yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML

Abstract

Ordinary differential equations (ODE) models are used throughout natural sciences to describe dynamic processes. In systems biology, ODEs are mostly stored and exchanged using the Systems Biology Markup Language (SBML), a widely adopted community standard based on XML. The Parameter Estimation table (PEtab) format extends SBML to parameter estimation problems. A large number of software tools support simulation of SBML models and parameter estimation for PEtab problems. Specifying ODE models in SBML and parameter estimation problems in PEtab provides access to these tools. However, SBML is considered to be neither human-readable nor human-writable. An easy-to-use approach to construct the SBML/PEtab models tailored to ODE models will facilitate model generation.

Periportal steatosis in mice affects distinct parameters of pericentral drug metabolism

“…The model was interpreted as solution of an ordinary differential equation (ODE) and implemented in the Systems Biology Markup Language (SBML) 60 , 61 format. A PEtab 62 parameter estimation problem was created via yaml2sbml 63 . Maximum likelihood estimation was employed for parameter estimation.…”