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From: mridul on 14 Jun 2010 15:41
Dear Team,

I'm working on a mathematical model of cellular signaling pathway and needs to do simulations in a hybrid fashion which means certain reactions as deterministic (ODE) while others are stochastic in nature. This mixed behavior is a feature of the signaling pathway and I guess, most of biological signaling processes falls into this category.

I'm using SimBiology of MATLAB R2008b on Windows XP for my model formulation and simulations. I can use it very well for ODE simulations but I'm unable to find any program/feature where I can run a hybrid simulation. Is there anyway to perform that??

Thanks for your timely suggestion and help.
Regards
Mridul KK
From: Arthur Goldsipe on 15 Jun 2010 08:58
Hi Mridul,

SimBiology supports three algorithms for stochastic simulations: the Stochastic Solver Algorithm (SSA), Explicit Tau-Leaping, and Implicit Tau-Leaping. These algorithms are appropriate when the stochastic behavior happens because there is a small number of molecules of a reacting species. As the number of molecules increases, the behavior of the stochastic model approaches that of the deterministic (ODE) model.

So, when you say you have a "hybrid" model, I interpret that to mean that your physical system has a small number of molecules of some reactants but a large number of molecules of other reactants. If so, then you should be able to model your "hybrid" system using one of the tau-leaping algorithms. However, these algorithms require that you write all reactions using mass-action kinetics. For example, rather than using Michaelis-Menten kinetics, you would need to explicitly model the underlying reactions (binding, unbinding, and conversion).

Good luck with your modeling!

-Arthur

"mridul " <desperadomkk(a)gmail.com> wrote in message <hv60kg$ck8$1(a)fred.mathworks.com>...
> Dear Team,
>
> I'm working on a mathematical model of cellular signaling pathway and needs to do simulations in a hybrid fashion which means certain reactions as deterministic (ODE) while others are stochastic in nature. This mixed behavior is a feature of the signaling pathway and I guess, most of biological signaling processes falls into this category.
>
> I'm using SimBiology of MATLAB R2008b on Windows XP for my model formulation and simulations. I can use it very well for ODE simulations but I'm unable to find any program/feature where I can run a hybrid simulation. Is there anyway to perform that??
>
> Thanks for your timely suggestion and help.
> Regards
> Mridul KK
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