'''''See page [[Cytoscape_2.5]] for the latest updates on release 2.5.''''' == Features == * Meta Nodes, Phase 2 * ID Mapping (was planned for 2.3) * Generic Plugin-state saving * Attribute Based Layout (e.g. cell localization based layout) * editor support for hyperedges * editor support for graphic labels, custom graphical nodes * Multi-colored nodes * Better hide/show for edges/ nodes * Real-time vizmapper update * Vizmapper map-by-filter value (e.g. color nodes by value of function) * KEGG Reader / Reaction node + editor * Expression Matrix reader for more data formats (MIAME) * Interactive Slider Widget * 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 * BioPAX output * editor support for connecting edges to metanodes and their children * editor support for adding "templates" (e.g. metanode templates, network motifs) to canvas * Headless mode, Phase 2 (Web Service?) == Refactoring / Design Issues == * 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 * Expression Matrix must use CyAttribute instead of redundant data structure. * Unit tests/swing unit tests + more automated build system that includes building of plugins.