Reproducibility of model-based results in systems biology

Abstract

Science requires that results are reproducible. This is naturally expected for wet-lab experiments and it is equally important for model-based results published in the literature. Reproducibility, in general, requires standards that provide the information necessary and tools that enable others to re-use this information. In computational biology, reproducibility requires not only a coded form of the model but also a coded form of the experimental setup to reproduce the analysis of the model. Well-established databases and repositories store and provide mathematical models. Recently, these databases started to distribute simulation setups together with the model code. These developments facilitate the reproduction of results. In this chapter, we outline the necessary steps towards reproducing model-based results in computational biology. We exemplify the workflow using a prominent example model of the Cell Cycle and state-of-the-art tools and standards.