How to consider steady state concentration of biomarker in Simbiology

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I'm trying to develop the QSP model for endogenous biomarker dynamics in the body with simbiology app (R2021). This biomarker remains to be 5 mM in the tissue under untreatment condition, whereas the concentration is gradually increased up to 10 mM and deacreased to 5mM by administrating the some precursor molecules. I would like to fit the parameter for the production and metabolism of this biomarker. How can I set the steady state concentation (in this case; 5mM) in simbiology app?

Answers (2)

Arthur Goldsipe
Arthur Goldsipe on 16 Dec 2021
The SimBiology app does not currently provide any direct way to automatically fit steady state data. However, if I'm correctly understanding what you want to do, then I think it may not be a well-posed fitting problem. It sounds like you are trying to estimate 2 parameters (one for production and another for metabolism) using a single measurement (steady state concentration). If that's an accurate description, you have too many degrees of freedom, and there could be many combinations of parameter values that would result in the desired steady state concentration.
That said, the SimBiology app does have a feature to calculate steady states of a model. Steady state is a step that you can add to a simulation program. And there's an Explorer that makes it easy to interactively change parameter values and see how these changes affect your results.
If it would be helpful, I can attach a sample project that illustrates this. If you want that, let me know what version of MATLAB you are using. (If I use a project from a newer version, you might not be able to open it.)

和孝 関口
和孝 関口 on 17 Dec 2021
Dear Arthur
Thank you very much for your kind reply. I would like to explain in detail.
The metabolic pathway of molecules is here;
Untreated condition
Molecule A (initial/steady state; 5mM) -> Molecule B (initial/steady state; 100uM) -> null
When molecule A is orally administered, the concentration of A goes up to 10mM at 15 min from 5mM and then decreases to 5mM to 60 min and B goes up to 1mM at 15 min from 100uM and then decreases to 100uM to 60 min. I would like to develop the model for molecule A and B with their time profiles by considering the steady state conc of A and B (5mM, 100uM)
If my understandg is correct, the steay state concentration also should be obtained by fitting production and metabolism parameters? I'm wondering if I would be able to develop this model by constrain the minimum values for A and B. It would be appreciated if you could ask me further questions.
My matlab and Simbiology is R2021a (9.10.0) and version 6.1.
和孝 関口
和孝 関口 on 21 Dec 2021
Thank you so much! Infully understand what you meant about the steady state constraints.

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