Model fitting using different data sets in SimBiology

Hi there,

I have a three compartment model for three different drugs that I would like to caliberate using a single parameter set for biological reactions. However, I cannot use the SimBiology tool to fit all three data sets because one of the drugs breaks down into several components before finally being cleared in the blood. A simplified version of the model looks similar to the one attached below. I would like to estimate EC50 values in the model for model caliberation and then simulate the model to compare results with actual data. For the two other drugs the equation for k1 would look similar but with Drug_Ctr instead of M3_Ctr

Answer 1

[Arthur Goldsipe]

Would it be possible for you to upgrade to R2021b? There's a new feature in that release that would make it much easier to do what you want. It's described in the SimBiology release notes as "Specify different parameter values for different groups during fitting". Basically, you can specify a different variant for each time course in your data (similar to how you specify a different dose for each time course in previous releases). You could use this variant to turn certain reactions on or off for specific time courses. You would also need to "merge" the two different models of interest into a single model and add a parameter to the relevant reactions or rules that enable you to turn them on or off for specific data sets.

For example, let's say you want to toggle between using M3_Ctr and Drug_Ctr in your rule for k1. You could update your rule to something like k1 = Emax*EC50/( X*M3_Ctr + (1-X)*Drug_Ctr +EC50). Then, for each time course where you want to use M3_Ctr you use a variant that sets X to 1, and for each time course where you want to use Drug_Ctr you use a variant that sets X to 0. You could make similar change to reaction rates if you need to turn certain reactions on or off for different time courses.

[Fearass Zieneddin]

Is there a way to specify two different doses with different targets in Simbiology or this should be done using MATLAB code? For exmaple, drug_s is being dosed and then drug_Ctr is being dosed. I've created a column for each dose in my data set but not sure how to set up different target species for each dose.

[Arthur Goldsipe]

Sorry for the delayed reply. I was on vacation last week. In the future, feel free to contact Technical Support if you don't get a timely answer via MATLAB Answers.

Yes, you can do this in the SimBiology Analysis App. Each dose target needs to be a different column in your data. In your fit program, you then configure the table that maps columns of your data. The name and location of this section is slightly different in R2021a and R2021b. In R2021a, the section is called "Definition," and in R2021b it's called "Data Map." In both cases, there's a button underneat this table labeled "Dose" that you click on to add a new dose to the table. Then, you select the name of the column and the name of the species. Here's a screenshot of a table I configured in R2021b: