Differences between revisions 10 and 16 (spanning 6 versions)
Revision 10 as of 2006-06-09 21:11:24
Size: 1211
Editor: KeiichiroOno
Comment:
Revision 16 as of 2006-07-12 23:01:43
Size: 1999
Editor: KeiichiroOno
Comment:
Deletions are marked like this. Additions are marked like this.
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 * Attribute Based Layout  * 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
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 * Vizmapper map-by-filter value (e.g. color nodes by value of function)
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 * Tree Object viewer in Browser (For GO data, etc.)  * Complex object (tree, map, etc.) viewer in Attribute Browser
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 * Background Task support (for compressing huge session file)  * 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.
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 * Migration to [http://java.sun.com/j2se/1.5.0/index.jsp Java version 5] and lib directory cleanup (especially XML-related files)
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 * Define what the Edge ID is  * Define ''Invisible CyAttributes ''(CyAttributes which is not shown on the Browser. Used internally)
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 * Remove legacy code from GO Server

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.

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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