We have seen how to implement the Gillespie algorithm. However, writing down the update and propensity functions is tedious and error prone. Let's use a tool that does this for us.
In this lecture we chose to go with MobsPy - a model tool for reactions based on the Copasi simulator.
Take a look at the tutorial examples on the MobsPy GitHub Page.
Check out the next homework. It is based on a paper that proposes an algorithm that leads to oscillation of bacterial concentrations. The design makes use of communication among the bacteria via a small diffusible signaling molecule AHL.
We propose to start reading the homework assignment with the following questions in mind: