Use cases addressed:
- First steps towards drawing pathways / metabolic networks.
- Support for large networks
- Key Usability Issues
- Save State, Undo
- Viz Mapper / Filters Specific Issues
New Features:
- New rendering engine; lots of plugin dependencies
- (Nerius, Allan as consultant) Also includes Layout algorithms for large networks
- Meta-Nodes; Phase I
- (Iliana, Allan, Melissa, Aditya, Alex Pico, Scooter)
- Saving Project State (["Save current session as XML file"]) (Kei, Iliana); Depends on Meta-Nodes
- Undo Manager (Allan w/ help from friends)
- Attribute browser
- link attribute browser to network view (Kei)
- Meta-node compatible browser window (expand/collapse) (Kei)
- New, improved Cytoscape Tutorials (Melissa)
- Graph Merge, moved to core (already a plugin) (Ryan, UCSD)
- [6. Clean-up Viz Mapper and Filter UIs (["VizMapUI"]); make friendlier; move to cytopanels] [Mike S, Allan, (possibly Alex?)]
TIMELINE
- [7. ID Mapping Services, Phase I] [Optional?] (Gary)
Refactoring / Design Issues:
(["Node id issue"]) – creation of a default “label” CyAttribute (Ben)
- New documentation options; docbook, wiki, etc. (Gary, Mike)
- Take care of delete/hide/remove situation (Allan, in conjunction with Cytoscape Editor)
- Flagging/selection of nodes/edges (Iliana)
Misc. Small Items
- Ability to rename networks (Brad K at UCSD)
- Brad is adding code to allow networks to be renamed. They are currently named based on the input file. This change will change that name throughout the system.
TIMELINE Nearly complete. All of the underlying code is in place, we just need to figure out how refresh the name in the network panel.
- Script to update source license
- Some of the Cytoscape source is missing copyright and license information. This needs to be fixed.
TIMELINE We have a script that needs to be updated with the proper information and tweaked so that it doesn't stomp on existing copyrights.
- Generic Linkout Pop-up Menu (Doron B, MSKCC)
- Re-organize save/load/import/export menu items (["New File Menu"]) (Kei)