Abstract
Recent technological and theoretical advances are only now allowing
the simulation of detailed kinetic models of biological systems that
reflect the stochastic movement and reactivity of individual molecules
within cellular compartments. The behavior of many systems could
not be properly understood without this level of resolution, opening
up new perspectives of using computer simulations to accelerate biological
research. We review the modeling methodology applied to stochastic
spatial models, also to the attention of non-expert potential users.
Modeling choices, current limitations and perspectives of improvement
of current general-purpose modeling/simulation platforms for biological
systems are discussed.
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