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Team:NCTU Formosa/Test
From 2014.igem.org
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Contents |
MATLAB Introduction
ANFIS Introduction
Adaptive-Network-Based Fuzzy Inference System, in short ANFIS, is a power tool for constructing a set of fuzzy if-then rules to generate stipulated output and input pairs. Unlike system modeling using mathematical rules that lacks the ability to deal with ill-defined and uncertain system, ANFIS can transform human knowledge into rule base, and therefore, ANFIS can effectively tune membership functions, minimizing the output error.
Single Unit
Red Promoter
As shown in Figure 2, the red promoter is consisted of Pompc and Plac. By multiplying the experimental data of Pompc + RBS + mGFP and Plac + RBS + mGFP, we would be able to build a model for the red promoter. This model, however, wouldn't be so accurate. To solve this problem, we used this model to train the actual experimental data of the red promoter by using ANFIS. Figure 2 is the result of such a training. We obtained a curve between our model and the actual experimental data. This curve is the representation of the new model that has been trained and supported by the actually experimental data of Pred. This new model definitely contains a high degree of accuracy.
Lux Promoter
We did the following modeling based on the data obtained from Imperial 2007 iGEM team. The data notes the strength of Plux under different concentrations of AHL and different time frames.
Using ANFIS to train 76 sets of data and to test 20 sets of data, we ontained Figure 4. It shows that our training data exhibits a similar trend as the testing data, even though the computer has no based knowledge of the trend. This simply means that our modeling has successfully simulated the actually data.
Figure 5 is the resultant graph from input 1 (time) and input 2 (AHL concentration). According to this graph, we can observe the output (fluorescence) has two peaks about AHL concentration(at concentration of 4 nM and 40 nM). That means we could achieve our regulation goal with little AHL. Also, pleas note that there is more output as time passes.
37 °C RBS
We used Figure 6 biobrick to model our 37oC RBS's function at different temperatures.
First, we did a experiment that test the fluroscence at different temperature and different time. Choosing 100 sets of data to do machine learning, then we tested 20 sets of data. As Figure 7 shown, the curve can classify 4 groups fit in 27oC,32oC,37oC and 42oC.
To test the accuracy of our model, we randomly chose 20 pairs of data which is not include in our training data to do the independent test, and the test result is shown in Figure 8. The blue dot in the figure represents the real experimental data that we randomly choose from our whole dataset, and the red star represents simulated result of our model. It is obviously showed that our model can accurately predict the biobrick function in any condition by using ANFIS.
From Figure 9, the maximum output is obtained at 37 oC. Under the same time frame, the output (the normalized expression of the reporter gene) is maximized at 37 oC while minimized at 25 oC. There is a dramatic decrease in the output below 30 oC and the outputs around 37oC are much higher. This modeling demonstrates that using 37 oC RBS is a plausible approach for achieving gene expression through temperature.
Reference
- iGEM 2007 Imperial https://2007.igem.org/Imperial
E.colightuner Simulation
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