Differences between revisions 6 and 11 (spanning 5 versions)
Revision 6 as of 2006-05-24 17:50:43
Size: 972
Editor: KeiichiroOno
Comment:
Revision 11 as of 2006-06-12 20:03:07
Size: 1256
Editor: KeiichiroOno
Comment:
Deletions are marked like this. Additions are marked like this.
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 * Generic Plugin-state saving
Line 10: Line 11:
 * Visual Legend  * Visual Legend automatic generator
Line 14: Line 15:
 * Tree Object viewer in Browser (For GO data)
 * Background Task support (for compressing session file)
 * Complex object (tree, map, etc.) viewer in Attribute Browser

 * ''Cytoscape Theme
(Skin)''
 * Background Task support (for compressing huge session file)
Line 17: Line 20:
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 * Define what the Edge ID is
 * Performance tuning for save/load huge sessions
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 * Unit tests/swing unit tests + more automated build system that includes building of plugins.

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)

  • 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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