Cytoscape 2.3
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, 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)
- New, improved Cytoscape Tutorials (Melissa)
- Graph Merge, moved to core (already a plugin) (Ryan, UCSD)
- [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)
Misc. Small Items
- Ability to rename networks
- Script to update source license
- Generic Linkout Pop-up Menu (Doron B, MSKCC)
Cytoscape 2.4 and Beyond
Features
MetaNodes, Phase 2
- 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