Journal
INTERFACE FOCUS
Volume 1, Issue 1, Pages 16-23Publisher
ROYAL SOC
DOI: 10.1098/rsfs.2010.0011
Keywords
computational; systems; biology; pharmacokinetics; pharmacodynamics
Categories
Funding
- FP7 BioSim
- UNICELLSYS
- NucSys
- ECMOAN
- BBSRC's Sysmo/SysMO2/MCISB
- DTC
- EPSRC
- NWO-GBMW
- Biotechnology and Biological Sciences Research Council [BB/C008219/1] Funding Source: researchfish
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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.
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