Within-host stochastic viral dynamics code

Description

This repo contains a couple of programmes which may be used to simulate the early stochastic dynamics of within-host viral infection. The parameters are set by default to approximate those applicable to HIV-1 infection dynamics.

File descriptions

The most important files are:

• hiv_gillespie.cc: Gillespie SSA simulation code (C++)
• hiv_tauleap_hybrid.cc: Hybrid tau-leaping simulation code (C++)
• deterministic.py: Integrator for deterministic model (Python)
• poissonian.cc: Methods to sample from Poissonian distributions (C++)

Requirements

Both the SSA and tau-leaping programmes use MPI to coordinate the parallel calculation of trajectories. (Multithreading is adequate for a single machine, but MPI allows one to easily use a cluster as well.) You'll thus need some MPI implementation installed (eg. openMPI or mpich), even if you don't plan to use the parallel feature.

The deterministic integrator needs Python 2.x with Numpy installed.

Directions

Edit one of the above files to ensure the parameters are close to what you want, then use make to generate the executables. Running each executable without any arguments generates instructions on how to use it.