Software

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

Tomáš Helikar¹ and Jim A Rogers^1,2

¹Department of Pathology and Microbiology, University of Nebraska Medical Center, 983135 Nebraska Medical Center, Omaha, NE 68198, USA

²Department of Mathematics, University of Nebraska, 6001 Dodge Street, Omaha, NE 68182, USA

author email corresponding author email

BMC Systems Biology 2009, 3:58doi:10.1186/1752-0509-3-58

Published:	6 June 2009

Abstract

Background

New mathematical models of complex biological structures and computer simulation software allow modelers to simulate and analyze biochemical systems in silico and form mathematical predictions. Due to this potential predictive ability, the use of these models and software has the possibility to compliment laboratory investigations and help refine, or even develop, new hypotheses. However, the existing mathematical modeling techniques and simulation tools are often difficult to use by laboratory biologists without training in high-level mathematics, limiting their use to trained modelers.

Results

We have developed a Boolean network-based simulation and analysis software tool, ChemChains, which combines the advantages of the parameter-free nature of logical models while providing the ability for users to interact with their models in a continuous manner, similar to the way laboratory biologists interact with laboratory data. ChemChains allows users to simulate models in an automatic fashion under tens of thousands of different external environments, as well as perform various mutational studies.

Conclusion

ChemChains combines the advantages of logical and continuous modeling and provides a way for laboratory biologists to perform in silico experiments on mathematical models easily, a necessary component of laboratory research in the systems biology era.