General Technique
Cytoscape is a general-purpose software platform for biological network data integration, visualization, and analysis in a unified conceptual framework. Though applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of gene-expression data and protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms.
Purpose/use/application of the technique:
Cytoscape embodies the systems biology idea that system-level biological properties are determined by networks rather than individual molecules and interactions. Cytoscape is designed to extract biological information from large sets of data of disparate types. The software provides basic functionality to: 1) layout and query networks. 2) visually integrate the network with expression profiles, phenotypes, and other molecular states; and, 3) link the network to databases of functional annotations. It is open-source, platform-independent (Java), and structured as a core that is readily extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features.
Example(s) of projects at ISB that use this technique:
Cytoscape is an integral part of many ISB projects, including:
Modeling predictive biological networks in Halobacteria (Baliga Lab)
Systems biology of yeast filamentation (Galitski Lab)
GLUE grant (Aderem/Bolouri Labs)
Ongoing area of technology development:
The Cytoscape project is based at a consortium of institutions including the Institute for Systems Biology, the University of California at San Diego, The Memorial Sloan-Kettering Cancer Center in New York City and the Institut Pasteur in Paris. In addition, there is an extended open-source development community. Some major areas of development include the representation of alternative network states, the integration of logical elements, and the analysis of network dynamics.
Representative publication(s):
http://www.cytoscape.org
Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, Avila-Campillo I, Shannon P, Galitski T. Derivation of genetic interaction networks from quantitative phenotype data. (2005) Genome Biol. 6:R38.
Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. (2004) Genome Res. 14:2221.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. (2003) Genome Res. 13:2498.
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