Difference between revisions of "Team:NCTU Formosa/Collaborations"

Collaborations

Collaborations among iGEM teams are one of the essential parts in Human Practices, for we have become companions with other iGEMers because of the reciprocal interactions. This year, we have done some collaborations including experience assistance, mentoring a new team.

TaiwanPP_FTP

Overview

TaiwanPP_FTP is a software collaboration between NYMU-Taipei and NCTU_Formosa. As the teams that both care about agricultural issues, we collaborated with NYMU-Taipei iGEM team to create innovative software that can predict the tendency of pest prospering shortly. The software will able to give detailed information of farm condition and give advice for farmers to prepare earlier before the threat.

We built up a prediction model by using the most popular way called machine learning for a variety insects. Through training a computer with a great amount of data, the computer will be able to analyze the relationship between input conditions and the outcomes. Finally, it can provide an accurate prediction which is the useful information for farm owners.(go to Website)

Figure 1. The screenshot of the website.

The Aim of TaiwanPP_FTP

We hope this tool could be user-friendly. All the information could be accessed through the Internet freely. It is remarkable if users could use the existing data to recreate another great application for the world. The product was a convenient web page that will show the predicted number of pests in the following three days of each observation station in Taiwan. All the source code and data are already on GitHub.(see on GitHub1 and GitHub2)

The Process of Collaboration

This software is the cooperated product of National Chiao Tung University and National Yang-Ming University. The member of NYMU first developed this idea. The member of NYMU was responsible for developing the software including raw coding for data collection, data processing, prediction voting establishment and web development, while the member of NCTU was acting as a consultant and advisor that refined the code and debugged including stuff such as streamlining the program, database connection. During the cooperation, we had several discussions through video chats on Facebook and had discussions in person. Finally, we made it an open source software and collaborated on GiHub.

How does it work

• Objective:
        By inputing weather data of the past few days, users can get the population size of pests. The types of pest include Bactrocera dorsalis, Bactrocera cucurbatae, Spodoptera litura, and Spodoptera exgua Hiibner.
• Data sources:

Data	Pests	Weather
Type	Open Source	Query Website
Duration	Collected every ten days	Collected every day
Data Type	Number	Temperature, Rainfall
Source	Taiwan Agricultural Research Institute	CWB Observation Data Inquire System

• Hypothesis:
        According to a great amount of research paper, the weather condition influences the maturation of pests to some extents. Take oriental fruit fly as an example; rainy days lead to their maturation. In contrast, low temperature results in a small group of oriental fruit fly. As a whole, in building this model, we presumed that there exists the connection between weather and group size of the pest.
• Features:
        The features we chose to utilize included average day temperature, the highest day temperature, the lowest day temperature, rainfall, pressure, wind velocity and relative humidity.
• Model selection:
        We are using two famous and frequently used models, Supported Vector Machine (SVM) and Random Forest (RF) in building the prediction system. In processing and testing data, the member of NYMU discovered that SVM made an incredibly great prediction (~100%) when the datasets are big enough, while RF has an average score of 80%. However, in some cases, when RF model reached 60~70% of accuracy score, SVM has 50% or worse. Thus, we decided to build a simple ensemble prediction model, with different hyperparameters and classifier. Moreover, choose the pest population size that most classifiers agree.

Characterization of Biobricks

NCTU_Formosa & Mingdao Senior High School Collaboration

We helped Mingdao iGEM team to confirm their BioBrick. We cultivated the E.coli according to their protocol. This year Mingdao iGEM team constructs a biobrick that can express enzyme, alcohol oxidase (AOX), on the surface of E.coli. The long anchor of the E.coli is from the concept of 2015 NCTU_FORMOSA.

Method: We cultivated E.coli BL21 3mL containing the biobrick selecting with Chloromycetin, and the other one is the control which doesn’t have the plasmid. Then we centrifuged 1mL bacteria solution and added PBS to adjust the OD values are almost the same. Then we added TMB, a substrate of oxidase and react in the dark. The product can be analysis by OD650. Ultimately, we proved their biobrick is valid.

On the other hand, Mingdao iGEM team also characterized our Biobrick is valid to express the target protein. They run an SDS-PAGE of our Pantide and no plasmid bacteria. The result shows that our Pantide is successfully expressed.

Figure 2. Collaboration with Mingdao.

Distribution Kit

NTHU_Taiwan iGEM team

We provided NTHU_Taiwan iGEM team with BBa_B0012.
(go to the wiki of NTHU_Taiwan)

Tongji_Shanghai iGEM team

We provided Tongji_Shanghai iGEM team with BBa_K1694005.
(go to the wiki of Tongji_Shanghai)

TCU_Taiwan iGEM team

We provided TCU_Taiwan iGEM team with BBa_K592012.
(go to the wiki of TCU_Taiwan)

Mingdao iGEM team

We sent the biobricks BBa_K1694002, BBa_K1694010, BBa_K1694035, BBa_K1694044 and BBa_K1694045, which was registry by 2015 NCTU_Formosa, to help them express the outer membrane protein.
(go to the wiki of Mingdao)

NCKU_Tainan iGEM team

This year, it is the first time for NCKU_Tainan to participate in Giant Jamboree. Therefore, we provided them with the Part BBa_K861171, BBa_I712667, BBa_I712015, BBa_R0010, BBa_R0040, BBa_C0040, BBa_C0051, BBa_C0061, BBa_C0062, BBa_R0065, BBa_K592009 and BBa_R0052 to them.
(go to the wiki of NCKU_Tainan)

Figure 2. We provided biobricks to these iGEM teams.

Mentoring New Teams

We have helped Taichung First Senior High School and Chung Cheng University set up their iGEM teams next year. (see Education)

Newsletter

This year, we were honored to take part in the Newsletter team collaboration edited by XMU-China iGEM team. We have penned an article in the Newsletter describing our project. (see the link for the Newsletter)

Survey Collaboration

International Survey aims to investigate the background knowledge of synthetic biology and the experience about genetic engineering across the world. There are 11 iGEM teams from different continents in the collaboration. The idea of the survey was first proposed by iGEM Aachen 2016, and fortunately, we had had online meetups in August. So we gladly accepted the offer as a principal team in Asia. We surveyed people on the street. Finally, we collected more than 500 samples and got some great result. Here are the teams that participate in the survey.