dummy variables in simbiology

Hi,

I have a model in simbiology where I am using a dummy parameter to control the concentration of an inhibitor in a reaction (michaelis-menten inhibitor function).

Basically, I have a rate rule controlling the concentration of the inhibitor species that sets it to 0 at a certain time, and this instantaneous change to 0 is controlled by the dummy parameter "event" (time>=24 & event == 1) which enables me to run my model according to 2 sets of experimental configurations; with and without the event.

I want to fit this model against experimental data in which 1 of the columns in my data set contains a 0 or 1 depending on whether the event was performed.

Is it possible to fit the model parameters using the "fit data" task, setting it up such that the dummy "event" parameter I have placed in the model is set using the value 0 or 1 in the column in the data set? (i.e IF data = 1, event = 1).

I use IF statements with dummy parameter values as switches quite a lot to control parameter and variable values when modelling with Matlab itself, is there a recommended way of doing this in simbiology so they can be coupled with values in specific data set columns for fitting?

Thanks for any help.

Answer 1

[Arthur Goldsipe]

Hi,

Currently (as of R2016a), the data in a fit task can only affect a model via dosing. So I think you could do what you want if you change your dummy parameter to a dummy species and configure the fit task to use the 0/1 data column as dosing for this species.

-Arthur

[micronaut]

Thanks for your help, this is much appreciated.

Currently, I have an experiment with compound at varying doses that are either constant throughout the experiment or washed out at time x. I have the dose in 1 column which is mapped to dose in "fit data". If I map washout to another species could they mapped together with inhibitor and washout? I'm guessing not (?).

In other tools I've just mapped the value of a parameter in a model to a value in the data, is this kind of assignment possible in simbiology?

Thanks again for your help.

[Arthur Goldsipe]

I don't fully understand this question: "If I map washout to another species could they mapped together with inhibitor and washout?" Can you explain in a little more detail or provide an example. What is "they" in the sentence?

Regarding mapping the value of a parameter to a value in the data: Today, this is not possible in SimBiology. As I mentioned, you can only map the data to dosing information that is applied to the model.