Applying the Benchmark Models using SBML

The Systems Biology Markup Language (SBML) is a general standard for defining models. Many tools and software enviroments support loading of models based on the SBML format. However, SBML does not provide comprehensive functionalitiy concerning loading of data as well as for defining the mathematical link from model to data (e.g. including error models).

As an example, we describe loading of a benchmark model using COPASI.

Loading SBML models in COPASI

We provide one SBML model for each corresponding data file in the subfolder SBML.The file can directly be improted under File/Import SBML. The parameters are already set to the optimal parameter values and the model can directly be simulated for these parameter values.

Remarks

In order to provide a clear 1:1 relationship between data sets and the respective mathematical model (which might comprise experiment specific parameters) we provide an individual SBML file for each data set.

We suggest testing proper implementation/loading by comparing your custom model simulations with the simulations which are provided in this benchmark collection as a reference. These noise-free simulations are provided in 'MODEL_NAME/data/*.xlsx' in sheet 'Simulation' for all experimental observations.