RE: [copasi-user-forum] ODE expression for Species and defining their parameters
Frank T. Bergmann
You were almost there, the formula you want to type is:
{[G]}/(1+{Values[k]}*{[ERK]})
Or
Best
Frank
From: 'Terrell' via COPASI User Forum <copasi-u...@googlegroups.com>
Sent: Thursday, October 29, 2020 6:45 AM
To: COPASI User Forum <copasi-u...@googlegroups.com>
Subject: [copasi-user-forum] ODE expression for Species and defining their parameters
Hi COPASI community,
I am using a somewhat non-traditional formalism for my model. I am having trouble defining an ODE expression for my species. When there is no rate constant in the denominator, the error goes away; but when it is there, the problem reappears.
The Error says "Variable not found". So I believe it was pertaining to that rate constant. I then tried to correctly define it by putting an arbitrary initial value; while I am not sure if the units placed is correct - I believe the units of k should be such that the fractional term in my ODE ends up with a unit of mol/l*s.
Please help.
Best regards,
Terrell
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Terrell
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Frank T. Bergmann
It is certainly fine to use ODE’s for systems that can only be represented by ODE’s. The only thing to note, when going that route, is that several analysis techniques will not be available later on. (MCA, TSSA, LNA and some stochastic solvers will not handle such a model).
Best
Frank
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Terrell
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Frank T. Bergmann
Sorry about that, those were the tasks in COPASI that won’t work with ODEs:
- Metabolic Control Analysis
- Time Scale Separation Analysis
- Linear Noise Approximation
Best
Frank
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Terrell
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