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Revision as of 14:03, 24 October 2017


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Modeling

Modeling in synthetic biology and iGEM Freiburg 2017

In synthetic biology, modeling can be applied to a wide range of topics, for example modeling of genetic circuits to predict their outcome and to support, if enough data is available, further development such as optimizing genetic circuits for a desired outcome.

In this subfield of mathematical and computational biology, ordinary differential equations (ODEs) are used to describe the transcriptional and translational process (Chen et al., 1999). ODEs consist of a set of parameters and a system of functions and their derivatives. How they can be set up in their simplest form is shown below.

f'(t)=y(z)-k1*f(t) (1) z'(x)=k2*f(t)-k3*z(t) (2)

The variables are functions of time t where f(t) describes the mRNA concentration, y(z)the transcription function and z(t)the protein concentration. Rate constants are enlisted in the following table. \[RNA_{pol} + g_{C4R} \rightarrow RNA_{pol} + g_{C4R} + mRNA_{C4R}\]

f't=yz-k1*ft