This page describes the Cytoscape architecture and a vision for where we want the architecture to be in the long-term.

Note: While we need to clearly decribe Cytoscape subsystems, it is important that most sections of this page not go into too much detail so that the overall architecture is apparent.

Why are there no biological semantics in the core, given that Cytoscape is targeted to biologists?

Core data structures

This section provides a very brief summary of core data structures meant as an executive summary, not exhaustive documentation.

Refactoring status

Miscellaneous data structures

This section briefly describes data structures that are part of the Cytoscape application, but are not considered core concepts. This generally means that the typical developer does not need to know about them because they are useful mainly for internal Cytoscape use or are planned to be removed.

Refactoring status

Cytoscape Core Subsystems

Refactoring Status

Cytoscape Core Plugin Systems

Many new systems are needed, as described in Future_Cytoscape_Features

Wiki page TODO

Cytoscape_architecture (last edited 2009-05-21 13:28:33 by 142)

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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