bioPN
bioPN is a R library of C functions that can be used to simulate time-dependent evolution of biochemical reactions. The model is defined as a place/transition Petri Net. It can either be deterministically solved using an explicit Runge Kutta Dormand Prince 45 method, or simulated using four variants of the Gillespie algorithm, executed as a hybrid of the two, according to the Haseltine and Rawlings' algorithm, or using the Partitioned Leaping Algorithm. The library has been designed for speed and flexibility.
Authors
Roberto Bertolusso (roberto *at* rice.edu) and Marek Kimmel (kimmel *at* rice.edu), Department of Statistics, Rice University, Houston, TX, USA.
Licence
The library is licenced under GPLv3.
Documentation
Manual
Download
Source
bioPN_1.0.0.tar.gz (2010-10-21)
Windows Binary Package
bioPN_1.0.0.zip (2010-10-21)
Code for Examples in Manual
Example 1: Stochasticity in Gene Regulation
Example 2: Cross-talk between P53 and NFkB
Download all the files to the same folder and make that folder the current one on R. Open main.R and run it. It will source the rest.
constants.R - places_transitions.R - model.R - fast_slow.R - initcond.R - protocol_propensities.c - main.R
See the manual for explanation on how to compile the c file. Follow this link for detailed information on utilities and setting PATH variable needed in Windows to compile c and fortran files (1.1 and 1.3). To avoid compiling protocol_propensities.c, to run the example an already binary protocol_propensities.dll is provided (for 32 bit systems. Tested on Windows XP).
