原创cytoscape简单操作

Tutoral 1 of Cytoscape
1. make a file: Sample.xls 2. Open the file, sample.xls
3. Visual Styles One of Cytoscape's strengths in network visualization is the ability to allow users to encode any attribute of their data (name, type, degree, weight, expression data, etc.) as a visual property (such as color, size, transparency, or font type). A set of these encoded or mapped attributes is called a Visual Style and can be created or edited using the Cytoscape VizMapper. With the VizMapper, the visual appearance of your network is easily customized.
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) 0 – 70,000 70,000 – 150,000 Suggested memory sizes 512M(default) 800M
Start Cytoscape
• 2. Double click cytoscape.jar in c:\Program Files\Cytoscape_v2.8.0 • 3. Start menu
• Installation of Java SE 6/5
http://www.oracle.com/technetwork/java/javase/downloads/ index.html
Install Cytoscape
• Download Cytoscape (windows) • http://www.cytoscape.org/download.html
4. layout
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. Cytoscape's 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:
Hardwares Processor Memory Graphics Card Monitor Small network visualization 1GHz 512M On board video XGA(1024*768) Large network analysis ans visualization As fast as possible 2G+ Highend graphics card Wide or dual monitwenku.baidu.comr