![]() ![]() 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. Many of these steps could be reproduced in the same way for molecular networking from GC-MS data. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Launch the latest version of Cytoscape When you launch Cytoscape, the Starter Panel will open with some example session files to choose from. An online tutorial, created with Cytoscape 3.7, used for molecular networking generated with LC-MS/MS data, can be accessed here. 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 can create visualizations of a variety of different types of networks, including molecular and genetic, social networks, and semantic Web. 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. Cytoscape is a free, open source visualization tool for modeling complex networks and integrating network points with attribute data. ![]()
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