A data-driven framework for identifying nonlinear dynamic models of genetic parts

ACS Synth Biol. 2012 Aug 17;1(8):375-84. doi: 10.1021/sb300009t. Epub 2012 Apr 4.

Abstract

A key challenge in synthetic biology is the development of effective methodologies for characterization of component genetic parts in a form suitable for dynamic analysis and design. In this investigation we propose the use of a nonlinear dynamic modeling framework that is popular in the field of control engineering but is novel to the field of synthetic biology: Nonlinear AutoRegressive Moving Average model with eXogenous inputs (NARMAX). The framework is applied to the identification of a genetic part BBa_T9002 as a case study. A concise model is developed that exhibits accurate representation of the system dynamics and a structure that is compact and consistent across cell populations. A comparison is made with a biochemical model, derived from a simple enzymatic reaction scheme. The NARMAX model is shown to be comparably simple but exhibits much greater prediction accuracy on the experimental data. These results indicate that the data-driven NARMAX framework is an attractive technique for dynamic modeling of genetic parts.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Models, Biological
  • Models, Genetic*
  • Nonlinear Dynamics*
  • Quorum Sensing / genetics
  • Quorum Sensing / physiology
  • Synthetic Biology
  • Systems Biology