interpret

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interpret[reaction-list] converts a list of reactions

{{arrow-form₁, rate-information₁}, {arrow-form₁, rate-information₂,...}}

into differential equations

{{ode₁, ode₂,...},{var₁,var₂...}}

The variable Global`t is used for the time argument.

The output of interpret can be evaluate by NDSolve as in the following example (Download Mathematica .nb file):

The format of rate-information and arrow-form vary with the type of reaction being described. For more information see:

• Summary of basic arrow forms

• Flux Reactions - reactions for which only a flux and not a specific kinetic rate law is known.

• (Generalized) MWC reactions - kinetic descriptions based on the Monod-Wyman-Changeaux models.

• GRN functions - kinetics described by sigmoidal activating functions similar to those found in neural networks.

• Hill functions - kinetics described by hill functions.

• Mass Action reactions - law of mass action.

• Michaelis-Menten reactions

• NHCA reactions - non hierarchical cooperativee activation models.

• Rational function reactions - rate laws described by rational functions (ratios of polynomials).

• S-Systems - power law approximations.

• User-defined reactions - rate laws given by any user defined function, similar to those in SBML.

  See Also: ODE