Cytoscape Wiki|
← Revision 5 as of 2010-11-24 19:15:21
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← Revision 6 as of 2010-12-09 17:39:36 →
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* Cleaning up session files - implement a clear global vs. session separation - they are not well distinguished in 2.x (e.g. proxy settings are stored in the session file) * Develop a unified settings/preferences system that supports global and session specific settings. Also, make available as an API for plugin developers. * Unify bookmarks and linkout systems - currently we have both, but we should have one. Need to support editing of linkouts, setting in configuration files - may be easily made part of a general system for settings |
- Place and time TBD, probably California in early 2011
- Focus: Get feedback on Cytoscape 3.0 alpha developer pre-release and continue API design.
- Agenda
Need a concept of how to link/join tables to networks and how these are synchronized (e.g. how selection state is synchronized - do we need a CyTable that can't be unlinked from a CyNetwork that stores e.g. selection state and then enable developers to link additional data tables as local tables for that network? This would set up a one to many relationship between networks and tables) - added Oct.2010
- Filter API - added Oct.2010
CyTable views - added Oct.2010
- How nested networks, subnetworks, groups, metanodes, compound graphs all play well together - added Oct.2010
- We should create an acceptance test suite to help us know if cyto3 is ready e.g. select 100,000 edges using the filters API and see how fast it is. This could be used to test Cytoscape from release to release.
- we should have a code test writing jamboree - write tests to capture specific behavior
- could be opened up to the plugin writing community, like we did in the past with 'day of bug testing' with people distributed and asking questions on IRC
- we should have a code test writing jamboree - write tests to capture specific behavior
- How would SBGN be supported in Cytoscape e.g. edges connecting to other edges? (should there be dummy nodes for the join points? We need to evaluate solutions other SBGN software have to this issue)
- Cleaning up session files - implement a clear global vs. session separation - they are not well distinguished in 2.x (e.g. proxy settings are stored in the session file)
- Develop a unified settings/preferences system that supports global and session specific settings. Also, make available as an API for plugin developers.
- Unify bookmarks and linkout systems - currently we have both, but we should have one. Need to support editing of linkouts, setting in configuration files - may be easily made part of a general system for settings