A cell is composed of many intertwined regulatory and signaling networks.
Proteins, RNA, and DNA act upon one another to control cellular processes and
responses to changes in the environment. In this module, we study a model of
a synthetic regulatory circuit, the Repressilator
, which consists
of a loop of three proteins, each of which represses the transcription of the
next (akin to the rock-paper-scissors game). As in the
module, we compare stochastic and deterministic representations of the
Repressilator dynamics, here in a much more complex system, where
good software design allows seamless conversion between two very different
simulation strategies. We also study the difference between shot noise
and telegraph noise
- Download the file RepressilatorHints.py and rename it "Repressilator.py".
- Open this file in a text editor (kate or emacs -- we
recommend against using kedit) or load it into the IPython dashboard (started with ipython notebook --pylab inline.
- Open a terminal window, move to the correct directory and start ipython,
or click on the notebook in the dashboard. You will find it convenient
to start python with the --pylab flag -- ie type ipython --pylab or ipython notebook --pylab.
- Follow the directions in Repressilator Exercise