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| * Place and time TBD, probably California in early 2011 | * Place and time TBD, probably California in early 2011 (after everyone has had a chance to play with milestone 1) |
- Place and time TBD, probably California in early 2011 (after everyone has had a chance to play with milestone 1)
- 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
- Develop a unified settings/preferences system that supports global and session specific settings/properties. Also, make available as an API for plugin developers.
- Implement a clear global vs. session separation for properties - they are not well distinguished in 2.x (e.g. proxy settings are stored in the session file)
- This would allow the session IO system to access global properties, which it currently can't do, so is forced to take these from the current active set (which can be changed by the user). Thus, when you create a new session, you may save some global and edited properties that don't make sense to save in the session.
- 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
- Create a cytoscape 3.0 session format?
- Better format for serializing visual styles - not just properties. E.g. XML
- Re-evaluate XGMML?
Should we have separate XML serializable objects for CyTable vs. CyNetwork? Other objects that are stored in XGMML? Would be more flexible and modular.
- XGMML is not maintained, was always a draft standard.
- Cytoscape stores all visual and data properties as attributes and doesn't make use of the XGMML graphics system for storing node/edge graphics.
- IDs are very messy with XGMML, because it requires IDs to be numbers, not strings, while Cytoscape uses strings, so Cytoscape is forced to store its unique IDs in the label field, which is not unique in XGMML.
- Develop a unified settings/preferences system that supports global and session specific settings/properties. Also, make available as an API for plugin developers.