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
• AND-tRNA → simulation results / sensitivity analysis
• IPTG Sensing →simulation results
• PoPS Duplexer →simulation results
• Compound module: IPTG Sensing → PoPS Duplexer →simulation results

All scripts: [http://csb.inf.ethz.ch/igem-2006/matlab_modules.zip 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).

• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and1.zip matlab_sim_and1.zip] (<0.1M) →simulation results → abandoned
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and2.zip matlab_sim_and2.zip] (<0.1M) →simulation results → the pursued version A
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and3.zip matlab_sim_and3.zip] (<0.1M) →simulation results → the pursued version B
• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and4.zip 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.

• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_xor1.zip matlab_sim_xor1.zip] (<0.1M) →simulation results → the only pursued version
• [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor2.zip matlab_sim_xor2.zip] (<0.1M) →simulation results → abandoned
• [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor3.zip matlab_sim_xor3.zip] (<0.1M) →simulation results → abandoned

Sensoring

• [http://csb.inf.ethz.ch/igem-2006/matlab_sim_iptg.zip matlab_sim_iptg.zip] (<0.2M) →simulation results