Retrieve Reaction Rate Dynamics from Metabolite Concentration Time Courses.

dynafluxr

Reaction rate dynamics can be retrieved from time-series measurements of chemical species and/or their isotopes. User has to provide corresponding stoechiometric matrix but not a regulation model (Michaelis-Menten or similar). Instead of solving an ODE system describing the evolution of concentrations, we use B-splines to catch the concentration and rate dynamics then solve a least square problem on their coefficients with optional constraints. Constraints can be set on initial values of concentration and/or monotonicity of B-spline coefficients. Positivity of these coefficients is always enforced. The package 'dynafluxr' can be used as a library providing appropriate functions but also as a stand alone application with command line interface.