regarding doubt

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Ritika Saxena

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Jun 24, 2022, 4:35:10 AMJun 24
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good afternoon 
I've a doubt regarding COPASI .please rectify it .
copasi doubt.jfif

Frank Bergmann

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Jun 24, 2022, 4:53:36 AMJun 24
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Hello, 

I'm afraid all we can tell from the picture is that the model is in an invalid state. That means that one or more of the concentrations (or rates) have NaN values. We would need to see the model to tell you more about it. 

all the best
Frank

Ritika Saxena

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Jun 24, 2022, 4:59:40 AMJun 24
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This is my model. it showing error in glucose transport for that I've taken rate law as reversible Michalis Menten . but then to its showing error in time scale separation analysis.
ecoli.cps

Frank Bergmann

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Jun 24, 2022, 8:45:00 AMJun 24
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Hello, 

* the error in the `glucose transport` reaction comes from the fact, that the rate law uses a volume element, and that is not yet mapped. once you map it to for example the 'cell' compartment, that error will go away. 

there is a couple of other things that you might want to have a look at: 

* your reaction 'glyceraldehyde phosphate dehydrogenase [TDH2]' has a rate of -inf at start, this does not seem right. 
* your `phosphofructokinase` reaction will be NaN, whenever F6P or ATP is 0, this will cause issues. 
* the `glucose transport` reaction is marked as reversible, however that is not reflected in the ratelaw. maybe use it as irreversible for now. 

Once these issues are solved, i would start with running time courses, since this is the basis for the time scale separation. Once that is working, the TSSA method can be used. 

The 'Check Model` option from the Tools Menu, is really helpful in discovering these things. 

best
Frank
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