Team:Freiburg/Model

Overview Motivation CAR T Cells Tumor Microenvironment AND Gate Outlook Achievements References

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Main Project Modeling Applied Design Proof of Concept BioBricks Basic Part BioBrick Improvement Interlab Study

Safety Cloning HIF1A Knockdown Cell Culture Lab Book

Human Practice Integrated Human Practice Collaborations

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.

$f^{\text{'}}\left(t\right)=y\left(z\right)-k1*f\left(t\right)$

$f^{\text{'}}\left(t\right)=y\left(z\right)-k1*f\left(t\right)$

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.