoscape.wodaklab.org/wiki/Cytoscape_2.7 --Code freeze ---Noel: changes to be checked in with data file encoding --If you want specific things tested, then put instructions on this page for Farzana before Feb.8 http://cytoscape.wodaklab.org/wiki/Cytoscape_2.7/Test%20Plan%20-%202.7 --Please fix bugs - the earlier, the better - we will begin assigning bugs in 1-2 weeks. -Test release: 1. tag SVN 2. make a zip file available in a centralized place for testing and communicate that to Farzana and others (mailing lists?) -Testing on 3 different platforms - important for file related bug fixes - Google Summer of Code updates? -- Organization application due March 12th -- We will put together an Ideas page, etc during the first week of march
January 21, 2010
Participants: Samad, Brian, Mike, Scooter, Allan, Kei, Peng, Johannes, Gary Agenda 3.0 plans: Piet: I cannot make it to the call but at the presentation I gave last week there were several people asking about the e.t.a for 3.0. Furthermore these people (myself included! :-) were pleasantly surprised when I showed the current state of 3.0, running and all with a considerable amount of functionality included. -Currently on hold until board makes a strategy decision. Anyone have any comments on the development process? So far no, so people seem to be happy with it. Brief update on retreat. -Looks like Michigan is working on it, will have more information next week. Ideker Lab Progress -http://cytoscape.wodaklab.org/wiki/IdekerLabProgress March.25 is the NCRR site visit 2.7 TODO: -Create 2.7 wiki page - based on http://cytoscape.wodaklab.org/wiki/Cytoscape_2.6 --Scooter will start this page -Development process - 'best we can' before process approved - check back on the status of this in 2 weeks - Feb.4, update Jan.28 (scooter will update via the wave) -Testing --Gary to ask Farzana about running through the test plan for 2.7 release - how long will this take. Estimate 2 weeks. --Testing can start right now. --Testing needs a list of pointers to new features for Farzana -Bug fixing. Lots of little things, but not aware of any show stopper bugs. Not sure how long bug fixing will take. -Update manual with new features --CyCommands and NestedNetworks, lots of minor features e.g. new edge types. --UCSD will add to manual - part of next sprint starting Feb.1. --CyCommand will not impact the manual -General aim for end of Feb for 2.7 release - main motivation is the site visit. Development process -Separate process for reviewing the manual Broken links from the old Cytoscape wiki - how can we fix these? Old URL: http://www.cytoscape.org/cgi-bin/moin.cgi/RecentChanges -Gary will ask Harold (sys admin) to look at http://sourceforge.net/apps/trac/sourceforge/wiki/Project%20web Talk about Cytoscape Launcher -UCSD will write an RFC for this. Will allow users to set the amount of memory allocated to Cytoscape from within Cytoscape. Start a Java process that will read a config file to launch the main application.
Thursday, January 14, 2010
Participants: Scooter, Brian, Sarah, Noel, Mike, Johannes, Peng, Kei, Daniel, Piet, Allan, Samad Agenda retreat update: no news. Still likely July in Michigan. board meetings updates (none) 2.7 plans: still targeting end of February 3.0 plans (post 2.7 & board meeting) teaching/training (CST?) : Scooter is going, One day training, maybe offsite, February 1st. 20 people signed up. Will do the basic online tutorial. An hour seminar, here is Cytoscape, generate interest beyond the initial 20.then 2-hour standard session. Afternoon is for special topics. They'll bring their own data. Piet will be giving an introduction to Cytoscape for software developers from the BioAssist programme of the Netherlands Bioinformatics Centre (http://www.nbic.nl/support/bioassist/) This is a collaborative endeavour in which biologists and (bio)informaticians organise bioinformatics support in a collaborative fashion.
Thursday, January 7, 2010 (Happy New Year)
Participants: Allan, Alex, Gary, Brian, Sarah, Mike, Kei, Peng, Johannes, Samad
Agenda:
how is google wave working out?
brian: seems ok, and it will likely get better and get more features
Etherpad code is now at http://code.google.com/p/etherpad/
update on board meeting?
documents that were sent to the board will be sent to the discussion list, includes something about process
retreat? No update. Still looking at Michigan in June.
Google Adwords for Cytoscape - anyone interested in getting access to the account to create ads, update keywords? (Gary) Interested: Allan, Mike, Alex. Gary will try to add google account
upcoming conferences/trainings. Cell signaling technology (CST) Scooter is interested and has contacted CST (scheduled for Feb 2 -- 20 participants have signed up) - need to follow up to see if anything is planned yet. Conferences: ISMB (Boston) andICSB (Edinburgh). Cytoscape Deadline for tutorial submissions for ICSB is January 15th!
Cytoweb status - nearing release - temporary/draft website available now at http://cytoweb.baderlab.org/ (URL will hopefully change to be on the cytoscape.org domain)
Migrate to Java 1.6?
(Not for now)
Cytoscape 2.7
end of february as a release target, end of january for feature freeze
ucsd - subnets
ucsf - cycommands
feature list will be added to wiki (Mike)
Cytoscape 3.0
need process thing finalized before site visit?
http://cytoscape.wodaklab.org/wiki/Cytoscape_3.0/DevelopmentModules
Cytoscape 2.8 Equation attributes RFC - Johannes - add excel like expressions in attributes. (making the attribute browser more excel like). Proposal would not modifyCyAttributes, but would add a new equation attribute type. http://cytoscape.wodaklab.org/wiki/Cytoscape_2.8/EquationAttributes
GSOC 2010? Org applications will be due ~mid-March. Alex will rename our effort as "Cytoscape, GenMAPP, and WikiPathways". Generating an "Ideas Page" is a year-round activity... never to early to start. Alex will look into using AdWords for GSoC.