To represent multivariate data associated with a node, Cytoscape can control the visualization of each node using a custom graphical image (since version 2.3) through a programming API. Scalar data can be linked to simple visualization properties such as node color, shape, or size as node and edge attributes. 2 INTEGRATED VISUALIZATION 2.1 Custom Node Graphics A key function of Cytoscape is to allow diverse types of attribute data to be visualized on the nodes and edges of a biological network. Taken together, however, these features provide a mechanism for expressing relationships between sets of data while simultaneously visualizing the integrated results. Separately, each of these features provides useful new capabilities to Cytoscape. The second feature is the introduction of spreadsheet-like equations into Cytoscape’s Attribute Browser to enable advanced transformation and combination of data sets directly within Cytoscape. The first feature allows non-programmers to map graphical images onto nodes, which greatly increases the power and flexibility with which integrated data can be visualized. Version 2.8 of Cytoscape has introduced two significant new features that improve its ability to integrate and visualize complex data sets. shape, color, size) as well as to perform complex network searches, filtering operations, and other analysis. Attribute values can be used to control visual aspects of nodes and edges (e.g. Data are integrated with the network using attributes, which map nodes or edges to specific data values such as gene expression levels or protein functions. genes, proteins, cells, patients) represented as nodes and biological interactions represented as edges between nodes. Its central organizing principle is a network graph, with biological entities (e.g. Cytoscape, now in its eighth year of development, has become a standard tool for integrated analysis and visualization of biological networks (Cline, et al., 2007 Shannon, et al., 2003). Thus data integration, along with integrated visualization, is key. Although various data sets can appear quite different in quality and quantity, they all are reflections of the same underlying biological system and its responses. These network data extend and compliment a great deal of other information available in the biomedical sciences. Vast data sets are being gathered to delineate networks of various types and levels, including networks of genetic and protein-protein interactions networks of transcriptional and post-transcriptional regulation, social networks, and multiscale networks that span several of these domains (Fowler, et al., 2009 Tan, et al., 2007). Contact: 1 INTRODUCTION Networks are pervasive in biology. Binary install bundles and source code for Cytoscape 2.8 are available for download from. Availability and Implementation: Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL). Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties. Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. Version 2.8 introduces two powerful new features Custom Node Graphics and Attribute Equations which can be used jointly to greatly enhance Cytoscape’s data integration and visualization capabilities. Joaquin Dopazo ABSTRACT Summary: Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Bioinformatics Advance Access published DecemCytoscape 2.8: New Features for Data Integration and Network Visualization * Associate Editor: Dr.
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