Computational challenges in systems biology

Systems biology is a broad field that incorporates both computational and experimental approaches to provide a system level understanding of biological function. Initial forays into computational systems biology have focused on a variety of biological networks such as protein–protein interaction, signaling, transcription and metabolic networks. In this review we will provide an overview of available data relevant to systems biology, properties of biological networks, algorithms to compare and align networks and simulation and modeling techniques. Looking towards the future, we will discuss work on integrating additional functional information with biological networks, such as three dimensional structures and the complex environment of the cell. Combining and understanding this information requires development of novel algorithms and data integration techniques and solving these difficult computational problems will advance both computational and biological research.