Graphical Analysis and Visualization Tools for Protein Interaction Networks

Sirisha Gollapudi, Alex Marshall, Daniel Zadik & Charlie Hodgman

Software for the visualization and analysis of protein-protein interaction (PPI) networks can enable general exploration, as well as providing graph-theoretic algorithms for specific tasks. Analyses can include reduction of complexity or the scope of the network in order to make it more manageable, or increase in complexity by integration with other datasets, to represent biology more accurately. Two software approaches are outlined in this chapter: desktop applications and web services. Desktop applications have attractive user interfaces with a wide range of analysis tools, and often capabilities for integration of other bio-molecular data. Web services provide a newer approach to network analysis. They have the advantages of a broader range of potential functionalities and a more extensible framework than standalone desktop tools. However, their relative infancy means that they are not as well developed. This chapter provides an evaluation of some common desktop applications, compared to and contrasted with several examples of web services.