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Team:NCTU Formosa/modeling
From 2014.igem.org
Contents |
Modeling Introduction
In the modeling part, we make two models in our project to optimize our result and enhance the convenience of the device usage. In the first model, we demonstrate a model for our biobricks which is composed of Pcons, RBS, 9 PBAN, BFP, and terminator. And in the second model, we model our device with two kinds of natural factor which are temperature and the wavelength of light. Before introducing the model, we would like to make a brief introduction for our modeling method and the modeling tool we used.
The following contents we can devided into three parts:
(1)Modeling Software: First, we introduce the tool we use. ANFIS, a tool involved in MATLAB
(2)Modeling for PBAN: Second, we use ANFIS to build a PBAN model that can fit to a theoretical and real condition at the same time
(3)Modeling for Device: At last, a device model is also established. This model can let the user know the insect capture performance in any condition.
Modeling for PBAN
In this project, 9 kinds of PBAN are used to attract 9 different kinds of insects into our device. Even though these 9 PBAN(PBAN(BM), PBAN(MB), PBAN(AI), PBAN(LD), PBAN(HAH), PBAN(AS), PBAN(SI), PBAN(AA), PBAN(SL)) facilitates the production of pheromone through different pathways, 9 PBAN are translated with the same promoter and RBS in E. Coli, and therefore, the production rate for each PBAN should be the same. With that said, we use a “Pcons + RBS + BFP + Term” as the theoretical condition to simulate PBAN biobrick (Pcons + RBS + PBAN + BFP + Term) expression. By detecting the expression value from the theoretical biobrick, and modified by our PBAN biobrick expression, this modified model can not only fit a theoretical condition that prevents our model from operating bias, but also fit to a real condition. To make a brief introduction of our PBAN model, the following contents are divided into two parts: (1) Theoretical biobrick (2) 9 PBAN biobrick and modeling result.
Theoretical biobrick
9 different kinds of PBAN biobrick and modeling result
Pcons + RBS + PBAN + PBAN(BM) + BFP + Term
Modeling for Device
We not only built a model for biobricks but also a customized model due to concern for users, such as farmers or engineers. However, finding a good condition for our device becomes a problem for the users due to the lack of information for the parameters we set.
To make the users easily use our operation debug device, we make a device model to let the user input the condition value and they can know the performance of the device under such condition. Here, we make a briefly introduction for our debug device and the parameters we used for modeling. In this device modeling, the wavelength of light and the surrounding temperature are used for modeling. The following contents we devided into three parts:
(1) Wave Length (2) Temperature (3) Experiment Data
Wave Length
According to the reference, insects have chemotactic properties of light, and different degrees of light will have different attractive effect, so we use the different kinds of wave lengths for the same moths. To evaluate a best wave length for the insect. Variable Light－we divide the wave of visible light into five parts－475, 510, 570 and 650 nm, hoping to modeling all of visible light condition.
Temperature
Temperature is key factor that can significantly influence the performance of a device, and it is hard to change the surrounding temperature if you put the device to the field. Thus, we take temperature into consider, and we select five temperature between the highest and lowest average temperature last year (17.03。C / 30.1。C) of the major city in Taiwan, and want to model all of temperature condition.
Experiment Data
In the experiment part, we use CCW no.1 that we introduce in "Result/Insect Aspects" to perform the attracting ability by changing the light wavelength and surrounding temperature. The insect will choose a bottle based on the favor light color in a consist temperature. Repeat the experiment by changing the temperature from 17 to 29 Celsius degree. And the following table is the result of the insect capture ability by using CCW no.1.
After experiment, the modeling using these data can simulate the capture ability in all condition.
The device model are aim to let the user easily input the condition value and know the device performance by this simulating surface. And the user can also find the local optima between the light wavelength 475nm to 650nm and the temperature between 17 to 29 Celsius degree.
Reference
- Central Weather Bureau of Taiwan http://stat.motc.gov.tw/mocdb/stmain.jsp?sys=100&funid=b8101
Modeling Software
MATLAB
MATLAB (matrix laboratory) is a numerical computing environment and fourth-generation programming language. It is developed by MathWorks, a company in United States. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, and Fortran. Although MATLAB is intended primarily for numerical computing, an optional toolbox uses the MuPAD symbolic engine, allowing access to symbolic computing capabilities. An additional package, Simulink, adds graphical multi-domain simulation and Model-Based Design for dynamic and embedded systems.
ANFIS
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.
