Cytoscape Wiki
Features
- Meta Nodes, Phase 2
- Generic Plugin-state saving
- Attribute Based Layout
- Multi-colored nodes
- Better hide/show for edges/ nodes
- Real-time vizmapper update
- KEGG Reader / Reaction node + editor
- Expression Matrix reader for more data formats (MIAME)
- Interactive Slider Widget
- Visual Legend automatic generator
- Standardize context menus for nodes/edges
- Network specific node and edge attributes
- Generic Preference System and inteligent UI for the new preference data structure
- Complex object (tree, map, etc.) viewer in Attribute Browser
Cytoscape Theme (Skin)
Logging system (maybe [http://jakarta.apache.org/commons/logging/ Commons Logging]?), instead of using tons of System.out.print
New BioDataServer to fully support entries in OBO and Gene Asociation file.
- Headless mode, Phase 2 (Web Service?)
Refactoring / Design Issues
Migration to [http://java.sun.com/j2se/1.5.0/index.jsp Java version 5] and lib directory cleanup (especially XML-related files)
New GraphObject class; for nodes/edges
Define Invisible CyAttributes (CyAttributes which is not shown on the Browser. Used internally)
- Performance tuning for save/load huge sessions
- Formalize what goes in the core
- Improving / Refactoring Event Model
- Remove the "GO Level" idea from Gene Ontology Server
Expression Matrix must use CyAttribute instead of redundant data structure.
- Unit tests/swing unit tests + more automated build system that includes building of plugins.