Cytoscape is an open-source software for creation, visualization and analysis of biological networks. Cytoscape is a systems biology software used for integrating biomolecular interaction networks with high-throughput expression data and other molecular state information. Cytoscape is an amazing tool when used with large databases of protein-protein, protein-DNA or genetic interactions. With Cytoscape its possible to have visual integration of the network with expression profiles, phenotypes and other molecular state information and link the network to databases of functional annotations.
Cytoscape basically consists of a "core" software that provides basic functionality and is extensible through plug-in architecture. There are various plug-ins available based on your need. And believe me, some of the plug-ins have great functionality and can do wonders with your data. The central organizing concept of Cytoscape is a network (graph), with nodes representing genes, proteins and molecules and edges or links between the nodes representing interactions between them.
Biology in a post-genomic era is an information science and converting the vast amount of biological information into useful knowledge is the key in today's world. Cytoscape allows you to do just that! It even has a functionality to do free text search across large number of databases! According to me Cytoscape is a very good tool for organizing and analyzing the ocean of biological information that is available today. Not only that, with the help of Cytoscape you can build your prediction models which can then be used to design your wet lab experiments. Well as they say it, Knowledge is Power, in that case Cytoscape is certainly a powerful computational systems biology tool.
Cytoscape is a collaborative project between the Institute for Systems Biology (Leroy Hood lab), the University of California San Diego (Trey Ideker lab), Memorial Sloan-Kettering Cancer Center (Chris Sander lab), the Institute Pasteur (Benno Schwikowski lab), Agilent Technologies (Annette Adler lab) and the University of California, San Francisco (Bruce Conklin lab).
For further information and download please visit http://www.cytoscape.org.
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