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

Tomáš Helikar, Jim A. Rogers

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


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.

Original languageEnglish (US)
Article number58
JournalBMC systems biology
StatePublished - 2009
Externally publishedYes

ASJC Scopus subject areas

  • Structural Biology
  • Modeling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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