Concepts in Mechanism Based Modeling
When we talk about biological organisms as systems we refer to the enormous number of mutually reinforcing, competing and counter acting feedback mechanisms that regulate the biological processes in space and time. We cannot hope to capture all aspects of
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Concepts in Mechanism Based Modeling Ole Lund, Jakob L. Laugesen, and Erik Mosekilde
We assume that biological phenomena in principle can be explained in terms of physical and chemical processes. The challenge is ’just’ to understand how this can be done.
2.1 Problem Definition When we talk about biological organisms as systems we refer to the enormous number of mutually reinforcing, competing and counter acting feedback mechanisms that regulate the biological processes in space and time. We cannot hope to capture all aspects of such a highly integrated system in any model. The first and most important step in the biological modeling process must, therefore, be to establish a clear picture of the purpose of the project. In general terms, the purpose of a modeling effort could be to examine the mechanisms underlying a specific phenomenon and to suggest new critical experiments that could provide insights into these mechanisms. In the health care sector, the purpose could be to design an individualized treatment of a particular disease, and in the pharmaceutical industry the purpose could be to predict parameters
O. Lund () Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet 208, 2800 Lyngby, Denmark e-mail: [email protected] J.L. Laugesen E. Mosekilde Department of Physics, Technical University of Denmark, Fysikvej 309, DK-2800 Lyngby, Denmark e-mail: [email protected]; [email protected] E. Mosekilde et al. (eds.), Biosimulation in Biomedical Research, Health Care and Drug Development, DOI 10.1007/978-3-7091-0418-7 2, © Springer-Verlag/Wien 2012
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characterizing the pharmacokinetics of a new drug or to foresee situations where the drug would give rise to adverse side effects. The parameters characterizing the subcutaneous absorption of insulin represent, together with parameters related to the distribution and metabolism of insulin, typical pharmacokinetic parameters. A clear picture of the purpose of the modeling effort or, in other words, a clear problem definition is required to sort out those processes and interactions we need to take into account from all of those that can be neglected. In most cases this delineation cannot be performed by means of spatial boundaries alone. The kidneys and the liver, for instance, are by themselves complicated systems that support many different processes and when we talk about a heart model, we implicitly refer to particular functions that this organ performs. Other processes that take place in response, for instance, to changes in physical activity, to interactions with the lungs or the nervous system, or to drug administration may or may not be accounted for. The causal aspects of the problem definition are closely linked to the establishment of a dynamic hypothesis, i.e. a description of how the considered phenomenon can be explained in terms of the proposed mechanisms. This explanation may include a so-called reference mode, i.e. a graph that specifies how the main var
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