Cytoscape geography software#

Conceptually, Diffusion applies heat to each node in the set, and lets the heat flow through connecting edges to adjacent nodes.

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. Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. Cytoscape’s Diffusion algorithm attempts to use a set of nodes and an entire interaction network to find the nodes most relevant to the original set. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features.

Cytoscape geography software#

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. 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 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. Introduction Cytoscape is a fairly complex application and its core distribution has multiple repositories for managing its code.