Cytoscape Wiki|
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= Cytoscape 2.4 and Beyond = |
<!> '''''See page [[Cytoscape_2.5]] for the latest updates on release 2.5.''''' <!> |
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* 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 |
* 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?) |
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* New GraphObject class; for nodes/edges * Formalize what goes in the core * Improving / Refactoring Event Model |
* 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. |
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 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.