Modeling

Synthetic biologists engineer bacteria to carry out logical operations and functions that are not found in nature. In order model genetically engineered functions, synthetic biologists use computer aided design (CAD) applications to bridge the gap between computational modeling and biological data. In order to accomplish this, we have modeled our circuit in two ways: 1. Ordinary Differential Equations 2. Tinker Cell Tinker Cell is a CAD software used by synthetic biologists to determine the rates of activity in bacteria. Tinker Cell makes it possible to design and model synthetic networks based upon reaction rates and DNA sequences. It is a visual tool that allows scientists to input custom algorithms for biological circuits they have developed.

Modeling the Etch-a-Sketch Circuit using MATLAB

MATLAB is a programming language commonly used by engineers solve technical computing problems in a wide variety of applications. MATLAB provides an interactive workspace that allows programmers to work with image processing, control design, financial modeling and computational biology. With our project, we used MATLAB to graph Ordinary Differential Equations (ODEs). mRNA Protein 1 lovTAP 7 lovTAP 2 cl434 8 lovTAP* 3 T7P 9 CL434 4 trpR 10 T7P 5 cl434 11 trpR 6 mRFP1 12 CL434 13 mRFP1   Parameters k transcription rate a translation rate u u protein degradation y mRNA degradation K dissociation constant n hill coefficent b for all of x B sub x = .01 a sub x o 0 if light off, 1 if light on c rate of light induced lovTAP to lovTAP*