Home

Benchmark Models for Dynamic Modelling of Intracellular Processes

This repository presents a collection of 20 ODE models developed given experimental data as benchmark problems in order to evaluate new and existing methodologies, e.g. for parameter estimation or uncertainty analysis. In addition to the equations of the dynamical system, the benchmark collection provides experimental measurements as well as observation functions and assumptions about measurement noise distributions and parameters. The presented benchmark models comprise problems of different size, complexity and numerical demands. Important characteristics of the models and methodological requirements are summarized and estimated parameters are provided.

This benchmark collection has been published incluging example studies for illustrating the capabilities of the presented benchmark collection as preprint in

• Helge Hass, Carolin Loos, Elba Raimundez Alvarez, Jens Timmer, Jan Hasenauer, Clemens Kreutz Benchmark Problems for Dynamic Modeling of Intracellular Processes BioRXiv (2018), https://doi.org/10.1101/404590

Usage of the Benchmark Collection

The benchmark models can be used

1. based on the Data2Dynamics modelling framework as decribed here.
2. in Matlab based on basic code for simulating the models as described here.
3. based your custom modelling software by loading models in the SBML format. Guidelines are provided here.