From 2007.igem.org

Useful Tools

During this summer the Imperial iGEM team has developed several routines in MATLAB. We are happy to share them with the rest of Synthetic Biology Community and hope they will prove useful.

Analysis of the Degradation of a Protein

Constitutive synthesis of a Protein

The experimental setup involves tagging a constitutive promoter with a fluorescent protein; the resultant fluorescence is then recorded and it is up to the user now to perform some analysis. This routine loads the experimental data as an excel sheet, allows for graphic visualization of the results, and if need be, elimination of some samples which may seem suspect (outliers). The synthesis rate and degradation term of the milieu are defined/estimated by the user. The routine was developed so the user may supervise all the operations.

Infector Detector

In the design phase, two possible system constructs were proposed, as a solution to the problem of detecting AHL-producing biofilm.
Our modelling team established that the system is governed by a set of energy-dependent coupled ODEs, which hold true for both system constructs. Numerous simulations were consequently performed on the system, for a particular set of biologically plausible parameters.
The routines employed in these simulations are now presented.

1 sub section per piece of code

Description of the code + images if possible ==

Cell-by-Date

Cell-by-Date is a Temperature-Time-Integrator, which serves to expose cold-chain breaks in the propagation of highly-perishible foodstuffs, e.g. freshly ground-beef. An investigation of its behaviour was necessarily first performed by way of simulations; the following routines were employed in this process.

CBD_EnergyODE.m

This function presents the vector of energy-dependent ODEs governing Cell-by-Date. The representative parameters are passed globally.

CBD_Sim.m

Here, MATLAB's ode23 is employed in the time-solution of the vector of ODEs passed by CBD_EnergyODE. Plots of resultant GFP expression and depletion of energy(E) are generated.

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