title: Understanding dynamics using sensitivity analysis: caveat and solution.
abstract: BACKGROUND
  Parametric sensitivity analysis (PSA) has become one of the most commonly used tools in computational systems biology, in which the sensitivity coefficients are used to study the parametric dependence of biological models. As many of these models describe dynamical behaviour of biological systems, the PSA has subsequently been used to elucidate important cellular processes that regulate this dynamics. However, in this paper, we show that the PSA coefficients are not suitable in inferring the mechanisms by which dynamical behaviour arises and in fact it can even lead to incorrect conclusions.
  
  
  RESULTS
  A careful interpretation of parametric perturbations used in the PSA is presented here to explain the issue of using this analysis in inferring dynamics. In short, the PSA coefficients quantify the integrated change in the system behaviour due to persistent parametric perturbations, and thus the dynamical information of when a parameter perturbation matters is lost. To get around this issue, we present a new sensitivity analysis based on impulse perturbations on system parameters, which is named impulse parametric sensitivity analysis (iPSA). The inability of PSA and the efficacy of iPSA in revealing mechanistic information of a dynamical system are illustrated using two examples involving switch activation.
  
  
  CONCLUSIONS
  The interpretation of the PSA coefficients of dynamical systems should take into account the persistent nature of parametric perturbations involved in the derivation of this analysis. The application of PSA to identify the controlling mechanism of dynamical behaviour can be misleading. By using impulse perturbations, introduced at different times, the iPSA provides the necessary information to understand how dynamics is achieved, i.e. which parameters are essential and when they become important.
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore.
authors.forename: Thanneer M
authors.initials: TM
authors.lastname: Perumal
authors.forename: Rudiyanto
authors.initials: R
authors.lastname: Gunawan
mesh_terms: D016923:Cell Death / Q000502:physiology; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D019169:Jurkat Cells; D007700:Kinetics; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D049490:Systems Biology / Q000379:methods*