Re: [copasi-user-forum] Time course simulation error
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Hoops, Stefan (sh9cq)
Aug 13, 2023, 11:18:03 AM8/13/23
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Hello Renad,
muscle.cps:
COPASI tells you what the problem is:
>ERROR 2023-08-13T11:11:34<
CMathModel (3): Recursive prerequisites encountered for object
'CN=Root,Model=New
Model,Vector=Values[sigmoid],Reference=InitialValue'.
The value sigmoid is recursively defined. It depends on the rate of Mn.
But also influences the rate through reaction: Production of Mn. You
need to decide what comes first.
Model 2 which uses ODEs instead of species and reactions has far more
of those circular dependencies.
I hope that helps,
Stefan
On Sat, 2023-08-12 at 18:47 -0700, Renad Al-Ghazawi wrote:
> Hi everyone,
>
> I'm a graduate student in bioinformatics, I've made a large system of
> (10)
> ODE's with approx. 20 parameters. I've successfully simulated this
> model in
> different coding languages however I wanted to use COPASI to simulate
> and
> potentially optimize my system parameters (if possible). Granted the
> system
> is quite complex and still in the works. I keep getting an error in
> my time
> course model.
>
> I've attached two CPS files. Any help would be much appreciated!
>
> Best,
> Renad
>
--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911
Phone: +1 540 570 1301
Email: sho...@virginia.edu
muscle.cps:
COPASI tells you what the problem is:
>ERROR 2023-08-13T11:11:34<
CMathModel (3): Recursive prerequisites encountered for object
'CN=Root,Model=New
Model,Vector=Values[sigmoid],Reference=InitialValue'.
The value sigmoid is recursively defined. It depends on the rate of Mn.
But also influences the rate through reaction: Production of Mn. You
need to decide what comes first.
Model 2 which uses ODEs instead of species and reactions has far more
of those circular dependencies.
I hope that helps,
Stefan
On Sat, 2023-08-12 at 18:47 -0700, Renad Al-Ghazawi wrote:
> Hi everyone,
>
> I'm a graduate student in bioinformatics, I've made a large system of
> (10)
> ODE's with approx. 20 parameters. I've successfully simulated this
> model in
> different coding languages however I wanted to use COPASI to simulate
> and
> potentially optimize my system parameters (if possible). Granted the
> system
> is quite complex and still in the works. I keep getting an error in
> my time
> course model.
>
> I've attached two CPS files. Any help would be much appreciated!
>
> Best,
> Renad
>
--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911
Phone: +1 540 570 1301
Email: sho...@virginia.edu
Montano, Nieves M - (nievesmontano)
Aug 14, 2023, 12:17:12 PM8/14/23
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From: 'Hoops, Stefan (sh9cq)' via COPASI User Forum <copasi-u...@googlegroups.com>
Sent: Sunday, August 13, 2023 8:17 AM
To: copasi-u...@googlegroups.com <copasi-u...@googlegroups.com>
Subject: [EXT]Re: [copasi-user-forum] Time course simulation error
Sent: Sunday, August 13, 2023 8:17 AM
To: copasi-u...@googlegroups.com <copasi-u...@googlegroups.com>
Subject: [EXT]Re: [copasi-user-forum] Time course simulation error
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