Is there a good tutorial for incorporating some of the MCMC code into a custom task in Simbiology?

I Am looking to add MCMC as a custom task and have no idea where to start in creating this - I Assume a custom task -but I am looking for a guid in how to even start writing this code.

Any direction is helpful.

Answer 1

[Fulden Buyukozturk]

Hi Andrew,

You can implement this, or custom analyses in general, in SimBiology either by creating a custom task on SimBiology desktop as you've suggested or by using a MATLAB script. I would suggest using a MATLAB script at least initially because it will be easier to debug your code.

To help start with this, you can configure a task and then check out the MATLAB/SimBiology code behind that task in SImBiology. This could serve as a starting point for your custom analysis. You can see the code by clicking on Task Code -> View Task Code on any built-in task on task editor. Please see below.

For example, to run a simple simulation, the programmatic workflow that you can run directly via a MATLAB script could look something like the following (you can run this example too since i'm using a shipped project):

% Load model from SimBiology project called AntibacterialPKPD
project = sbioloadproject('AntibacterialPKPD','m1');
model = project.m1

% Get model simulation settings and set stop time to 336
settings = getconfigset(model);
settings.StopTime = 336;

% Get the dosing schedule from the model
dose = getdose(model, '500 mg tid')

% Simulate with the dose
simdata = sbiosimulate(model, settings, dose);

% Plot all states
sbioplot(simdata)

For implementing MCMC specifically, I suggest you take a look at simfunction and Hamiltonian Monte Carlo sampler from the Statistics and Machine Learning Toolbox.

Does this help?

Fulden

Answer 2

[Andrew Heitman]

Yes, this is a great place to start. Thanks!