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Stochastic simulations

This directory is the code needed to run the stochastic simulations, and the data from it.

Running the stochastic simulations requires this simple C++ library for the Gillespie algorithm, which you must install separately.

drawing

Load data from DVC

To just load the data from DVC, run dvc pull. Otherwise you must run the stochastic simulations from scratch - this can take a while!

Running stochastic simulations

Running the stochastic simulations requires this simple C++ library for the Gillespie algorithm, which you must install separately.

The source files are in the src directory. They are built with CMake from a dedicated build directory:

mkdir build
cd build
cmake ..

or, you can use your favorite generator like cmake .. -GXcode.

The binaries are in the bin directory:

cd bin
./run_gillespie

The default output directories are the data_gillespie and data_tau_leaping folders. You can see how to plot the trajectories using the Mathematica notebooks in the mathematica directory.