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 […]

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 […]