  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. 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. 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
http://www.iim.csic.es/%7egingproc/biopredynbench/.
