We present an approach for constructing dynamic models for the simulation of
gene regulatory networks from simple computational elements. Each element is
called a ``gene gate'' and defines an input/output-relationship corresponding
to the binding and production of transcription factors. The proposed reaction
kinetics of the gene gates can be mapped onto stochastic processes and the
standard ode-description. While the ode-approach requires fixing the system's
topology before its correct implementation, expressing them in stochastic
pi-calculus leads to a fully compositional scheme: network elements become
autonomous and only the input/output relationships fix their wiring. The
modularity of our approach allows to pass easily from a basic first-level
description to refined models which capture more details of the biological
system. As an illustrative application we present the stochastic repressilator,
an artificial cellular clock, which oscillates readily without any cooperative
effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07