Simple Stochastic Code in Python

It’s been a while since I blogged (grant writing etc gets int he way of actual thinking and doing) so here is a quick post that uses Python to model a simple reaction A -> B using the Gillespie next reaction method.

I know importing pylab is discouraged but I can never remember how to import matplotlib. pylab is an easy way to get matplotlib. It also imports scipy and numpy but I import numpy separately.

I use lists instead of array to accumulate the results because they are faster to extend as the data comes in. Note that with a Gillespie algorithm you don’t know beforehand how many data points you’ll get.

I’ll also make a shameless plug to my book Enzyme Kinetics for Systems Biology which explains the algorithm.

This entry was posted in General Science Interest, Modeling, Programming, Python, Software. Bookmark the permalink.

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