Imperial/Dry Lab/Software
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.
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.
Simulations
ID_EnergyODE.m
This function presents the vector of energy-dependent ODEs governing Infector Detector(ID). The set of representative parameters is passed globally.
ID_Sim_Transfer.m
This script allows for user-defined simulation of the transfer functions of both system constructs, which can either be visualized independently, or simultaneously, for comparison. The routine defines a set of parameter values and simulates the dynamic behaviour of the system by invoking the ODE set, ID_EnergyODE, for use by MATLAB's ode15s solver. The transfer functions, [GFP] vs [AHL], are computed and plotted on a semi-logarithmic scale. The user maintains control over the range of [AHL] over which the computation should occur.
ID_Sim_InputVar.m
A user-defined routine, performing simulations of the dynamic behaviour of the system, where the user maintains control over which inputs are to be investigated. e.g. varying initial [LuxR] of construct 2, to observe its resultant behaviour, in terms of GFP expression and/or Energy depletion.
Data Analysis
- Chassis Characterisation with the Classic Promoter Model
The routine allows you to load the results of several experiments at the same time. These data are then analysed by shape matching . Once the best fit is identified, the results are returned and the corresponding graphs are plotted.
Download ID Routines
The above routines may be downloaded together in zipped form. Please access the following link.
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.
Simulations
CBD_EnergyODE.m
This function presents the vector of energy-dependent ODEs governing Cell-by-Date(CBD). 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 the function,CBD_EnergyODE. Plots of resultant GFP expression and depletion of energy(E) are generated.
Data Analysis
Download CBD Routines
The above routines may be downloaded together in zipped form. Please access the following link.
