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.
- Change to the
src
directory
cd src
- Type
make
should build the code with no errors and create an executable called pmcmc
.
Note the gsl
math library is needed.
- The
pmcmc
executable has a number of options:
-s
the simulator used - eithergillespie
,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
- Running the
pmcmc
executable will create two files:
name_of_simulator.csv
- mcmc output;timing.csv
- run time (in seconds)