Team:SYSU-Software/HP/Silver

SYSU-Software:Project

SILVER

  • During our project, we brainstormed on how we can share our project or spread ideas in synthetic biology to

  • the public. We finally participated in nine Human Practice activities, covering Scientific and Social Thinking,

  • Project Assessment and Public Engagement. These activities also helped us improve our software design on

  • safety and model.

Scientific & Social Thinking

  • Central China iGEM Consortium

  •    In order to promote the communication between iGEM teams around China and prepare for the incoming Giant

  • Jamboree, SYSU-CHINA and SYSU-Software organized Sun Yat-sen University Central China iGEM Consortium in

  • Hedanqing Lecture Hall, with 28 teams participating in. The consortium lasted for 3 days, consisting of the presentation

  • section and poster section, simulating the agenda of Giant Jamboree.

  •    We invited Yan Zhang, the vice president of our school to make a speech at the beginning of the opening ceremony.

  • We also invited Haoqian Zhang to share his iGEM experience and give his precious advice.

  •    In this consortium, we also presented our software, sharing our ideas with other teams and introducing our

  • Genexplorer.

  • Promoters and RBSs Calculation

  •    Our previous idea had found it was impossible to construct satisfied circuits by retrieving the promoter and RBS se-

  • quences from iGEM Registry and combining with CDS directly because most of the records in Registry lacking strength,

  • and we can’t determine which part we should use. Thus we developed a model from previous work to calculate the

  • strength of these parts through their sequences.

  •    Apart from the main project, we also wonder if we can use our model to calculate the strength of promoters of

  • RBSs in Registry. So we downloaded all sequence data from Registry and use our model calculating their strength.

  • We would develop this model into a small tool so that every team can use it to calculate the strength of their con-

  • structed promoters or RBSs.

Project Assessment

  • Consulting to the professors

  •    We consulted to teacher Jie Zhang in Biosafety Committee, Sun Yat-sen University about the biosafety problems and

  • regulations in our college, country and our software.

  •    Teacher Jie Zhang told us that in our college, Sun Yat-sen University, also in our country, a series of strict regulations

  • on biosafety have been issued and operated for many years.

  •    However, nearly all of these regulations are concerned about the biosafety problems in experiment, and few regulation

  • or guidance relating to software operation has not been formulated. Thus, suggested by teacher Jie Zhang, we should ensure

  • that the users of our software can avoid any biosafety problems.

  • Risk Self Assessment

  •    To eliminate the potential safety problems, we restricted the data in our software from three aspects: chemicals,

  • parts and chassis species. To reach the targets, we made a ban list originally depending on the Catalogues of Hazardous

  • Chemicals, and a warning system to remind the user if their products were harmful. We wrote a small program to re-

  • trieve the label data of promoters and RBSs in iGEM Registry, not using those with red flags. We also found a list of

  • Risk Group 3 and 4 organisms, and we abnegated them in our software. For more details see our Safety.

  •    Then we tested our software if the system worked well, and if there were other missing problems.

  •    We tested where the chassis species belonged, and found that all species are in Risk Group 1 and 2.

  •    We tested the system if it would stop the operation and warn when we input some chemicals with potential safety

  • problems.

Public Engagement

  • Garden party for introduction of synbio to the public.

  •    We, together with SYSU-CHINA, held a parade in the campus to introduce synthetic biology to the public. Our

  • audiences were all enthusiastic, including not only students from life sciences and many other majors, but teachers of

  • different backgrounds. Also, some residents and tourists showed an enormous interest in our garden party. This time,

  • we divided our parade into 2 parts. First, you could splice a fundamental Circuit Project in the “Splice a Circuit” part.

  • What you need to do is to put the genetic parts in the right orders to complete a circuit. By using the electronic bricks

  • to symbolize the different parts in synbio, we managed to introduce the four fundamental parts to the public by visual-

  • ized approaches. If a circuit is completed correctly, a light bulb which symbolizing a certain functional CDS would be

  • lightened. By turning the microcosmic process into the visible and operable way, we successfully attracted many partici-

  • pants to get involved in our game, especially some kids and teenagers who got the pure pleasure of scientific research.

  • “This is absolutely the most exciting game I’ve ever played. “It inspires me to take more time in biology study as a stu-

  • dent of senior high”, said by one student.

  •    As to the second part “Design a Circuit”, you must use the synbio knowledge you’ve already learned in the first

  • game and your imagination to design a much more complicated circuit. Made up of more than twenty biobricks and re-

  • lated to Toggle Switch, the circuit was so hard that even some of our team members were stumped. However, to our

  • surprise, some participants did finish the circuit with least effort, including a pupil. During this garden party, we’ve seen

  • more and more Chinese teenagers devoting themselves in the joy of life sciences, and our team will try our best to

  • make contributions to spreading this joy to the public without any doubt.

  • Biological Contest in Modeling.

  •    As a good instance in the collaboration between outstanding universities in Guangdong Province, the “Bio-5-Talk” is

  • a series of activities which really make difference in developing communications among college students in Guangdong.

  • The highlight during “Bio-5-Talk” is absolutely the Biological Contest in Modeling. This year the annual party attracted

  • 15 teams. By using fruits, styrofoam and other materials which are common in daily life, the participants are asked to

  • make a fabricated eukaryotic cell by hand. Our team used toothpicks to imitate the cytoskeleton together with plasti-

  • cine as the organelles, making a patterned and simple eukaryotic cell. We managed to use the cell model to illustrate

  • the basic process of transcription and translation, together with the knowledge of synbio to the other teams. At the

  • same time, we surely made some other participants interested in synthetic biology.

  • Presentation for High School Summer Camp

  •    During the summer vacation, School of Life Sciences, Sun Yat-sen University held a Summer Camp for high school

  • students in China, introducing biology related researches and activities to them. SYSU-Software also grasped this op-

  • portunity and attended to this camp, presenting an one-hour introduction about synthetic biology and iGEM competi-

  • tion to them.

  •    Considering what they have learnt in senior high school, we organized our presentation as a small lecture, from

  • DNA, RNA sequence and genetic engineering to the principles and target strata in synthetic biology. Our presentation

  • explained three main factors that led to success in synthetic biology: standardization, decoupling and abstraction. We

  • emphasized the importance of standardization, which enabled the biologists to create circuits having specific functions

  • with “Bio-bricks” like building constructions with bricks. This principle was also most familiar with these students be-

  • cause they had learnt something about genetic biology, and noticed the deficiencies in digested operation if restriction.

  • sites unspecific between gene parts. Although the other two principles, decoupling and abstraction, was hard to image

  • their roles in synthetic biology for these students, we believed their main idea would help students when they had to

  • face some complex problems in the future.

  •    We also introduced the target strata in synthetic biology, including sequence, part, device and system. From se-

  • quence to higher stratum, we thoroughly explained how a intact synthetic system form, and mentioned standardization

  • again. At last, we presented a brief introduction on iGEM competition, including its history, tracks and awards. We also

  • introduced the software track and what we have done in this track.

  •    After the presentation, many students showed their interests in synthetic biology and iGEM. One of them even said

  • that he was excited because he had played LEGO for years but had never imaged functions in creatures can be built

  • like the toy bricks, and he wanted to know more about synthetic biology and iGEM.

  •    Even in Biology Festival we used toy electronic components symbolizing the genetic circuits, some participants also

  • felt confused about synthetic systems and their function in reality because electric circuits also had slight differences

  • from genetic circuit. Thus we decided to develop a video game in which genetic circuits coming from real projects and

  • their parts are shown as those in SBOLv.

  •    Then Genexplorer came into being, in which the player can built a circuit following the order of parts shown in the

  • game, and all circuits were retrieved from eminent projects in previous competition. Target players of this game is

  • people who have not ever learned synthetic biology but have interested in it.

  •    We have promoted this to other iGEM teams, and to the public in High School Summer Camp and CCiC, where

  • the attending students and teams showed great interest in this simple and enjoyable game. With their suggestions, we

  • even developed a more difficult version later. For more details or if you want to play this game, please click here.

  • Mini lecture to 2016 freshmen

  •    We presented a mini lecture for 2016 freshmen shortly after the start of the new semester, in which we introduced

  • iGEM competition, synthetic biology, our team project as well as our Human Practice activities, especially the game

  • Genexplorer. We exemplified GFP to illustrate four basic elements in synthetic biology and how they work in real bac-

  • terium.

  •    After the lecture, with the freshmen, we also discussed the biosafety and ethics problems that brought from syn-

  • thetic biology. The freshmen raised some problems that our project should concern or may ignore.