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Methods Mol Biol. 2016;1386:441-63. doi: 10.1007/978-1-4939-3283-2_19.

Modeling and Simulation Tools: From Systems Biology to Systems Medicine.

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Systems Bioinformatics, VU University Amsterdam, Amsterdam, The Netherlands.
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands.
Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands.


Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of "Software as a Medical Device" and what this may imply for the migration of research-oriented, simulation software into the domain of human health.In our second perspective, we see how in practice hundreds of computational tools already accompany drug discovery and development at every stage of the process. Standardized exchange formats are required to streamline the model exchange between tools, which would minimize translation errors and reduce the required time. With the emergence, almost 15 years ago, of the SBML standard, a large part of the domain of interest is already covered and models can be shared and passed from software to software without recoding them. Until recently the last stage of the process, the pharmacometric analysis used in clinical studies carried out on subject populations, lacked such an exchange medium. We describe a new emerging exchange format in Pharmacometrics which covers the non-linear mixed effects models, the standard statistical model type used in this area. By interfacing these two formats the entire domain can be covered by complementary standards and subsequently the according tools.


Constraint-based modeling; Kinetic modeling; Pharmacodynamics; Pharmacometrics; Physiology-based pharmacokinetics; Quantitative and systems pharmacology; SBML; Software design; Standards development; Systems biology

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