zhenglei-gao / hybrid-pmcmc

Bayesian Inference for Hybrid Discrete-Continuous Systems Biology Models

This repository contains the source code for the paper

Sherlock, C., Golightly, A., Gillespie, C.S. (2013) Bayesian Inference for Hybrid Discrete-Continuous Systems Biology Models (arXiv)

To download the code, either clone this repository or download the zip file and unpack.

1. Change to the src directory

cd src

2. Type

make

should build the code with no errors and create an executable called pmcmc. Note the gsl math library is needed.

3. The pmcmc executable has a number of options:

• -s the simulator used - either gillespie, hybridLNA, hybridSDE
• -n the number of iterations
• -d the input directory. This directory should contain a sub-directory with the name of the simulator used.
• -b the burnin - default 0
• -t thin - default 1

For example

./pmcmc -s gillespie -n 1000 -d ../input/inference/run1/ -t 2

4. Running the pmcmc executable will create two files:

• name_of_simulator.csv - mcmc output;
• timing.csv - run time (in seconds)