To create a simple network model and to visualize the network.
Cell is the most important principle unit of life, where several reactions take place. Cell contains genetic material DNA that encodes for proteins. Proteins carry out many important functions, some of which include: acting as enzymes, providing energy for metabolic activities, giving shape to the cell, and enabling motility to cell. Along with these activities, it plays a very important role in cell signalling. All these functions and processes can be well understood with the help of genome analysis. During the last few years, we have witnessed the availability of complete genome sequences and post-genomics experimental data. With the availability of huge data, several networks at molecular level like gene regulatory network, metabolic network, etc., have come into existence. Targeting modeling at these networks would help us to understand the underlying phenomena in detail.
How to represent these complex pathways or networks on a computer?
In mathematics or computer science perspective, a network is represented as a graph. It has nodes otherwise called as vertices, which are linked to each other through edges.
What is a Biological Pathway?
Biological pathway is a series of actions among different molecules in a cell. It triggers certain product or assembles new molecules, which regulates some genes by turning on and off.
Figure 1: An example for biological pathway
( Image source: en.wikipedia.org/wiki/File:Signal_transduction_pathways.svg )
What is a network?
Network is simply a collection of links connecting nodes in the network. Minimum information required to form a network is connectivity rule i.e., which node connects to which node. Speaking in biological terms, the links might refer to function of a particular protein or gene (nodes) or their expression patterns. Networks are collections of interactions, which contain pathways that are interlinked. All the pathways are subsets of networks, which means in a network pathways are interlinked.
Why to design or model biological networks?
Modeling a biological network would represent a biological scenario like a pathway and can help us to bring out the hidden properties of that system. This model can help us predict the dynamic behavor of the network which could be comparable with the experimental results. Accuracy of the model can be increased or it can be corrected with these predictions.
Biological pathways are grouped into networks and these networks are classified into metabolic networks, cell signalling networks, gene regulatory networks and protein-protein interaction networks.
To study such a complex process, visualisation of entire process is very much important. Modelling, reverse engineering and analysis of these macromolecular complex networks have interested the computational biologists, which lead them to develop specific tools like cytoscape, cell designer, E-cell, J-Designer etc.
Cytoscape is an open source platform to visualise and analyse complex networks, which is protected under the GNU LGPL (Lesser General Public License). It is available to all platforms. It is also extensible through plug-in architecture for different computational analyses. These biological networks are organised as graphs, connecting each node to another node through edges (called as interactions). This software becomes more powerful when it is used in connection with large databases of genetic interactions, protein-protein interactions.