原创cytoscape简单操作.pptVIP

Maunal of Cytoscape 2.8.0 Wangercheng Introduction Cytoscape is a project dedicated to building open-source network visualization and analysis software. A software Core provides basic functionality to layout and query the network and to visually integrate the network with state data. The Core is extensible through a plug-in architecture, allowing rapid development of additional computational analyses and features. Cytoscapes roots are in Systems Biology, where it is used for integrating biomolecular interaction networks with high-throughput expression data and other molecular state information. 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 allows the visual integration of the network with expression profiles, phenotypes, and other molecular state information, and links the network to databases of functional annotations. The central organizing metaphor of Cytoscape is a network (graph), with genes, proteins, and molecules represented as nodes and interactions represented as links, i.e. edges, between nodes. Preparation Requirement of system: Installation of Java SE 6/5 /technetwork/java/javase/downloads/index.html Hardwares Small network visualization Large network analysis ans visualization Processor 1GHz As fast as possible Memory 512M 2G+ Graphics Card On board video Highend graphics card Monitor XGA(1024*768) Wide or dual monitor Install Cytoscape Download Cytoscape (windows) /download.html Start Cytoscape 1. java –Xmx512M -jar cytoscape.jar -p plugins windows+r, input: cmd cd c:\Program Files\Cytoscape_v2.8.0 java -Xmx512M(1GB) -jar cytoscape.jar -p plugins Recommendation Number of objects (nodes + edges) Suggested memory sizes 0 – 70,000 512M(default) 70,000 – 150,000 800M Start Cytoscape 2. Double click cytoscape.jar in c:\Pro