Team:XMU-China/Content4

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What is synthetic biology on earth? Most people will present a confused expression when hearing this subject. Before the lecture we made a survey, finding that in fact nearly 100% of the respondents didn’t understand the meaning of the term. Fortunately through our lecture, we got our audience across to the basic principle and a general situation of synthetic biology. The lecture was held in the chemistry lecture hall, Xiamen University on July 7th. There was no empty seat in the hall. Lots of students even stood the whole lecture. The lecture has five parts, including introduction of synthetic biology, iGEM, iGEM-XMU , iGEM-HS program and our following activity——garden party.<br/>
 
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Synthetic biology is a newly-developing subject. Our iGEM-XMU team used simple words with vivid pictures to illustrate the generation and development of this discipline. What’s more, we introduced some basic knowledge of genetic safety in an interesting video. These unfamiliar words such as bacteria and gene got across well in our lecture. <br/>
 
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In addition, we introduced iGEM, including the start, development and goal of this competition to have the high school students know what we are crazy about. After that we presented some excellent teams, from biosynthesis to software, to stimulate them to enjoy this game. Every program included has its specialty, from bacteria with fluorescence to E.coli that can detect spoiled meat, as well as a kind of automatic LegoTM robot. They were all impressed by the charm synthetic biology shows. iGEM-XMU, a good team with two gold medals in Asia division in the last two years was invited to MIT to compete with the top undergraduates all over the world and achieved a great success. We then introduced our development and our 2013 team, including our project.<br/>
 
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  We got to know that China had four teams entering the 2012 iGEM-HS competition and made a brilliant achievement. In order to get a better popularization of iGEM-HS in China, we show these high school students some interesting iGEM-HS programs to draw their attention to this competition. Our efforts paid off. Inspired by what they saw, these high school students hoped to popularize synthetic biology and iGEM to make contributions to the development of this interesting project. They believed they can organize a next Chinese iGEM-HS team as well with our help in lab and other aspects. They wished that we can keep a long interaction and cooperation.<br/>
 
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During the lecture there was a really positive interaction between these high school students and our team. Every student participates in the competition, answering questions related to biological safety and some lucky dogs won our special rewards. In order to have a better and deeper communication, our team members and high school students exchanged E-mail address and telephone number with each other.
 
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做微流体实验中,我们多次连续8小时左右通过荧光显微镜拍到了大量的照片.但是更大的工作量是处理照片得到我们想要的数据.之前我们使用的软件只能进行手动处理,并且最大的瓶颈在于不能批量处理照片.因此我们使用MATLAB编码了自己的新程序,批量处理实验照片得到数据,大大节约了我们的时间.</p>
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We held a garden party and related exhibition with the theme of synthetic biology and iGEM in the Gui Huashan Building, Xiamen University on July 17th afternoon. The whole activity included three parts——synthetic biology exhibition, game and the Killers of Three Kingdoms cards presentation. To help the participants learn synthetic biology is a challenging but attractive process. These high school students could enjoy the interests in science and technology, know the knowledge about biology and think over ethics in life science through our activities. <br/>
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We ushered the students to our conference theatre, having them participate in any activities they are interested in and giving them attracting presents. We also gave every participant our badge.<br/>
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The synthetic biology exhibition was composed by some display boards including knowledge of synthetic biology, program display on iGEM, biological safety and genetic engineering. Some information and pictures were from iGEM wiki. We made this exhibition following the lecture to improve our HP effects. <br/>
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Garden party game was the most important parts in order to enhance the interest. It was composed with three parts—Riddles written on lanterns，Foldit computer games and finding the differences between DNA molecules. In the first game, we find some riddles related to gene and biology and wrote them on lanterns. If the participant could find the answer then he would win a prize. Foldit, a computer game liked by the high school students since they can learn from entertainment, folds proteins and tests their stabilities with four people competing in it.  Finding the differences between DNA molecules, is to find two or three differences between two analogous DNA pictures. From this game participants could be aware of DNA structure more deeply and practice their precision. We accumulated every students’ points and the final top 10 won the prize.<br/>
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Our special prize is the cards——Killers of Three Kingdoms, very popular in China. There are abundant role-relationship and mutual promotion and restraint between every cards, just like Bong in America！！！Our team designed this kind of cards particularly for the HP, combining synthetic biology with the cards. Some high school students even play the cards with our plain guidance, making us think it’s an interesting and enjoyable game. Participants hoped that we could  send to them more cards and give them designing pictures. From this game we had a better interaction.<br/>
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Finally our team organized a special link for these high school students. We show them our culture strains so that they can get an access to germiculture.  <br/>
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After the garden party as well as the exhibition, these senior high school students signed on our whiteboard and had a group photo taken with us at our request. We made informal interviews with some of them and get a satisfactory feedback. They wished we could hold the activities next year and they would try their best to popularize synthetic biology and iGEM. A student, from Shaowu No.1 Middle School Of Fujian, expressed his hope that we could come to their hometown to help people in the countryside to get a correct understanding of genetic engineering. As I know, some people even regard transgenosis as poisons. This is also our hope that more and more people can learn something about transgenic products via this competition and have a better understanding of genetic engineering. After all, we, as iGEMers, not only need to do experiments in laboratory, but also help synthetic biology understood by the public. <br/>
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<h4>Surveys on The Popularization of Synthetic Biology and iGEM
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in high school students of Fujian Province<br/>
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Our team conducted a synthetic biology survey before our lecture entitled "Contemporary introduction to synthetic biology". hWe wanted to compare how much they knew about synthetic biology and iGEM before the lecture with what their knowledge about them after our presentation in order to assess our work. We’ve prepared 300 questionnaires and handed out 227 of them. Among these drew-back questionnaires, 180 of them are valid. We put 12 questions on the questionnaire as below.<br/>
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ImageMe的主要算法是先将读入的照片进行灰度化处理,之后进行边缘处理从而得到照片中图形的边缘,接着寻找每个格子的边界,最后对每个格子的灰度进行积分.
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1. Have you ever heard about synthetic biology before our lecture? <br/>
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2. If you have, in which way it was accessible to you?<br/>
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3. Which parts do you think are the most intriguing about synthetic biology after our lecture?<br/>
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4. Have you ever heard about iGEM before our lecture? <br/>
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5. If you have, in which way it was accessible to you? <br/>
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6. Are you willing to participate in iGEM after our lecture? <br/>
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7. If your answer is no, why? <br/>
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8. What’s your reason for participation, why? <br/>
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9. If you participate in iGEM in which aspects do to want to get supports? <br/>
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10. How much time can you spend on iGEM?<br/>
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11. If you participate, you and your family are willing to afford in which aspects? Some survey results are shown as below:<br/>
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Two major findings have been obtained from this analysis.<br/>
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First of all, we drew a conclusion that almost everyone learned a lot from our lecture although they tended to be unfamiliar about the details of synthetic biology. Comparing the number of people who know about iGEM and the number of people who are willing to participate in iGEM we think the number of people who are interested in iGEM increases nearly 60%. Just look at the reasons why they don’t want to participate, most people chose no time and no supports. Only few people claimed that they were not interested in it and far less people said they didn’t like biology at all. Considering that our high school students are under so much pressure from National College Entrance Examination and some high school are too poor to afford technologies and apparatus, our results indicated a really good reality that almost everyone was willing to accept this new science and technology. <br/>
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Second, as for how to popularize iGEM and synthetic biology, we summarize two points. <br/>
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On the one hand, popularizing iGEM and synthetic biology via internet can reach a good effect because nearly half of these high school students said they heard iGEM and synthetic biology from the internet. We all think wiki is really a good platform to popularize synthetic biology and communicate with other iGEMers. What’s more, publishing more books relating to synthetic biology and iGEM is also a good conduit to let synthetic biology and iGEM known by other people, especially the young. <br/>
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  On the other hand, teacher and parents seem to have difficulties in accepting a new technology in China or in the whole world so that students can’t learn some interesting and impressive new science and technologies from adults. It’s very common in China but we, as a new generation, should try our best to realize the rapid changing of our society.<br/>  
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Future plans<br/>
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Finally we drew some conclusion to improve our survey next time. In order to obtain results that are more valid we should launch a more widely circulated survey. In addition, perhaps more copies can be distributed at random to the general public. On the other hand, it’s really important to make an effective and smart questionnaire to get a more cogent result. Maybe we can make two kinds of questionnaire to hand out before and after the lecture to compare to get a better conclusion. <br/>
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We collaborated with Purdue iGEM team to create a definitive characterization standard for the parts registry. All the teams participated required to fill out a survey which about the important items in the registry page. Purdue iGEM team worked out a standard protocol which contains all of the details. The other teams need to complete it better or put forward some questions and problems. To make this work easy, we had a video meeting with the Purdue iGEM team and USP Brazil team though the GOOGLE HANGOUTS. It really helped us to exchange the opinions just like face to face.<br/>
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As we know, the members of this collaboration are currently over 50 teams so that it is the biggest collaboration in the iGEM history. We feel awesome about what we did!<br/>
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We provided parts BBa_C0061 and BBa_I0462 to the Toulouse iGEM team due to the high transform difficulty they described using this year’s distribution. Toulouse could directly use them for their cloning and we got some useful feedback about our parts.<br/> 
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We had a short meeting with 4 members of NJU iGEM team that visited us. During it, we introduced this year’s project to each other and exchanged the opinions. We welcome all other visitors as well.<br/>
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In the summer vacation, we drew a doodle about 2013 iGEM in Furong tunnel in the camp with the member of software team of our university. This tunnel is not only a main stem but also a famous scenic spots, so that more than 30,000 people per day will pass by and look our doodle. In addition, the doodle is a quite novel approach to introduce synthetic biology and we believe that no team did it before.<br/>
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We also held a garden party with software team where introduced iGEM and synthetic biology to 200 students of senior high school from the whole Fujian Province. Go to page…to see more<br/>
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In the wet lab, we helped them to structure their plasmids, such as teaching how to ligation and digestion.<br/>
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We’ve also had a really good communication with the iGEM team of Peking University. From August 11th to August 19th ,one of our team members went to Peking University to get a deep cooperation with them. Firstly we introduced our own project in this year and exchanged the opinions .They gave us some good suggestions in experiments and models. What’s more, they gave us one BioBrick of sfGFP (BBa_...), which gave a great help to our structure. This sfGFP allowed our circuit to generated a brighter fluorescence and made easier to obverse in the microfluidics.<br/>
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Revision as of 00:57, 23 September 2013

LinkUp - Multipurpose HTML Template

Abstract

Modeling in Matlab

We used Matlab to help us solve the four DDEs and draw the graphs. In addition, we developed a GUI user interface after finishing the main DDE code. The user interface makes people easier to modify and adjust the parameters without recoding the .m files and any Matlab language knowledge. We called this software “Gene oscillate simulator”.

Gene Os

“Gene oscillate simulator” has two main modes of simulations. The basic simulation is designed for the oscillate circuit with LuxI, aiiA and LuxR, while the advanced simulation adds the effect of ndh gene. In each of the modes, users can make a series of graphs though designing the different parameters. The numbers of graphs mainly depend on the different parameters and the modes.

The meaning of each parameter can be displayed when click each parameter or right click each input box. For the people first use this software, we designed the “one example” function which can set the parameters suitably in a single time.
To get an idea about the different conditions in which oscillations could occur, we created a function which allows users to enter the range in which the variables should be varied and compare their results in the results. Due to the arithmetic speed, we finally apply this function in fluid flow speed and cell density, which are the most important parameters in the model. For example, people can set the cell density range from 0.1 to 0.9 with the step 0.2 by not selecting the ’Fix the cell density’ item.
A white noise system was coded to simulate the noisy environment in the medium. This function makes the model closer to the actual environment. Users can set the strength by clicking “add white noise” box and inputting the decibels.
A script calculates amplify and period of the oscillation is also added as an additional function. This allows our software detect and compare the characteristic of certain oscillation.
After setting all the parameters, users can save and output these settings into a standard 2003 excel file through the file menu. Loading is also supported which makes more convince for transmitting the parameters.
Before draw the graphs users need to choose the plot mode when range parameters exist. For example, when set the cell density the software will ask user to draw separately or put curves with different cell density together.

Then clicking the “draw” button, the software iterates over the values and plots graphs of all combinations possible for that range of values. After calculating, at most 3 kinds of graphs can be given, (1) concentration alteration of four main protein (2) fluorescence alteration under different cell density and fluid flow speed (3) amplify and period alteration under different cell density and fluid flow speed.

To protect the software and computer, we designed an error-stop system which could stop the simulation as soon as one error was detected. This system also is called when users click “cancel” button to stop the calculation. But different with error happened; this stop process takes about 1 min. The arithmetic speed of this software depends on the complexity of the parameters. Choosing both cell density range and fluid flow range to calculate can sometimes take more than 10 minutes. It is mainly because the large numbers of nested for-loops in the script and the slowly calculate speed about Matlab core.

ImageMe

Microfludic Image Analyser

做微流体实验中,我们多次连续8小时左右通过荧光显微镜拍到了大量的照片.但是更大的工作量是处理照片得到我们想要的数据.之前我们使用的软件只能进行手动处理,并且最大的瓶颈在于不能批量处理照片.因此我们使用MATLAB编码了自己的新程序,批量处理实验照片得到数据,大大节约了我们的时间.

原理

ImageMe的主要算法是先将读入的照片进行灰度化处理,之后进行边缘处理从而得到照片中图形的边缘,接着寻找每个格子的边界,最后对每个格子的灰度进行积分.

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