Differences between revisions 5 and 10 (spanning 5 versions)
Revision 5 as of 2006-04-29 01:37:44
Size: 919
Editor: KeiichiroOno
Comment:
Revision 10 as of 2006-06-09 21:11:24
Size: 1211
Editor: KeiichiroOno
Comment:
Deletions are marked like this. Additions are marked like this.
Line 10: Line 10:
 * Visual Legend  * Visual Legend automatic generator
Line 14: Line 14:
 * Tree Object Support in CyAttributes (for GO data)  * Tree Object viewer in Browser (For GO data, etc.)
 * ''Cytoscape Theme (Skin)''
 * Background Task support (for compressing huge session file)
Line 16: Line 18:
Line 19: Line 20:
 * Define what the Edge ID is
 * Performance tuning for save/load huge sessions
Line 24: Line 27:
 * Unit tests/swing unit tests + more automated build system that includes building of plugins.

Features

  • Meta Nodes, Phase 2
  • 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
  • Tree Object viewer in Browser (For GO data, etc.)
  • Cytoscape Theme (Skin)

  • Background Task support (for compressing huge session file)
  • Headless mode, Phase 2 (Web Service?)

Refactoring / Design Issues

  • New GraphObject class; for nodes/edges

  • Define what the Edge ID is
  • 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
  • Remove legacy code from GO 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.

Cytoscape_2.4_and_Beyond (last edited 2009-02-12 01:03:05 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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