BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

Villaverde, Alejandro F; Henriques, David; Smallbone, Kieran; Bongard, Sophia; Schmid, Joachim; Cicin Sain, Damjan; Crombach, Anton; Sáez Rodríguez, Julio; Mauch, Klaus; Balsa Canto, Eva; Mendes, Pedro; Jaeger, Johannes, 1973-; Banga, Julio R.

doi:http://dx.doi.org/10.1186/s12918-015-0144-4

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

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Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D et al. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology. 2015;9:8. DOI: 10.1186/s12918-015-0144-4

Abstract

Background: 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. Results: Here we present BioPreDyn-bench, a set of challenging parameter estimation problems which aspire to serve as reference test cases in this area. This set comprises six problems including medium and large-scale kinetic models of the bacterium E. coli, baker’s yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network. The level of description includes metabolism, transcription, signal transduction, and development. For each problem we provide (i) a basic description and formulation, (ii) implementations ready-to-run in several formats, (iii) computational results obtained with specific solvers, (iv) a basic analysis and interpretation. Conclusions: This suite of benchmark problems can be readily used to evaluate and compare parameter estimation methods. Further, it can also be used to build test problems for sensitivity and identifiability analysis, model reduction and optimal experimental design methods. The suite, including codes and documentation, can be freely downloaded from the BioPreDyn-bench website, https://sites.google.com/site/biopredynbenchmarks/.