Segmentation Fault while customizing output plot specification

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Hikmet Emre Kaya

Oct 4, 2023, 5:19:12 AM10/4/23
to COPASI User Forum

I am trying to run a parameter estimation for the attached model. I have the starting model (ERK_Akt_Wnt_SBML.cps), and I added one reaction and modified another reaction (ERK_AKT_Wnt_SBML_Muc1NGal.cps), but the lack of kinetics studies leaves me no choice but to estimate the parameters computationally to normalize the second model with respect to the original one.

Basically, I added the reaction Galectin Binding, for which I don't really know the parameters except the ratio kf/kr, and modified the reaction v2 (so I want to estimate its k1 and k2).

As experimental data, I uploaded the time course txt file from the original model (the one before I made the changes mentioned above).

I wanted to view only the weighted errors in the plot, so when I go to the output specifications to delete the measured and fitted curves, COPASI crashes and gives the following error: ./CopasiUI: line 28: 29722 Segmentation fault      "${CopasiUI}" "$@"

I am not sure what is causing this error. I am using the latest version for Linux64.

Thanks for the help in advance


Frank Bergmann

Oct 4, 2023, 7:33:11 AM10/4/23
to COPASI User Forum
Hello Emre, 

I'm traveling currently and wasn't able to reproduce the crash you described. However, what you could do is regenerate a new plot, with just the errors you'd like to see. In the latest version we changed the dialog, so that you can more easily choose what you want to see for the parameter estimation result plot. 

I'll get back to you in a week or so when I'm back from my travels. 

Output Assistent 2023-10-04 at 7.31.23 AM.jpg

Hikmet Emre Kaya

Oct 4, 2023, 8:13:02 AM10/4/23
Hello Frank,

OH I cannot believe I skipped it (lack of morning coffee). That should work fine, then.

A more generic question: besides the curves for the weighted errors, what are the ways of interpreting how good the fit is? E.g., is there a universal objective value threshold or does it depend on the model?

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Hikmet Emre Kaya

Professional Science & Wellness Writer

PhD Candidate in Computational Glycoenzymology at the University of Cape Town

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