Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks

Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. Results: We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuo...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: David Adalsteinsson, David McMillen, Timothy C. Elston
• Keywords: Biochemical Networks, BMCBI 2004, Random Variables, Stochastic