A biological simulator using a stochastic approach for synthetic biology

Abstract

Synthetic Biology is a new engineering discipline created by the development of genetic engineering technology. Part of a new engineering discipline is to create new tools to build an integrated engineering environment. In this thesis, I designed and implemented a biological system simulator that will enable synthetic biologists to simulate their systems before they put time into building actual physical cells. Improvements to the current simulators in use include a design that enables extensions in functionality, external input signals, and a GUI that allows user interaction. The significance of the simulation results was tested by comparing them to actual live cellular experiments. The results showed that the new simulator can successfully simulate the trends of a simple synthetic cell.