Design and Architecture of Web Services for Simulation of Biochemical Systems

Computer simulation of biochemical networks plays a central role in systems biology. While there are several software packages for modeling and simulation of these networks, they are based on graphical user interfaces that operate on the local computer. However, it is now often desirable to operate simulation tasks through a distributed computing framework where data can be gathered from different sources and distinct subtasks operated in different physical computers. In this paper we describe a, web services implementation for the COPASI biochemical network simulator (CopasiWS). COPASI provides a range of numerical methods for simulation, optimization and analysis of biochemical reaction networks. Our aim is to allow easy integration of these powerful functionalities with local and remote services to provide a distributed computing platform for the simulation and analysis of biochemical models. One immediate result of this work is that simulation tasks are now and language-independent manner available to be used in a platform as components of distributed workflows, for example using the Taverna workflow engine. We describe the CopasiWS architecture, key design and implementation issues, and illustrate the range of services available through a web portal interface (CopasiWeb).