![]() 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. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Im traying to contain the objects inside of cytoscape canvas without moving outside of max width and height, but if i drag the objects inside of canvas, they go outside of canvas border: Actually im not using the canvas from HTML5, instead im using the canvas from cytoscape.js plugin so this makes more complicated to fix it. 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 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 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 also has an edit functionality that enables you to build and modify networks interactively within the network canvas. ![]()
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