THE CIRCADIAN CLOCK – A BioSPI MODEL

We are studying the circadian clock based on a generalized model presented by Naama Barkai and Stanislas Leibler. A positive element, protein A, increases its own expression and that of a negative element, protein R. Strong binding of R to A inhibits A’s activity and so represses the expression of both elements by binding to the promoters P_A and P_R. The autoactivation of A results in a hysteresis: a bi-stable dependence of A concentration on R. Slow kinetics of R then lead to oscillations, which can be described as successive transitions between 'induced' and 'repressed' states. Since this phenomenon is dependent on differential rates and stochastic effect, we use the BioSPI compiler for accurate stochastic simulations.

Full code for the clock is available here

The code can also be accessed through a clickable map

More details on the clock can be found in Barkai N. and Leibler S. (2000) Biological rhythms: Circadian clocks limited by noise, Nature 403, 267 - 268.

More on our work can be found in our ISMB00 poster, and in our presentations.

The work on the circadian clock is done in collaboration with Naama Barkai, at the departments of molecular genetics and physics of complex system at the Weizmann Institute of Science.