ETH Simulation Scripts
From 2006.igem.org
modular scripts
Each file contains a createXXX()
script for the device it contains. The created program object contains:
 function handles for reaction rates: r
 stoichiometric matrix: N
 constants (inside of the function handles)
 state (concentration) changes (the ode dy values) can be computed by: N · r
The modules can then be "connected" using the createInOutConnector()
function. The result is again a device object, consisting of the connected basic device objects.
sim_1_1
and sim_1_2
can be used to simulate devices with 1 input/1 output and 1 input/2 outputs respectively, both basic and composite devices.
simulations
contains the first examples, simulating
 XOR → simulation results / sensitivity analysis
 ANDtRNA → simulation results / sensitivity analysis
 IPTG Sensing →simulation results
 PoPS Duplexer →simulation results
 Compound module: IPTG Sensing → PoPS Duplexer →simulation results
All scripts: matlab_modules.zip (<0.1M)
older scripts
unzip the file, each zip file contains 2 files: sim_xxx.m
and ode_xxx.m
.

ode_xxx.m
: contains the differential equations, i.e. the model 
sim_xxx.m
: sets the parameters, calls the simulator and plots the result (this is the one to run, but the other is also needed).
 matlab_sim_and1.zip (<0.1M) →simulation results → abandoned
 matlab_sim_and2.zip (<0.1M) →simulation results → the pursued version A
 matlab_sim_and3.zip (<0.1M) →simulation results → the pursued version B
 matlab_sim_and4.zip (<0.1M) →simulation results → abandoned
As a result of the meeting on August 17, we will from now on concentrate on the AND versions 2 and 3.
 matlab_sim_xor1.zip (<0.1M) →simulation results → the only pursued version
 matlab_sim_xor2.zip (<0.1M) →simulation results → abandoned
 matlab_sim_xor3.zip (<0.1M) →simulation results → abandoned
Sensoring
 matlab_sim_iptg.zip (<0.2M) →simulation results