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= 1. Introduction = Cytoscape is an open-source community software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular state information for visualization and analysis. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. A software “Core” provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular state information; and to link the network to databases of functional annotations. The Core is extensible through a plug-in architecture, allowing rapid development of additional computational analyses and features. '''The central organizing metaphor of Cytoscape is a network (graph), with genes, proteins, and molecules represented as nodes and interactions represented as links, i.e. edges, between nodes.''' __'''Development'''__ Cytoscape is a collaborative project between the Institute for Systems Biology (Dr. Leroy Hood), the University of California San Diego (Dr. Trey Ideker), Memorial Sloan-Kettering Cancer Center (Dr. Chris Sander) and the Institut Pasteur (Dr. Benno Schwikowski). Visit http://www.cytoscape.org for more information. __'''License'''__ Cytoscape is protected under the GNU LGPL (Lesser General Public License). The License is included as an appendix to this manual, but can also be found online: http://www.gnu.org/copyleft/lesser.txt Cytoscape also includes a number of other open source libraries, which are detailed in Section 10, Acknowledgements below. __'''What’s New in 2.2'''__ Cytoscape version 2.2. contains several new features, plus improvements in the performance and usability of the software. These include: *Enhanced support for node and edge attribute handling, including a powerful new attribute browser, for navigating, defining, and editing node and edge attributes. For plugin coders, this also includes a greatly improved API (cytoscape.data.CyAttributes). *Support for dockable, tabbed panels (CytoPanels). *A set of Cytoscape editors for building and modifying networks interactively by adding nodes and edges to a drawing canvas. *Improved support for ontologies and other structured annotations. *Simplified mechanism for saving Visual Styles in between sessions. *A new GML visual style to manage visual properties from GML files *Many performance improvements and bug fixes. |