Developing a Rate Equation Simulation Environment Using Microsoft Silverlight

Abstract

The exponential growth of information demands the automated movement of data and software via new software models that are able to integrate data and components on their own without scientists’ direct involvement. However, current stand-alone software modeling environments do not support a secure software execution, nor do client server applications allow user customization of the software running on the servers. To address this problem, a biological pathway modeling environment was built as a stand-alone Rich Internet Application (RIA). The modeling environment was tested by constructing a simulation of the glycolysis pathways in the human erythrocytes, and the results were compared against one of the latest and richest erythrocyte metabolism models developed by Kuchel and Mulquiney. The working simulation was able to settle into a quasi-stable state, with substrate concentrations close to what Kuchel and Mulquiney presented. It was also found that while the browser environment does allow for dynamic applications to be developed, speed and performance do become major issues. In later versions, it is hoped that the performance of the simulator can be increased and that it will become possible to link models together and add collaboration tools.