Time course simulation, sliders and experimental data

[Matteo Scampicchio]

I am using the "Time-course" task with the sliders to guess the initial values of some kinetic parameters. However, I would like also to include in the time course plot also the experimental data that I would like to fit. This would help me to better adjust the sliders and match the experimental point. Is it that possible?

Many thanks! Matteo

[Frank Bergmann]

Hello Matteo, 

this is not directly supported, but you can make it work. I think it could be done like this: 

- create a new global variable for your measured element (say obs_a)

- map the experimental data to obs_a 

- click on tools\CreateEventsForTimeSeriesExperiment

- now add obs_a to your existing plot

when your run your simulation now, you will see the curve for obs_a matching your experimental data (with lines between points) and your existing simulation. 

let us know if you need help with setting this up. 

best

Frank

[Scampicchio Matteo Mario]

Dear Frank,

I am afraid I am lacking some basic terminology. I have checked in the documentation the meaning of “mapping the data”, but no meaning… And about the global quantities, do you mean fixed or assigned?

 

Just to make it simple, I can try to exemplify my question with a minimalistic dataset.

I have the following experimental data:

Time     [A]

0            100

10         37

20         13

30         5

Which I want to model with the following mass flow irreversible kinetic model:

A -> B

The initial concentrations (time zero) are:

A = 100

B = 0

Now, I would like to have a Time Course plot (Concentration vs time), where I can vary the rate constant “k1” with a slider, and visualize in the plot not only the resulting simulation, but also the points of the minimalistic dataset shown above.

 

Many thanks for your time and help! Matteo

 

 

From: copasi-u...@googlegroups.com <copasi-u...@googlegroups.com> On Behalf Of Frank Bergmann
Sent: Tuesday, May 2, 2023 1:59 PM
To: COPASI User Forum <copasi-u...@googlegroups.com>
Subject: [copasi-user-forum] Re: Time course simulation, sliders and experimental data

 

Non si ricevono spesso messaggi di posta elettronica da frank.thom...@gmail.com. Informazioni sul perché è importante

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[sven....@gmail.com]

Hello, 

I can think of another way (with a different set of drawbacks...): 

You could use the parameter estimation with "current solution statistics" as method (which basically does nothing). Then you can define sliders for the parameter estimation task, and when you change a slider the parameter estimation will redraw the parameter estimation result plot (if you have one defined). You will have to make sure that the parameters that you want to change with a slider are not included in the parameter estimation. The drawback is that you will only get a plot of the variables for which you have measurements.

Sven