Martin Meier-Schellersheim

Computational Biology Unit
Laboratory of Systems Biology
National Institute of Allergy and Infectious Diseases
National Institutes of Health

Title: Rule-based spatially resolved modeling of cellular signaling
processes

Abstract: While rule-based approaches are becoming increasingly popular
within the modeling community their application to problems involving
spatially heterogeneous cellular biochemistry has so far been limited to
stochastic simulations that apply rules to create reactions between
pairs of individual molecules. These techniques are currently too
expensive for simulations involving large numbers of molecules or large
spatial regions such as whole-cell geometries or even multi-cellular
systems. Especially in these cases, however, automated, rule-based
creation of reaction-diffusion networks can be highly advantageous
because the spatial aspects add a layer of complexity to the formal
representation of signaling pathways that is absent in non-spatial, well
stirred simulations. I will introduce a modeling environment that uses
rules specifying interactions between pairs of molecular binding sites
in combination with formal representations of cellular geometries to
automatically build and simulate cellular signaling pathways embedded
into their spatial contexts.