Inferring reaction systems from ordinary differential equations


In Mathematical Biology, many dynamical models of biochemical reaction systems are presented with Ordinary Differential Equations (ODE). Once kinetic parameter values are fixed, this simple mathematical formalism completely defines the dynamical behavior of a system of biochemical reactions and provides powerful tools for deterministic simulations, parameter sensitivity analysis, bifurcation analysis, etc. However, without requiring any in-formation on the reaction kinetics and parameter values, various qualitative analyses can be performed using the structure of the reactions, provided the reactants, products and mod-ifiers of each reaction are precisely defined. In order to apply these structural methods to parametric ODE models, we study a mathematical condition for expressing the consistency between the structure and the kinetics of a reaction, without restricting to Mass Action law kinetics. This condition, satisfied in particular by standard kinetic laws, entails a re-markable property of independence of the influence graph from the kinetics of the reactions. We derive from this study a heuristic algorithm which, given a system of ODEs as input, computes a system of reactions with the same ODE semantics, by inferring well-formed re-actions whenever possible. We show how this strategy is capable of automatically curating the writing of ODE models in SBML, and present some statistics obtained on the model repository .

Theoretical Computer Science, 599:64–78