Repeated parameter estimation task and output report

[Daniel Koch]

Hello everyone,

I'm working on a model for which I have plenty of data for parameter estimation. Unfortunately, not all parameters are identifiable and some of the resulting estimates vary a lot. So what I wanted to do is to create a set of about 50-100  parameter sets and repeat the simulations with each set to see how robust the model predictions are despite varying parameters.

As I don't want to run so many parameter estimation tasks manually in COPASI, I wanted to use the parameter scan function set on repeat. As output, I'd like to have a table of the form

parameter 1, ..., parameter n, obj func val

where each line contains the parameter values and the obj function value for one parameter estimation run. So I created a new output report (under report templates) and added the parameters from the report menu "Items -> reactions -> reaction parameters". However, the report only lists the initial value of the parameters, not the estimated values. Furthermore, I can't find the obj func val in this menu.

I actually expected to find the parameters values and the objective function somewhere in the report menu "Items -> Results", but oddly there's nothing on parameter estimation...

Many thanks in advance for any help!

Best regards,

Daniel

P.S.: My COPASI version is 4.31

[Frank Bergmann]

Hello Daniel, what you want to do is possible, but you will have to go in the expert mode, in oder to find that. Since that is a bit tricky, i've made a recording of it: 

https://share.getcloudapp.com/6quYJGJk

this gives you a table with the iteration of the scan in the first column, the objective value in the second, and all of the parameter values in the third column, like this: 

TaskList[Scan].Output counter TaskList[Parameter Estimation].(Problem)Parameter Estimation.Best Value TaskList[Parameter Estimation].(Problem)Parameter Estimation.Best Parameters
0 12.8574 ( 1.67662e-06 44.5005 0.0430289 0.0553515 -0.0509407 0.0580391 0.0481459 )
1 12.8441 ( 2.02566e-06 44.8104 0.0430058 0.0532896 -0.0509422 0.0348974 0.0479169 )
2 12.8442 ( 0.000470107 44.8178 0.0430054 0.0528828 -0.0509423 0.0338961 0.0478904 )
3 12.5023 ( 26.7281 46.6495 0.0465405 0.0789732 -0.0498038 0.0355239 0.0583371 )
4 12.844 ( 1.00848e-06 44.7722 0.0430089 0.0538379 -0.0509419 0.0376988 0.047947 )
5 12.8444 ( 1.60747e-06 44.7451 0.043009 0.0539655 -0.0509417 0.0401919 0.0479656 )
6 12.8445 ( 2.86071e-06 44.7329 0.043012 0.0538388 -0.0509415 0.040538 0.0479727 )
7 64.9511 ( 13387.7 968.82 0.12083 0.4 -0.0257434 -0.197784 0.275153 )
8 12.844 ( 2.31137e-06 44.785 0.0430075 0.0527802 -0.0509419 0.036971 0.0479468 )
9 12.8446 ( 1.0785e-06 44.7289 0.0430114 0.0542827 -0.0509417 0.0400607 0.0476609 )

I hope this helps, 

best

Frank

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[Daniel Koch]

Hi Frank,

That's exactly what I was looking for, many thanks for your help! :-)

Best,

Daniel