Setting up pre-simulation conditions for parameter estimation

[Deepa]

Dear All,

I would like to know if there is a way to set up pre-simulation conditions

for carrying out parameter estimation.

I am using time-course date in the parameter estimation task.

From the experiments, I have the information about pre-incubation (/pre-simulation)

condition. 

Example, pre-incubation (30 min) at 2.8 mM glucose concentration followed by

incubation (60 min) at 20 mM glucose concentration.

I'm not sure how to use the pre-incubation information (i.e. concentration) in the parameter estimation set up.

I'm currently not taking the pre-incubation condition into consideration and only the

incubation glucose dose is used for mapping dose -> independent variable in the parameter estimation set-up. Here, I am assuming the time-series data from 0 to 60 min corresponds to 20mM incubation glucose (I think I'm making a mistake here because the

data point at t=0 min corresponds to the pre-incubation glucose and not the incubation glucose).  

dose   dose_unit    time                                 time_unit     glucose-6-phosphate
20.0    mM              0.0                                    min        3.498419522886086
20.0    mM              20.849799367704243  min        3.0430039636938147
20.0    mM              55.7415795233463       min        2.6565907619549174

dose is mapped to the independent variable and glucose-6-phosphate is mapped to

the dependent variable.

Suggestions on how to include the pre-incubation condition and how to perform

pre-simulations will be of great help.

Thanks so much for your time and kind attention,

Deepa

[Frank Bergmann]

Hello Deepa, 

for this you would create a global quantity lets call it `dose`. Next you create an event `preincubation` that would trigger at `time > 30` and assign the value of `dose` to the glucose concentration. In the parameter estimation setup you would then map the dose column as independent value to the global quantity `dose`. And you can then repeat the same with another event for 60 minutes. 

I hope this helps, 

best

Frank

[Deepa]

Hello Frank,

Thanks a lot for the explanation.

I'm not sure if I understand the events correctly:

preincubation is from 0 to 30 min

incubation is from 30 min to 60 min

Would I trigger the pre-incubation at t=0 min and incubation at t=30 min?

Could you please clarify?

Thanks again,

Deepa

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[Frank Bergmann]

Would I trigger the pre-incubation at t=0 min and incubation at t=30 min?

Could you please clarify?

Yes that would work.  You also have the option of handling the pre-incubation (for t=0) directly as initial assignment, but the event will also work.  if you are using an event to t=0, please check 'fire at initial time if trigger is true'.

Frank

[Deepa]

Hi Frank,

Thanks a lot for the clarification.

I tried the following via the events.

I 

I'm thinking if I should be doing 0< Time < 30 for the preincubation event and trigger the incubation event at Time>30. Also, could you please tell me if we can

use negative time i.e  -30 < Time < 0? I would like to specify the incubation for all experiments at t=0. 

The pre-incubation time differs in each experiment (i.e. 30 min, 10 min, 60 min, etc.)

I would like to know if we could do 

 -30 < Time < 0 

 -60 < Time < 0 

 -10 < Time < 0 

Could you please also explain a bit about specifying via the initial assignment? 

Could we map the dose column in the parameter estimation task as an independent value to the initial assignment?

Thank you,

Deepa

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[Frank Bergmann]

Hello Deepa

* for an event to fire at the initial time .. you have to click on the checkbox, Fire at Initial Time... this is disabled in your image, so that event would not trigger

* no, you cannot make the time negative, as workaround you could make your most negative time 0, and add the offset to all your other times in your time series. 

* what you can do, is to create a global variable `trigger_time` for the time at which the event should be triggered, and then write the event as `Time > trigger_time`. then you'd map the actual time to be used as independent column from the experimental data. 

* what i meant with initial assignment, is that when you go to the glucose species in your model. You would check the 'initial expression' checkbox and select the initial value of the dose parameter in the expression. Now when the experiment sets the dose's initial value, the species value should change accordingly. 

best

Frank