Cytoscape 2.1
Introduction
Cytoscape is an open-source
community software project for integrating biomolecular interaction
networks with high-throughput expression data and other molecular
states into a unified conceptual framework. 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 states; and to link the network to
databases of functional annotations. The Core is extensible through a
straightforward 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. Hamid Bolouri), 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.