Backward simulation for inferring hidden biomolecular kinetic profiles

Abstract

Summary: Our backward simulation (BS) is an approach to infer the dynamics of individual components in ordinary differential equation (ODE) models, given the information on relatively downstream components or their sums. Here, we demonstrate the use of BS to infer protein synthesis rates with a given profile of protein concentrations over time in a circadian system. This protocol can also be applied to a wide range of problems with undetermined dynamics at the upstream levels.For complete details on the use and execution of this protocol, please refer to Lim et al. (2021).

Keywords

• Biophysics
• Systems biology
• Computer sciences