Computational Gene Circuit Design
The models for the Repressilator and the Toggle Switch that we have built in Chap. 8 are not based on the notion of DNA parts and the two circuits are treated just as biological systems made of interacting molecules. However, as we have seen in Chap. 1 , an ultimate goal of Synthetic Biology is to developed methods for the modular design and modeling of genetic circuits, where basic components – DNA sequences and pools of signal carriers – are linked together in a visual way, as it is usually done with electronic circuits. One of the first attempts in this direction is represented by the Parts & Pools software, the Synthetic Biology add-on of ProMoT, a computational tool for the modular design and analysis of complex systems. In the following, we will see how the Repressilator and the Toggle Switch can be designed in a “drag and drop” way with Parts & Pools. First, DNA parts and pools are displayed on the canvas provided by ProMoT. Then, they are connected to each other with wires were the signal carrier molecules are imagined to flow. Each circuit component is associated with a pre-existent mathematical model, in which a user can only change parameter values. A model for the whole circuit is generated by ProMoT via the composition of the models of the circuit components. The circuit model can be exported, finally, into the SBML format and used for simulations and analysis with COPASI.
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