Biology Reference
In-Depth Information
Chapter 14
Spatiotemporal Modeling
and Simulation in Biology
Ivo F. Sbalzarini
1. Introduction
Describing the dynamics of processes in both space and time simultane-
ously is referred to as spatiotemporal modeling. This is in contrast to
describing the dynamics of a system in time only as is, for example, usu-
ally done in chemical kinetics or pathway models. Solving spatiotempo-
ral models in a computer requires spatiotemporal computer simulations.
While computational data analysis allows unbiased and reproducible pro-
cessing of large amounts of data from, e.g. high-throughput assays,
computer simulations enable virtual experiments
in silico
that would not
be possible in reality. This greatly expands the range of possible pertur-
bations and observations. Computational experiments allow studying
systems whose complexity prohibits manual analysis, and they make
accessible time and length scales that cannot be reached by lab experi-
ments. Examples of the latter include molecular dynamics (MD) studies
in structural biology and studies in ecology or evolutionary biology.
In virtual experiments, all variables are controllable and observable.
We can thus measure everything and precisely control all influences and cross-
couplings. This allows disentangling coupled effects that could not be
separated in real experiments, greatly reduces or eliminates the need for
indirect control experiments, and facilitates interpretation of the results.
Finally, computational models do not involve living beings, thus enabling
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