ETH Simulation 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_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
- AND-tRNA → 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)
unzip the file, each zip file contains 2 files:
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