Cytoscape Wiki=Cytoscape 2.3=
==Use cases addressed:==
- First steps towards drawing pathways / metabolic networks.
- Support for large networks
- Key Usability Issues
- Save State, Undo
VizMapper / Filters Specific Issues
==New Features:==
- New rendering engine; lots of plugin dependencies
- (Nerius, Ethan, Allan as consultant; possibly Ben) Also includes Layout algorithms for large networks
- Meta-Nodes; Phase I
- (Iliana, Allan, Melissa, Aditya, Alex Pico, Scooter)
- Saving Project State (Kei, Iliana); Depends on Meta-Nodes
- Undo Manager (Allan w/ help from friends)
- Attribute browser; link attribute browser to network view
- (Kei)
- [6. Clean-up Viz Mapper UI; make friendlier; move to cytopanels]
- [Mike S; currently understaffed]
- [7. Clean-up Filter UI]
- [Mike S; currently understaffed]
- [8. 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)
=Cytoscape 2.4 and Beyond=
Features
MetaNodes; working as core
- Attribute Based Layout
- Multi-colored nodes
- Better hide/show for edges/ nodes
- Real-time vizmapper update
- KEGG Reader / Reaction node + editor
- Interactive Slider Widget
- Visual Legend
- Standardize context menus for nodes/edges
- Network specific node and edge attributes
==Refactoring / Design Issues==
New GraphObject class; for nodes/edges
- Formalize what goes in the core
- Improving / Refactoring Event Model