Applying the Benchmark Models using Matlab

Applying the Benchmark Models using Matlab

One possibility for applying the presented benchmark models is based on Matlab without any modelling environment or toolbox. On this page we describe how the models can be used in the Matlab programming environment.

An alternative strategy based on Data2Dynamics (which also runs in Matlab) is decribed here.

Another alternative is using SBML (described here).

Loading the models in Matlab

The following functions are providedfor loading models and data in Matlab:

• ReadBenchmarks can be used for loading the whole benchmark model including all data sets. This function calls all three functions briefly described in the following.
• ReadModelFiles only loads a model file as found in the folders
• ReadInfoFiles only loads the model information as stored in
• ReadDataFiles can be used to load specific data sets.

Remarks

Please note, that our Matlab tools only provide functionality for basic simulations of the models. This might be very helpful for testing correct implementations. However, please note that these tools do not provide advanced numerical or methodological functionalilty (like forward- or adjoint sensitivities) which is usually essential for high-performance analysis. The generated code is only based on Matlab's ode15s integrator which might generate numerically inaccurate solutions without any additional methodological considerations.