Cytoscape_2.4_and_Beyond

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
• 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

• 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

• 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.

Priority for 2.4 Release

1. Oficially release Metanode plugin
2. Automatic node label position adjustment (place labels outside of the node)
3. ID Mapping

4. [:VisualLegendGenerator:Automatic Visual Legend generator] (code is already available. Needs generic GUI)

5. Immutable/Invisible CyAttributes (mainly for Metanodes)

6. Migration to Java Version 5
   • Test core plugins in v5 environments
   • Replace old library files

   • Optional: use v5 features (such as generics, extended for loops, etc.) for writing more readable & stable codes