Figure 10.

Synthetic Biology Example. Shown here is a screenshot of an oscillator constructed using positive and negative feedback. The network design is the same as the one shown in Figure 9, but the difference is in the way the network is constructed. This network is constructed by connecting parts together; the kinetics is based on the properties of the parts, thus loading parts from a database would affect the network dynamics. This particular network has been constructed in E. coli and shown to oscillate [9]. Both genes, araC and lacI, are regulated by the same promoter, p1. The promoter is regulated by the proteins, AraC and LacI, thus forming the feedback loop. The dotted connection between the promoter region and the two genes indicates that the promoter p1 is situated upstream of both genes. Therefore, it is implied that there are two copies of the promoter in the physical DNA. The dotted lines from the gene to the proteins represent multiple reactions, which is meant to capture transcription, translation and protein folding stages, all of which contribute to the delay that is required for the oscillation. The bottom left corner shows the sequence of one of the contiguous sequences of DNA, starting from the promoter region and ending with the araC gene. A video demo showing how this network is constructed is available online at http://www.tinkercell.com webcite under the "Demos" link.