title: What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform.
abstract: The utility of model repositories is discussed in the context of systems biology (SB). It is shown how such repositories, and in particular their live versions, can be used for computational SB: we calculate the robustness of the yeast glycolytic network with respect to perturbations of one of its enzyme activities and one transport system. The robustness with respect to perturbations in the key enzyme phosphofructokinase is surprisingly large. We then note the upcoming convergence of pharmacokinetics-pharmacodynamics (PK-PD) and bottom-up SB. In PK alone, quite a few one-, two- or more compartment models provide valuable initial guesses and insights into the absorption, distribution, metabolism and excretion of particular drugs. These models are phenomenological however, forbidding implementation of molecule-based tools and network information. In order to facilitate a fruitful synergy between SB and PK-PD, and between PK and PD, we present a new platform that combines standard phenomenological models used in the PK/PD field with mechanism-based SB models and approaches.
authors.affiliation: Medical Biochemistry at Academic Medical Center ,  University of Amsterdam ,  Amsterdam ,  The Netherlands.
authors.forename: Maciej
authors.initials: M
authors.lastname: Swat
authors.forename: Szymon M
authors.initials: SM
authors.lastname: Kiełbasa
authors.forename: Sebastian
authors.initials: S
authors.lastname: Polak
authors.forename: Brett
authors.initials: B
authors.lastname: Olivier
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Bruggeman
authors.forename: Mark Quinton
authors.initials: MQ
authors.lastname: Tulloch
authors.forename: Jacky L
authors.initials: JL
authors.lastname: Snoep
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Verhoeven
authors.forename: Hans V
authors.initials: HV
authors.lastname: Westerhoff