Re: [Ecell-users] set up ODE for species directly.

[Lu L. <lu...@eb...>]

Hi Moriyoshi and Yuri

Thank you very much, yes I think ExpressionFluxProcess will be helpful.
But I have several questions:

1. ExpressionFluxProcess represents a customized reaction rate or it
directly presents flux?
e.g.
Process ExpressionFluxProcess(a2b)
{
k 33;
Expression "K^2";
VariableReferenceList [S0 Variable:/cell:a -1][P0 Variable:/cell:b 1]
}

Then, if we only consider this one reaction, which of the following
expression is correct?
da/dt = -K^2[a]   and    db/dt = K^2[a]
or
da/dt = -K^2   and  db/dt = K^2

2. Since the unit for Expression must be "number/second" instead of
"concentration/second", if, in the expression, the MolarConc of some
variables are used, I must multiply self.getSuperSystem().sizeN_A once, in
order to inform the system that I changed the unit?
I just wonder how e-cell do this consistency check ?
If under some circumstances, I need to multiply the size twice.....can
e-cell detect it?

3 In the case of multi-compartment model, in which way I can indicate that
I multiplied correct compartment/compartments?
e.g.
Process ExpressionFluxProcess(Ca_ER2Cytosol)
{
Kch 3;
K1 2;
Expression "(Kch*C1.MolarConc^2/(K1^2+C1.MolarConc^2)) *
(C2.MolarConc-C1.MolarConc)";   #this expression is wrong since I haven't
multiply any compartment size!#
VariableReferenceList [C1 Variable:/cytosol:Ca 1][C2 Variable:/ER:Ca -1];
}

* in this example I want to represent ER release Ca to cytosol.
the first part of this expression,
Kch*C1.MolarConc^2/(K1^2+C1.MolarConc^2) should have no unit problem,
since the unit for Kch is per-second, and the unit for K1 is
concentration.
However, for the second part C2.MolarConc-C1.MolarConc, I should convert
its unit into Number instead of concentration. Which compartment size, and
what kind of expression I should use here.

4 which stepper I should use for ExpressioFluxProcess?
should it must be a continuous stepper?
Can I use ODEstepper?


I am looking forward to your reply.
Thank you very much !

yours Lu


> Hi,
>
> In which sence did you say "directly" ? Sounds like
> it's ExpressionFluxProcess that fits to your case; did
> you try it yet?
>
> Moriyoshi
>
>
> 2008/3/18, Lu Li <lu...@eb...>:
>> Hello
>>
>>  I wonder in e-cell, can I directly set up ODE for some species?
>>  And these species, even can play a role in some reactions, their flux
>>  will not be influenced by these reactions?
>>
>>  I am looking forward to your reply.
>>
>>  Best Wishes
>>  yours Lu Li
>>  --
>>  Lu Li
>>  PhD student in Computational Neurobiology
>>  EMBL-European Bioinformatics Institute, Cambridge, UK
>>
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>
>
> --
> Moriyoshi Koizumi <mor...@gm...>
> (also reachable on <mo...@sf...>)
>


-- 
Lu Li
PhD student in Computational Neurobiology
EMBL-European Bioinformatics Institute
Cambridge, UK
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