Setting up parameter estimation using experiments with different initial conditions

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Stephen Sweeting

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Sep 29, 2023, 3:50:10 AM9/29/23
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Hello everyone,

I am trying to set up a model for my experiments. I have done a variety of different conditions, and want to put these into the model and then do a parameter estimation to calculate what some of the rate constants are for some of the elemental steps.

When I load all the experimental data into one file, the parameter estimation doesn't do a good job. However, when I group reactions together that have the same initial concentrations of various species, then the parameter estimation does a good job at predicting the curves from the data.

Is there a way to set up a COPASI model so that experiments with different initial conditions can be used in modelling? Any guidance in this is greatly appreciated, as I'm very new to using COPASI for modelling.

Sluka, James Patrick

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Sep 29, 2023, 12:54:28 PM9/29/23
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I’m sure there are COPASI expert that can help more, but quickly:

Your experimental data gets loaded into COPASI as a table, typically with columns of values for species and rows as time. You can also make a column for a parameter (like an initial condition, or an initial estimate of a k) and load it the same way. You might have to duplicate that value down the entire column.

 

James P. Sluka, PhD
Biocomplexity Institute

Intelligent Systems Engineering

School of Informatics, Computing and Engineering

Indiana University

Bloomington, IN   USA

Office: 812-855-2441

Cell: 317-331-7465

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