search

Open-Systems-Pharmacology / Forum

Discussion forum for the Open Systems Pharmacology Project
65 stars 19 forks source link

MoBi does not allow committing changes in organ protein expression #532

Closed yishuanwu closed 4 years ago

yishuanwu commented 4 years ago

Hi,

I have a simulation in MoBi for which I'd like to optimize the relative tissue expression (M_0) of the protein binding partner of a TMDD model. I am able to modify the parameter in the simulation and the simulation ran. However, when I attempt to commit the changes in MoBi by updating the below screenshot item, my simulation gives me an error (second screenshot) about parsing the 'M_0':

image

image

Where else should I modify the relative expression of the protein to avoid the error message?

Thanks again! Shirley

PavelBal commented 4 years ago

You should not optimize the "M_0" parameter but "Relative expression (normalized)" of the molecule in the respective compartment.

Yuri05 commented 4 years ago

What is "M_0"-parameter?

PavelBal commented 4 years ago

@Yuri05

image

Yuri05 commented 4 years ago

Well, in a "standard" model it's possible to optimize start amounts of proteins and commit the optimized values back into building blocks, so here the problem seems to be project-related. DummyModel_OptimizeStartAmount.zip

grafik

yishuanwu commented 4 years ago

Thank you for both of your help.

I did not realize that I can conduct parameter identification for the start amount in MoBi and was doing the optimization manually before.

When I do it by parameter identification, transferring to the simulation, and then commit the changes, I did not run into the error -- so maybe I was modifying the parameter at the wrong location? I went under Parameter > Organism > Individual Organ > Interstitial, and modify the M_0 from there, but the manual edit gives me the error message if I try to commit the change and rerun.

However, as my goal is to extrapolate the model to a different species, I would need to be able to manually modify the start amount. How else should I manually modify this parameter?

I wanted to try out the example you supplied. But it says that my application is too old (compatible version 13) and cannot load a project created with a newer version (project version 14).

I visited the download page and see that my version should be current (8.0.21, and installed after the release date of Jun 19, 2019). Is a new release being planned?

Yuri05 commented 4 years ago

Is a new release being planned?

Yes. For now you can use the portable version of MoBi9 (not released yet) to open the file.

yishuanwu commented 4 years ago

I am sorry to be a bother. It's telling me "Unable to load DLL 'OSPSuite.Func.ParserNative.dll": The specified module could not be found. (Exception from HRESULT: 0X8007007E)"

Pavel did say that I should not optimize the M_0 but should normalize the relative expression-- I finally found that parameter. It's under the parameter tab next to the initial value tab. Changing the relative expression changes the start amount, while changing the initial value M_0 does not change the start amount in the parameter tab, even though they both affect the current simulation. Therefore my issue is fixed. Thanks!

Shirley