A tool to construct simulation models of biochemical cascades

Conference Date
2017
Location
Lyon, France
ISBN
978-0-262-34633-7
Date Published
September 2017
Conference Date: 2017, Vol. 14, Pages 521-528.
(doi: 10.7551/ecal_a_084)
© 2017 Massachusetts Institute of Technology Published under a Creative Commons Attribution 4.0 International (CC BY 4.0) license
Article PDF (887.99 KB)
Abstract

Simulation models are extremely useful but can be difficult to construct. There are numerous biochemical cascades in the human body and simulation models would help our understanding of how they work. We have developed a new approach for constructing agent based simulation models of biochemical cascades that is both powerful and general. The approach has been implemented in the CASCADE system and has been used to develop simulation models for 12 biochemical cascades including one (TLR4-Myd88) that has two feedback mechanisms. Early results indicate that the tool can greatly help in students understanding how to model biological systems (biochemical cascades in particular) using agent based techniques. This paper describes our approach, the use of the system and our evaluation of the generality, power and use of the system. In addition, the simulation model for the TLR4-Myd88 cascade predicted a novel result that was subsequently validated with a lab experiment.