Team:NCTU Formosa/Test

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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 P_ompc and P_lac. By multiplying the experimental data of P_ompc + RBS + mGFP and P_lac + 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 P_red. This new model definitely contains a high degree of accuracy.

Figure 2. using ANFIS to modified the simulated data by experimental data to obtain a more accurate result.

Lux Promoter

We did the following modeling based on the data obtained from Imperial 2007 iGEM team. The data notes the strength of P_lux under different concentrations of AHL and different time frames.

Figure 3. the biobrick to test expression of the lux promoter

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 4. The training and testing data using ANFIS system

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.

Figure 5. Input 1 is time (min), input 2 is AHL concentration, and output is fluorescence.

37 °C RBS

We used Figure 6 biobrick to model our 37^oC RBS's function at different temperatures.

Figure 6. The biobrick used to test the temperature-regulated RBS function

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 27^oC,32^oC,37^oC and 42^oC.

Figure 7.The figure shows 100 training data composed by 4 different temperture (blue dot), and simulated result (red star).

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.

Figure 8. The blue dots represents the real experimental data. The red star represents simulated result of our model.

Figure 9. Input 1= Time (hr), Input 2= Temperature (degree Celsius), Output = Normalized expression (AU).

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 37^oC 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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 ===MATLAB Introduction===