Summary:

DYNSTOC implements a null-event kinetic Monte Carlo method for simulating chemical reactions in a homogenous reaction compartment. The method can be used to simulate a large-scale biochemical reaction network, provided reaction rules are used to represent the reactions in the network. DYNSTOC reads reaction rules written in the BioNetGen language (BNGL), which is useful, among other purposes, for modeling protein-protein interactions involved in signal transduction. The simulation method does not require that a network be specified explicitly but rather takes advan-tage of the availability of the reaction rules in a rule-based specification of a network to determine if a randomly selected set of molecules participates in a reaction during a time step. Time is advanced regardless of whether a reaction or null event occurs after selection of a set of potential reactants. The method of DYNSTOC is closely related to that of STOCHSIM. DYNSTOC differs from STOCHSIM by allowing for model specification in terms of BNGL, which extends the range of protein complexes that can be considered in a model. DYNSTOC enables the simulation of rule-based models that cannot be simulated by conventional methods.

Availability:

DYNSTOC is Copyright 2008 Northern Arizona University and Copyright 2008-2009 The Translational Genomics Research Institute, All Rights Reserved.

Contact:

dynstoc@tgen.org

Usage:

1. Download the current version using the download link below.
2. Open package:
   

   • $ tar xzf filename.tar.gz

3. If not using precompiled package, from the package directory, run autoconf script and compile executable:
   

   • $ ./configure

   • $ make

4. Run sample model:
   

   • $ src/ds_bngl models/egfr_simple.bngl

Supplemental material

Download Dynstoc For Non-Commercial Use

Sample models

BioNetGen (and bngl documentation)