ETH Simulation Scripts
From 2006.igem.org
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==== older scripts ==== | ==== older scripts ==== | ||
| - | [[ | + | unzip the file, each zip file contains 2 files: <code>sim_xxx.m</code> and <code>ode_xxx.m</code>. |
| + | : <code>ode_xxx.m</code> : contains the differential equations, i.e. the model | ||
| + | : <code>sim_xxx.m</code> : 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) →[[ETH_Sim_And1|simulation results]] → ''abandoned'' | ||
| + | * [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and2.zip matlab_sim_and2.zip] (<0.1M) →[[ETH_Sim_And2|simulation results]] → the pursued version '''A''' | ||
| + | * [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and3.zip matlab_sim_and3.zip] (<0.1M) →[[ETH_Sim_And3|simulation results]] → the pursued version '''B''' | ||
| + | * [http://csb.inf.ethz.ch/igem-2006/matlab_sim_and4.zip matlab_sim_and4.zip] (<0.1M) →[[ETH_Sim_And4|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) →[[ETH_Sim_Xor1|simulation results]] → the only pursued version | ||
| + | * [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor2.zip matlab_sim_xor2.zip] (<0.1M) →[[ETH_Sim_Xor2|simulation results]] → ''abandoned'' | ||
| + | * [http://www.tik.ee.ethz.ch/~brockho/igem2006/matlab_sim_xor3.zip matlab_sim_xor3.zip] (<0.1M) →[[ETH_Sim_Xor3|simulation results]] → ''abandoned'' | ||
| + | Sensoring | ||
| + | * [http://csb.inf.ethz.ch/igem-2006/matlab_sim_iptg.zip matlab_sim_iptg.zip] (<0.2M) →[[IPTG_1|simulation results]] | ||
Latest revision as of 16:34, 28 October 2006
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
