Team:NYMU-Taipei/Human Practice
TITLE
Besides the fungal killing switch and the functional prototype that help reduce concerns over GMO
Why web app?
Besides the fungal killing switch and the functional prototype that help reduce concerns over GMO, we wonder what else in iGEM we can do as social practice to really engage in growers’ life and help them diminish threats posed by those pests. So far in our project, the entomogenous fungus provides a biological, no-harm attempt to eradicate the pests, which is one of the most important components of our idea. The prototype makes applying these genetically-engineered fungi practical and perhaps better. Now that we have a software and a hardware, what can we do more for the growers?
The answer came to the app. A well-design, thoughtful and realistic web app. Growers, and well as government officials can simply check the “Taiwan Pest Prediction web”, where we provide 4 common pests in Taiwan with time scale from 1 day to 3 days. We offer the predicted pest scale from 0~64, 65~256, and above, totally 3 ranges, and the voting accuracy, for 61 stations around Taiwan. More important, we put all the code on github as open source, every one and every country can take advantage of our effort to establish a better and powerful prediction program.
Collaboration
This web is the outcome of National Chiao Tung University and National Yang-Ming University collaboration. NYMU member first developed this idea. In NCKU, the Asia-Pacific Conference, students from NCYU joined in and form a collaboration team. NYMU member are responsible for developing the software including raw coding for data collection, data processing, prediction voting establishment, and web development. NCTU members are in charge of streamlining the program, database connection and server establishment. We have several video chats through FB and having face-to-face chat. We exchange code often on the FB and later on github.
Collaboration
Data Collection
This web is the outcome of National Chiao Tung University and National Yang-Ming University collaboration. NYMU member first developed this idea. In NCKU, the Asia-Pacific Conference, students from NCYU joined in and form a collaboration team. NYMU member are responsible for developing the software including raw coding for data collection, data processing, prediction voting establishment, and web development. NCTU members are in charge of streamlining the program, database connection and server establishment. We have several video chats through FB and having face-to-face chat. We exchange code often on the FB and later on github.
Process and prediction
This web is the outcome of National Chiao Tung University and National Yang-Ming University collaboration. NYMU member first developed this idea. In NCKU, the Asia-Pacific Conference, students from NCYU joined in and form a collaboration team. NYMU member are responsible for developing the software including raw coding for data collection, data processing, prediction voting establishment, and web development. NCTU members are in charge of streamlining the program, database connection and server establishment. We have several video chats through FB and having face-to-face chat. We exchange code often on the FB and later on github.
upload
This web is the outcome of National Chiao Tung University and National Yang-Ming University collaboration. NYMU member first developed this idea. In NCKU, the Asia-Pacific Conference, students from NCYU joined in and form a collaboration team. NYMU member are responsible for developing the software including raw coding for data collection, data processing, prediction voting establishment, and web development. NCTU members are in charge of streamlining the program, database connection and server establishment. We have several video chats through FB and having face-to-face chat. We exchange code often on the FB and later on github.
2016/07/05 Interview Transcript
Location: National Yilan Senior High School
Staff: Kao, Chi-Hsiang Eric Kuo
Respondent: 黃國修 HUANG,KUO-HSIU
Q1: How do you encourage your students to enter the field of biology?
A: Students studying biology shouldn’t be disconnected from nature, especially those studying ecology. That’s why I often take my students out to the field in addition to giving traditional lectures. I also like to teach in an interdisciplinary way. For instance, I’ll often cooperate with the geology teacher, leading students to study organisms living in intertidal areas. This type of cooperation is dependent upon the subject matter at hand and the other teachers’ interests, of course. Through these field excursions, students often gain a deeper understanding and appreciation towards our environment.
In Yilan, we teach Applied Biosystems, a book regarding agriculture and biotechnology. During class, I encourage discussion among students and hands-on activities. For example, we have cooperated with the local farmers to let students participate in agricultural activities.
Throughout the student’s sophomore and junior years, biology class is more focused on exploration and discovery; but during their senior year, in preparation for the college entrance exam, we follow the textbook more closely. The school takes into account the needs of different students and recommends them not to take extra lessons outside of school (e.g. cram school).
Q2: How does the Information Age affect your teaching style?
A: We often assign research projects to students, but many of them only know how to search in Wikipedia. In many cases, a student already has an opinion in mind then goes online to search for evidence that confirms their opinion, often ignoring other evidence with different perspectives. For example, one of the research questions asks whether alcohol can kill viruses. During the first week, many students confidently said “yes”, but after some hints, they usually come up with a different answer. Multimedia use depends on the lesson at hand; some teachers use PowerPoint presentations to enhance the visual effect on specific chapter, while others choose to play a Youtube video to help students understand the lesson material.
Q3: iGEM is closely related to synthetic biology. What is your opinion on synthetic biology?
A: For many high school students, synthetic biology is a long way off. They only learn about the concept of synthetic biology during their senior year. I’m personally not in favor of teaching university material to high school students. However, I am very happy to see students go deep into research if they show interest in synthetic biology. The philosophy of synthetic biology: it allows one to play God and create lots of organisms using simple tools, almost like the putting legos together.
Q4: Science and Humanities
A: Biology can relate to lots of other issues: plastic waste in the ocean, agriculture and food safety… etc. I require students to participate in DFC: Design For Change Challenge. Looking around, students may feel disconnected from the society, but that is not actually the case. Through DFC, students can realize that they too have the power to change the ones around them, indirectly changing society in the process. For instance, a former student researched on the ingredients contained in each brand of instant noodles, compiling them into a table; allowing consumers to quickly and conveniently check for themselves. Another student did community service at a remote town, teaching the local children new scientific discoveries and playing little games etc. Some students found their direction in life through these activities. Once you step out of your comfort zone, the resources are there for you to use.
Summary
Mr. HUANG not only teaches students the basic subject but inspires them to love their environment and community by introducing them the field. We found KAP, knowledge, attitude, and practice, on Mr. HUANG. He delivers the knowledge in a brand new way to students, changing their attitude on biology and the environment. Last but not least, they do DFC to actually practice their thought. Through this kind of education, children would build a strong connection with nature and be inspired to protect her.
Teacher HUANG is unlike the other teacher in Taiwan because of his passion, effort, and responsibility.
2016/07/12 Interview Transcript
Time: July 12 th ,2016 3:00 pm
Interviewer: 郭宥陞 Recorder: 郭宥陞
Interviewed: 台灣農村陣線 (Taiwan Rural Front) 秘書處 蕭喬薇
Q&A:
Question1:
It seems that the government and the agricultural sector in Taiwan generally have a rather contentious relationship. What may be the cause of that?
A: The agricultural occupation generally isn’t perceived as an industry. In addition, in this small yet densely populated region, the government has the ability to purchase and acquire farmland through legal means for non-agricultural purposes. Asides from farmers, the intermediaries in the market also play a crucial role in influencing the relationship. Since the Taiwanese government does not implement adequate legal measures to guarantee the rights the agricultural industry, it creates a fragmented relationship.
Question2:
What contributions has Taiwan Rural Front made to advocate for land rights and changes to the current agricultural measures? We would like to hear your stories.
A: In 2008, the government issued a reform plan to transform the agricultural industry into one for tourism purposes, although the decision brings little to no benefits to the farmers. For instance, Taipei residents often choose to purchase cheaper land in Yilan to build elite housings or mansions. However, the tall buildings often block out the sunlight, and contaminated water are also not adequately regulated, thereby bringing detrimental consequences to people’s lives and the agricultural industry’s once persistent culture of purity and simplicity. As a result, the rural countryside essentially became a tourist site of little significance behind the urban city. Some people feel that there must be changes to these measures; we believe that those who hold the same belief should voice out their opinion together.
When we began to hear the thoughts and hopes of those who are directly involved in the agricultural industry, we decided to create the organization “Taiwan Rural Front”. Through social media and the internet, we bring these issues to light and attract supporters who are involved in different areas of occupations and industries. In addition, we have published some relevant works and communicated with international organizations; we hope that we can make a difference via politics and effective public relations.
Question3:
In the early ages, we didn’t use chemical fertilizers or pesticides in crop production. Then, there was an evident trend towards an increased use of pesticides and synthetic fertilizers. However, recently there are more and more farmers shifting their approach towards organic farming. What accounts for these trends and changes in agricultural methods?
A: In the past, farmers faced relatively less food scarcity issues, plus the technology back in the days was not advanced enough to invent chemical fertilizers and pesticides. After World War II, food shortage becomes a common issue, hence it becomes a goal for every country’s researchers to find alternatives to mass-produce crops. The United States, the European countries and Japan all have their own methods to deal with food shortage. During the Green Revolution in the 1960s, government from different countries encouraged farmers to use pesticides and synthetic fertilizer to improve agricultural output. However, with that comes many downsides. In Taiwan, such measures have not only brought harm to the quality of soil, it also increased farmers’ reliance on industrial products, and subsequently they lose their agency and become trapped in a cycle of debts.
Recently, more people have returned back to the traditional farming methods, taking soil quality and well-being of the consumers into account. Although the agricultural output is incomparable to that of the mass production, yet it raises the quality of living, and attracts young people to be willing to return back to the agricultural industry. As such, the relationship between land and mankind are gradually improving.
Question4:
What are your thoughts on genetically modified crops?
A: The agricultural industry, the consumers and the environment are the three essential areas that Taiwan Rural Front focus on. How has genetic modification impact the agricultural industry? Genetic modification has a huge implication for the Third World countries. The Monsanto company uses inexpensive and efficient plantation methods to solve food scarcity issues in these countries, and encourage the farmers to use their products. Nonetheless, despite the promising sign of good agricultural output at the start, once the soil fertility worsens, the crop yield decreases significantly. As a result, farmers have to use an even stronger fertilizer; this creates a viscous cycle. How is this different than the agricultural methods used long ago? in the early days, farmers save the left-over seeds and trade the seeds with the other farmers, thereby saving cost. Using the seeds from Monsanto, the cost of cultivating crops not only increases, the diversity and options also become limited. These seeds have no patent, so one cannot use them without approval; this limits the farmers’ agency to manage their own farmland. Hence, in our views on genetic modification, we are concerned with threats posed by monopolistic corporations on the rights and will of the farmers.
Question5:
As students, what can we do to contribute to the agricultural developments in Taiwan?
A: To solve an issue, one must first have a good understanding of that area. We hope that teenagers can visit the countryside more frequently and have a more thorough understanding of the farm life. As well, by promoting and advocating our cause, we hope to spread awareness about the importance of our connection to the land. We notice that parents in Taiwan commonly do not wish to have their kids stay in the countryside, most likely as a result of the lack of resources and opportunities when compared to the cities. Moreover, those of the younger generation who move from rural to urban area often lose connection with their home on the countryside. Hence, we will be planning activities and inviting teenagers to talk to the farmers about their work experiences and interesting lifestyle. Perhaps it will successfully convince some to return to the countryside; yet, the agricultural industry doesn’t only involve the famers, it requires the cooperation of people from different fields and studies. Not everyone will decide to return to the agricultural industry, but it is important for all of us, regardless of the field of study we pursue in, to appreciate and be grateful of our homeland.
We have a hardware, a software for Ios-i-GEM, yet …
Besides the fungal killing switch and the functional prototype that help reduce concerns over GMO, we wonder what else in iGEM we can do as social practice to really engage in growers’ life and help them diminish threats posed by those pests. So far in our project, the entomogenous fungus provides a biological, no-harm attempt to eradicate the pests, which is one of the most important components of our idea. The prototype makes applying these genetically-engineered fungi practical and perhaps better. Now that we have a software and a hardware, what can we do more for the growers?
The answer came to the app, a well-design, thoughtful and realistic app. Growers, as well as government officials can simply check the “Taiwan Pest Prediction web”, where we provide 4 common pests in Taiwan with time scale from 1 day to 3 days. We offer the predicted pest scale from 0~16, 16~64, and above 64, 4 ranges in total. We convert prediction question into classification question, by building numerous classifiers and perform voting, we can get the prediction that most classifiers agree to. More important, we put all the code on github as open source, everyone and from every country can take advantage of our efforts to establish a better and powerful prediction program.
Collaboration
This app is the outcome of our collaboration with NCTU. We first developed our idea of construct such a web app for social practice. In August, when we have done the web crawling part, we participated in Asia-Pacific iGEM conference hosted by NCKU, and met our friends from NCKU. It was incredible to meet friends with similar ideas and, most importantly, we decided to collaborate at that time. From then, we had several face-to-face talks in FB Messenger and frequent calls.
The attribution is listed as following:
NCTU
1. Provide us with expertise in FTP, web crawling, and the concept in pipeline
2. Streamline code, making it more readable and understandable.
3. Provide the idea of open source, and we did put our code on github.
NYMU
1. First come up with this idea
2. Write program for web-crawling, date processing, machine learning and FTP uploading.
3. Establish FTP host and write UI website.
Collaboration
Step 1: Update climatological data
Connect to Agriculture weather website. Crawl and store the newest climatological data.
Step 2: Data process and making prediction
Grasp necessary information from html, and build up several SVM and RandomForest classifiers for prediction. Merge the outcome with the web frame.
Step 3: upload to FTP
Upload the html files to FTP.
----icon credit: Freepik, Wissawa Khamsriwath, Madebyoliver, Gregor Cresnar
Data source
| Part Number | Type | Description | Length(bp) |
|---|---|---|---|
| BBa_K1769000 | composite | Dimeric FYVE | 426 |
| BBa_K1769001 | composite | Dimeric FYVE+GFP | 1152 |
| BBa_K1769002 | composite | J61051+RBS+LuxR+Ter+pLUX+RBS+LuxI+Ter+pLux+RBS+Aiia+Ter+pLux+RBS+GFP+Ter | 5050 |
| BBa_K1769003 | reporter | J61051+RBS+GFP+Ter | 2154 |
| BBa_K1769004 | coding | Monomeric FYVE | 204 |
| BBa_K1769005 | coding | mtrB | 2094 |
| BBa_K1769006 | coding | Dimeric FYVE (without stop codon) | 423 |
| BBa_K1769007 | reporter | Monomeric FYVE+GFP fusion protein | 1067 |
| BBa_K1769008 | coding | MtrB+LVA tag | 2127 |
| BBa_K1769009 | composite | T7+RBS+defensin | 196 |
| BBa_K1769010 | composite | J61051+RBS+LuxR+Ter+pLUX+RBS+LuxI+Ter+pLux+RBS+Aiia+Ter+pLux+RBS+Ter | 4301 |
Hypothesis
1. According to reports from Taiwan Agricultural Research Institute, the weather condition can directly or indirectly influence the maturation of pest. Take oriental fruit fly for example, days of raining can lead to the maturation. Low temperature, in contrast, resulting in small population size of oriental fruit fly. In building the model, we presumed that there is a relationship between weather and pest group size, such that there is a transformational matrix that transforms the weather information approximately to pest group size.
2. Feature selection: We choose average day temperature, highest day temperature, lowest day temperature, rainfall as feature.
Model selection
We are using two famous and frequently used model in building prediction model, SVM and RandomForest.
(A Gentle Introduction to Support Vector Machines in Biomedicine, Alexander Statnikov*, Douglas Hardin# , Isabelle Guyon†, Constantin F. Aliferis)
(ICCV TUTORIAL, BOOSTING and Random Forest for Visual Recognition, Tae-Kyun Kim , Jamie Shotton , Björn Stenger )
SVM is a machine learning method, by transforming data from dataspace into a hyper space, we can find a hyperplane that can separate these data with different labels. The SVM is trying to minimize the transformation matrix in some way. RandomForest is an ensembled decision forest. With building several decision trees, we are able to find out the best prediction that most decision tree agree.
In processing and testing data, member of NYMU discover that SVM made incredibly great prediction(~100%) when the datasets are big enough, while random forest got average score of 80%. However, in some cases, when randomforest model reached 60~70% of accuracy score, SVM got 50% or worse. We thus decide to build a simple ensembled prediction model, with different parameters and training datasets. And choose the pest population size that most classifiers agree.
Hypothesis
1. According to reports from Taiwan Agricultural Research Institute, the weather condition can directly or indirectly influence the maturation of pest. Take oriental fruit fly for example, days of raining can lead to the maturation. Low temperature, in contrast, resulting in small population size of oriental fruit fly. In building the model, we presumed that there is a relationship between weather and pest group size, such that there is a transformational matrix that transforms the weather information approximately to pest group size.
2. Feature selection: We choose average day temperature, highest day temperature, lowest day temperature, rainfall as feature.
The following links can be helpful in realizing how SVM and RandomForest work:
SVM
A clear intro to SVM
SVM without tears: page 19 is incredibly and clear
RandomForest
To realize RandomForest, it is recommended to understand
Here is an intro to RandomForest In Wikipedia
a pdf deliberates on RandomForest
Human Practice in Beijing
What we have achieved:
a. After conducting an interview at both the Beijing No.14 High School and National Yilan Senior High School, we analyzed the similarities and differences in their academic programs in the field of sciences.
b. In a visit to the Miyun District in Beijing, we surveyed to find out local farmers’ average expense on pest-control, as well as farmers’ awareness on the environmental implications of their methods of pest control.
c. Visits to Beijing No.57 High School and Beijing Institute of Technology allowed us to exchange and discuss the progress of our projects with the students.
d. We visited Professor Du Guei-Sen at the Capital Normal University to discuss the feasibility of our project, insight with regards to our fungi, as well as the topic of biosafety.
