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 [#acknowledgements Acknowledgements] below.

What’s New in 2.3

Cytoscape version 2.3. contains several new features, plus improvements to the performance and usability of the software. These include:

• A much faster rendering engine. Cytoscape can now render at interactive speed graphs with over 100,000 nodes and edges.
• The ability to save a session. You can now save all of your work in Cytoscape to a single file. When re-opened, this file will return Cytoscape to the state in which you left it including all networks, attributes, and properties.
• A node grouping plugin. This will allow one node to contain and display subnetworks.
• Enhanced Undo/Redo support.
• An enhanced attribute browser.
• An enhanced Ontology Server Wizard.
• An improved command line interface.
• The ability to rename networks.

• The GraphMerge plugin included by default.

• Enhanced context or pop-up menus for nodes.
• Many performance improvements and bug fixes.
• A rewritten "bird's eye view" of the network that is enabled by default.
• The ability to load expression data according to node attribute (such as a commercial probeset identifier) instead of ndoe ID.

Are you an experienced Cytoscape user? If so, you should definitely read the following sections because important parts of Cytoscape have changed and what used to work, may no longer work as you expect!!!

• [#properties Properties (cytoscape.props and vizmap.props) handling.]
• [#renderer Rendering Engine.]
• [#command_line_args Command line arguments.]
• [#menus The menu system.]
• [#navigation Network Panel Navigation.]