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Science  11 Mar 2005:
Vol. 307, Issue 5715, pp. 1539
DOI: 10.1126/science.307.5715.1539c

Tracing the interacting molecules that keep a cell running is trickier than keeping track of all the characters in Tolstoy's War and Peace. Puzzled readers can turn to Cliffs Notes, while researchers can keep their biochemical networks straight with Cytoscape, a free program for charting and analyzing inter-related genes, proteins, and other molecules. Created by the Institute for Systems Biology, the University of California, San Diego, and other organizations, the software lets users feed in their own data or standard files of molecular interactions from sites such as BIND. The program weaves the information into a map of molecular relationships. Cytoscape can also accept data on gene activity determined by microarrays, allowing users to infer hypotheses about which pathway produces a particular gene-expression pattern.

http://www.cytoscape.org/

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