Streamlining COPASI Workflow: Efficient Experiment Updates after Parameter Estimation

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Vincenzo Rosso

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Aug 23, 2023, 11:22:42 AM8/23/23
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Dear community,

I am currently engaged in utilizing COPASI for the precise determination of parameters within an enzymatic model featuring five distinct reactions. In the aftermath of executing the parameter estimation process, I encounter a pivotal step: the model update through the "update model" button. This action prompts a window to appear, necessitating the selection of an experiment from a pool of approximately 40 distinct experiments.

Herein lies my query: given the substantial number of experiments at hand, should I undertake the task of updating each experiment individually subsequent to parameter determination? My aspiration is to ensure the synchronization of the experiments with the refined parameters. Could you kindly guide me on the most efficient method to select and update these experiments in unison? I am particularly concerned that if I opt to update only one experiment, the remaining experiments might persist with outdated kinetic parameter values.

Thank you for your time and consideration.

Warm regards,
Vincenzo Rosso G.





Hoops, Stefan (sh9cq)

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Aug 23, 2023, 1:37:10 PM8/23/23
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Hello Vincenzo,

The easiest way for you is to check the 'Create Parameter Sets'
checkbox and run the 'Current Solution Statistics' in the Parameter
Estimation task. This will create a parameter set for each experiment
which you can apply to the model under Model->Biochemical->Parameter
Sets.

I hope that helps.

Thanks,
Stefan
--
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

Vincenzo Rosso

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Aug 24, 2023, 8:57:47 AM8/24/23
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Dear Hoops, 

Thank you for your swift and precise response to my previous email. Your help allowed me to move forward with my project in a timely manner.

Regards, 
Vincenzo Rosso G.
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