iBioSim: a CAD package for genetic circuits

iBioSim is a CAD package for the design, analysis, and simulation of genetic circuits. It can also be used for modeling metabolic networks, pathways, and other biological/chemical processes [1]. The tool provides a graphical user interface (GUI) for specifying circuit design and parameters, and a GUI for running simulations on the resulting models and viewing […]

synthetic biology: an emerging engineering discipline

In the last decade a new engineering disciple called “synthetic biology” has emerged. It differs from the science of biology in that it applies engineering strategies to the creation of cells that perform a desired task, such as the production of drugs or biofuels. It also differs from previous genetic engineering approaches by stressing the […]

simulating a synthetic biology circuit with system dynamics

McAdams and Arkin report the following synthetic biology oscillator circuit in their paper “Gene regulation: Towards a circuit engineering discipline” [1]: The circuit works by having gene R1’s protein inhibit production of R3, who’s protein inhibits production of R2, which in turn inhibits production of R1. Delays in the inhibition processes cause sufficient expression of […]