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BioPreDyn-Bench is a suite of benchmark problems for dynamic modelling in systems biology

BioPreDyn-Bench has been developed in the framework of BioPreDyn, an EU FP7 Cooperation project (Knowledge Based Bio-Economy, KBBE EU grant number 289434). BioPreDyn partners are developing data-driven computational models to analyze multi-scale biological networks, creating tools to help design and optimize complex biotechnological processes.

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Why

Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models.

The associated problems of parameter estimation (model calibration) and optimal experimental design are particularly challenging. The community has already developed many methods and software packages which aim to facilitate these tasks.

However, there is a lack of suitable benchmark problems which allow a fair and systematic evaluation and comparison of these contributions.
What

BioPreDyn-Bench is a suite of benchmark problems for dynamic modelling in systems biology, created by several partners from the EU project BioPreDyn.

Currently, it contains six challenging parameter estimation problems which aspire to serve as reference test cases in this area.

This set includes medium and large-scale kinetic models of E.coli, S. cerevisiae, D. melanogaster, Chinese Hamster Ovary (CHO) cells, and a generic signalling network.

The level of description includes metabolism, transcription, signal transduction, and development.
How

Regarding the implementations, we provide the following formats:

(1) ready-to-run implementations in Matlab, AMIGO (Matlab toolbox) and COPASI

(2) core implementations in C (which only need the user to write a small program as optimization driver, therefore allowing the use of any optimization code which can be interfaced with C)

(3) partial implementations (systems dynamics plus initial conditions) in SBML (so they can be imported into any of the many software packages that support this format)