ETHZ/Simulation

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(Difference between revisions)
(Simulation of Test Cases)
(Simulation of Test Cases)
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== Simulation of Test Cases ==
== Simulation of Test Cases ==
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To test for all conditions we run timing simulations for all 4 different branches in the flow diagram of our protocol.  
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To test for all conditions we run timing simulations for all 4 different branches in the flow diagram of our protocol and plotted the concentrations of the inducers, memory proteins and reporter proteins.
* During the first 1000 minutes of the simulation we did not add any inducers to the system to check for the baseline production of proteins.
* During the first 1000 minutes of the simulation we did not add any inducers to the system to check for the baseline production of proteins.
* Between 1000 and 2000 minutes we added the inducer that should be learned and let the system reach steady state.
* Between 1000 and 2000 minutes we added the inducer that should be learned and let the system reach steady state.
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* After the 2000<high>th</high> minute and 3000 minutes  
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* After the 2000<sup>th</sup> minute we added the inducer AHL for memory formation and run the simulation for additional 1000 minutes to reach again steady state.
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* Between 3000 and 4000 minutes we finally tested if the system reacts in the desired way by showing the right color.
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==== Test 1 ====
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==== Test 1: Learn and recognize IPTG ====
[[Image:ETHZTest1.png|center|thumb|Fig 1: Test 1: learn and recognize IPTG |720px]]
[[Image:ETHZTest1.png|center|thumb|Fig 1: Test 1: learn and recognize IPTG |720px]]
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==== Test 2 ====
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==== Test 2: Learn IPTG and get gested for aTc ====
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[[Image:ETHZTest2.png|center|thumb|Fig 2: Test 1: learn IPTG and get tested for aTc |720px]]
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[[Image:ETHZTest2.png|center|thumb|Fig 2: Test 2: learn IPTG and get tested for aTc |720px]]
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==== Test 3 ====
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==== Test 3: Learn and recognize aTc ====
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[[Image:ETHZTest3.png|center|thumb|Fig 3: Test 1: learn and recognize aTc |720px]]
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[[Image:ETHZTest3.png|center|thumb|Fig 3: Test 3: learn and recognize aTc |720px]]
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==== Test 4 ====
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==== Test 4: Learn aTc and get tested for IPTG ====
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[[Image:ETHZTest4.png|center|thumb|Fig 4: Test 1: learn aTc and get tested for IPTG |720px]]
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[[Image:ETHZTest4.png|center|thumb|Fig 4: Test 4: learn aTc and get tested for IPTG |720px]]
== Sensitivity Analysis ==
== Sensitivity Analysis ==

Revision as of 11:37, 15 October 2007

Contents

Protocol

Fig. 1: Flow diagram

Simulation of Test Cases

To test for all conditions we run timing simulations for all 4 different branches in the flow diagram of our protocol and plotted the concentrations of the inducers, memory proteins and reporter proteins.

  • During the first 1000 minutes of the simulation we did not add any inducers to the system to check for the baseline production of proteins.
  • Between 1000 and 2000 minutes we added the inducer that should be learned and let the system reach steady state.
  • After the 2000th minute we added the inducer AHL for memory formation and run the simulation for additional 1000 minutes to reach again steady state.
  • Between 3000 and 4000 minutes we finally tested if the system reacts in the desired way by showing the right color.

Test 1: Learn and recognize IPTG

Fig 1: Test 1: learn and recognize IPTG

Test 2: Learn IPTG and get gested for aTc

Fig 2: Test 2: learn IPTG and get tested for aTc

Test 3: Learn and recognize aTc

Fig 3: Test 3: learn and recognize aTc

Test 4: Learn aTc and get tested for IPTG

Fig 4: Test 4: learn aTc and get tested for IPTG

Sensitivity Analysis

For a system like our is is not enough to find a set of parameters for which it is working. To provide a stable performance also in the presence of noise and parameter missmatch we were interested in analysing the sensitivity of the system.

The results are plotted in Figure 5.

Fig. 5: Sensitivity analysis