Software Tools for Systems Biology

Publisher Summary This chapter surveys some of the software tools and emerging standards for representing, simulating, and analyzing cellular networks. Model databases, model exchange standards, ontologies, and computational approaches that are relevant to the study of dynamics in biochemical networks have also been discussed. There has been a significant increase in the availability of computer software to help in modeling, simulating, and analyzing dynamic models of cellular processes. Many tools have been developed by practicing scientists and are therefore available free, whereas others are commercial. The software discussed in this chapter is concerned with analyzing two particular types of problem. One is the classical problem of solving systems of differential equations that describe the deterministic evolution of molecular species concentrations in time. The second problem of interest is the realization of the master equation. This equation describes the time evolution of the concentration probabilities. However, because we need one time evolution equation for every particle state in the system, the system of equations becomes unwieldy very rapidly as the size of the system increases. There are still some areas that are lacking, most notably bifurcation analysis and model composition. There are some very notable tools for bifurcation analysis, but they have been written more for general use than specifically for systems biology. One of the issues that have plagued software development in systems biology is chronic reinvention. Many tools, particularly those listed at SBML.org, carry out similar functions at their core. The fact that each tool reimplements the same functionality is arguably a waste of resources, and it would be of great benefit to the community if some of the core functionality could be released in the form of reusable software libraries.