系统生物学软件（王栋）Cytoscape and its plugins.pdfVIP

Cytoscape and its plugins Aija Niissalo Department of Computer Science University of Helsinki Finland May 25, 2007 Abstract Cytoscape is a software environment for integrated models of biomolec- ular interaction networks. It is developed and continually developing as an open source software project and offers an graphical user interface (GUI) for network modeling. This Java-based framework can visualize and integrate protein-protein, protein-DNA and genetic interactions with high-throughput expression data and molecular state information. With the help of Cytoscape and its plugins a researcher can e.g. identifying functional subnetworks in large-scale datasets. The cell interactomics can be visualized. Additionally, the produced images with Cytoscape are high quality and can be used in scientific papers. This article gives an overview of the tool and its plugins. This writing is not a manual or de- tailed user tutorial, because these can be found in the Cytoscape website (), where also Cytoscape itself is downloadable. 1 Introduction If we want to develop predictive biology - e.g. in genomics, proteomics or metabolomics and further on in medical and physiological understanding - one important principle is that in most cases it is not individual genes but rather bi- ological pathways and networks that are responsible of the wide diversity of an organism’s response or its phenotype [Quackenbush, 2007]. We must develop tools to understand the structures of the networks and the rules that govern the inte