https://github.com/csgillespie/hybrid-pmcmc

Science Score: 10.0%

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Links to: arxiv.org
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Low similarity (7.6%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: csgillespie
Language: FORTRAN
Default Branch: master
Size: 459 KB

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Stars: 2
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Created over 12 years ago · Last pushed almost 12 years ago

Metadata Files

Readme

README.md

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.

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 - 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)

Owner

Name: Colin Gillespie
Login: csgillespie
Kind: user
Location: Newcastle, UK
Company: Newcastle University

Website: https://www.jumpingrivers.com
Twitter: csgillespie
Repositories: 62
Profile: https://github.com/csgillespie

Author of Efficient R programming. R consultant with Jumping Rivers and Senior Statistics lecturer at Newcastle University.

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