Automatic Transformation of Kinetic Equations into S-System and GMA Forms

Canonical models in S-system or GMA form are sets of differential equations which are consistent with a number of specific features of biochemical systems as well as with observations that are common to other branches of biology [3]. While these models are advantageous for their light-weighted structures which let us instantly derive steady-state concentrations of the metabolic intermediates involved, the accurate derivation of the parameters required — the kinetic orders and the rate constants — can become extremely time-consuming and a laborious task to perform manually. For these reasons, we have developed an automation tool to convert the kinetic models written in E-Cell [4] rule files into GMA formed models to be run in PLAS [3].