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Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Genome research | Nov 4, 2003

Cytoscape is an open source 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. Cytoscape's 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. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

Pubmed ID: 14597658 RIS Download

Mesh terms: Algorithms | Archaeal Proteins | Bacteriophage lambda | Computational Biology | Halobacterium | Internet | Models, Biological | Neural Networks (Computer) | Phenotype | Software | Software Design | Stochastic Processes