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quantumbrake / cayenne

Python package for stochastic simulations
https://cayenne.readthedocs.io/
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Support for custom rate equations #123

Open sriki18 opened 4 years ago

sriki18 commented 4 years ago

Currently the user can only specify rate constants and the rate equations are implicit from the structure of the reaction. There should be support for custom rate equations independent of structure.

sriki18 commented 4 years ago

There are a few reasons to avoid custom rate equations.

  1. Custom rate equations do not make theoretical sense. It is the structure of the reactions that determines the reaction kinetics. 2. Not being able to create custom rate equations reduces the probability of errors.
  2. Something like Michaelis Menten kinetics can be described by setting up the individual constituent reactions, i.e.
    • E + S <-> ES
    • E -> E + P and picking rate constants which satisfy the assumption of Michaelis Menten kinetics.
  3. Phenomnological models like Monod kinetics should be treated carefully. Such models typically violate the theoretical assumptions of Gillespie type stochastic simulations, and it may not be ideal to simply use the rate equations to determine kinetics in the stochastic realm. Presently such approaches are not supported.