Questions about CopasiUI and CopasiSE

[Konstantia Georgouli]

Hi,

I am sending this email because I have some questions regarding CopasiUI and CopasiSE. 

1. I am running stochastic simulation for a model using CopasiUI  and I am taking negative count species in the results of  the Time Course. Is it possible to change this?

The model does not contain mass action formulas but general reaction rate formulas. 

2. Is there any way to confirm that NativeJit is used when someone uses CopasiSE?

3. Last, I have created a cps file (executable) running stochastic simulation and  producing the particle numbers in the results. However, when I am trying to run this using CopasiSE, it returns the concentrations in the report file instead of the particle numbers. Is there any way to fix this?

Thank you.

Kind regards,

Konstantia

[Frank Bergmann]

Hello Konstantia

1) I think this would have to be done on the level of the rate formulas ... you could always consider to multiply your ratelaw with a parameter that has a piecewise assignment on it, being 1 whenever the substrates are non-zero, and 0 everywhere else. 

2) not without checking the symbols on the executable i'm afraid. If you tell me which platform you are on, I can tell you how to check. 

3) If you open your model file in the CopasiUI, you can specify on the task, to generate a Report in the output assistant that would use the particle numbers (its called "Time, Particle Numbers, Volumes, and Global Quantity Values"). 

I hope this helps, 

best

Frank

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[Mendes,Pedro]

Konstantia,

On 3/25/21 7:29 PM, Konstantia Georgouli wrote:
> 1. I am running stochastic simulation for a model using CopasiUI  and
> I am taking negative count species in the results of  the Time Course.
> Is it possible to change this?
> The model does not contain mass action formulas but general reaction
> rate formulas.

This should not happen if your rate laws have zero rates when the
substrate number is zero. I suspect you may have rate laws where this
does not happen. You can check your rate laws in the GUI by selecting
Tools/Check Model. Go through the report and identify any rate law where
the rate is not zero when one of the substrates is zero. Then you may
follow the advice Frank gave, of setting some kind of piecewise
assignment. Only those rate laws will need the piecewise trick, any rate
law that is zero when substrates are zero should not be a problem.

Pedro

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[Konstantia Georgouli]

Hi both,

Thank you very much for your help. I will try to follow your suggestions.

Is there any way to set this parameter with a piecewise assignment in CopasiUI? 

Frank, about your question of what platform I am using for checking the use of NativeJit, the answer is Linux. 

Thanks,

Konstantia

[Hoops, Stefan (sh9cq)]

Hello Kontantia,

You can see whether NativeJIT is enable when you open Help->About. It
will say:
NativeJIT just in time compiler (enabled)

Thanks,
Stefan

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Email: sho...@virginia.edu

[Frank Bergmann]

On linux, you could see if the jit was enabled on CopasiSE, you could run: 

strings CopasiSE | grep Jit

(potentially full path to the CopasiSE), if you get outputs like: 

_ZTS14CJitExpression

then that CopasiSE has been compiled with Jit support. 

best

Frank

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[Konstantia Georgouli]

Hi all,

Thank you very much for your help.

Frank, could you tell me how I can set this piecewise assignment for my model in CopasiUI please ?

On Friday, 26 March 2021 at 07:58:59 UTC-7 frank.thom...@gmail.com wrote:

Hello Konstantia

1) I think this would have to be done on the level of the rate formulas ... you could always consider to multiply your ratelaw with a parameter that has a piecewise assignment on it, being 1 whenever the substrates are non-zero, and 0 everywhere else. 

Thanks,

Konstantia

[Hoops, Stefan (sh9cq)]

Hello Konstantia,

Did you verify that all kinetic laws are correct, i.e., the model
checker did not complain about a reaction no being zero if a substrate
is zero.

Furthermore if you have higher order kinetics, i.e., your stoichiometry
is not 1 and you did not correct for this in your rate laws than you
should make sure that the check box 'Apply Stochastic Correction of
Rate Laws' is marked.

If you still have a problem, i.e., see negative numbers I would
appreciate if you could share your model with me so that I can
determine what is going wrong.

Thanks,
Stefan

[Konstantia Georgouli]

Hi Stefan,

Thank you very much for your answer. I have checked the model using the model checker and there are some messages for example

"The kinetic function is never zero for positive parameter values if substrate "c_MG_196_MONOMER" is set to zero."

For this reason, I want to set a parameter with piecewise assignment as Frank suggested.

I have already selected the  'Apply Stochastic Correction of Rate Laws' checkbox.

I am attaching the SBML model  as you suggested.

Please let me know if you need anything else.

Thanks,

Konstantia

[Frank Bergmann]

Hello Konstantina, to define such a piecewiese expression i'd create a global quantity, with an expression like: 

if({[A]} < 0,0,1)

where in this case {[A]} represents the substrate concentration (you could add an or expression, if you have multiple substrates). And then edit the function definition to use that global quantity and multiply your existing expression with it.

the complete allowed syntax is described here: 

http://copasi.org/Support/User_Manual/Model_Creation/User_Defined_Functions/

Cheers

Frank

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