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.
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 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.