Hi Nick,
Here is an example of a simple model with one mass action reaction, L <-> C, with initial amounts of L and C being 1 and 0, respectively. The goal is to estimate the forward, kf, and reverse, kr, reaction rate parameters from data:
ID TIME LDATA CDATA DOSING
'1' 0 NaN NaN 1
'1' 0.056515 1.896 0.10399 NaN
'1' 0.2819 1.6196 0.38043 NaN
'1' 0.43163 1.5161 0.48388 NaN
'1' 2.1167 1.3346 0.66538 NaN
'1' 2.666 1.3336 0.66638 NaN
'1' 10 1.3333 0.66667 NaN
'2' 0 NaN NaN 2
'2' 10 2 1 NaN
'3' 0 NaN NaN 3
'3' 10 2.6667 1.3333 NaN
'4' 0 NaN NaN 4
'4' 10 3.3333 1.6667 NaN
This table contains data for four different experiments (ID). Each experiment corresponds to a different dose (DOSING) and has different data for L and C (LDATA/CDATA). In this example, we have steady state data (at time 10) for all experiments, but transient data is only available for the first experiment. Missing or not applicable data is indicated using NaN.
I am assuming you already have the model in the SimBiology desktop. The following steps give you a high-level overview of how to set up the fit task:
In the "Data" section, choose "Import Data from MATLAB workspace..." to add the table to the task. The "Independent Variable" should be TIME and the "Group" should be ID.
Next, click on the little + in section "Estimated Parameters" and add kf and kr to the list. Since this example is well-scaled, I suggest choosing no transformation.
Next, in section "Dosing Information", enter DOSING as "Dose Column Name" and L as "Dose Component Name".
In section "Response and Error Model Information" add "Response Column Name"s LDATA and CDATA with "Response Component Name"s L and C, respectively.
Lastly, expand section "Estimation Method" and check "Pool data". This tells the fit that all of your experiments share the same parameters, i.e. you can combine data from multiple experiments to inform the estimation of the rate parameters.
Now click the "Run" button in the tool strip on the top of the Task Editor. You should obtain rate parameters [kf, kr] close to [1, 2], which I used to create the data in the first place.
I hope this helps.
Best
-Florian
