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
