Utilizing Example Collection

Benchmark collection

The Benchmark collection is a set of independently published ODE-models calibrated with experimental data from the field of computational cell biology. The set of models is available in D2D, they are part of the Examples folder.

The introduction and analysis of the benchmark problem collection is published in Bioinformatics: Helge Hass et al. Benchmark Problems for Dynamic Modeling of Intracellular Processes

There also is a github page that collects the information about the benchmark models:.

Utilizing the example collection

Arbitrary subsets of the Benchmark collection (or other subsets of the example folder) can be used to perform method comparisons and performance assessments regarding parameter estimation and uncertainty quantification across different models. Here, we give a showcase example in how such an analysis could be implemented using D2D functionality:

First, a copy of the chosen subset (here, the ten fastest) of the benchmark collection is moved to a new folder:

mkdir('myFolder')
arCopyBenchmarkModels('fast10','myFolder')
cd('myFolder')

Secondly, all the setup files need to be compiled:

arCompileAllSetups

In the last step we want to run an analysis on all the models:

arEvalToAllExamples('arFitLHS','LHS100',[],1,100);

Here, a LHS 100 is performed for all the chosen models.

By specifying a more refined analysis function (e.g. @userfun), a straightforward performance assessment across various models is available.

addpath(path_to_userfun); % add path to the working dir to find the user-function
arEvalToAllExamples(@userfun,'none',[],2);

Via this approach you can now utilize the model collection to perform your own analysis. In the respective function documentations, you can find more details.