Team:SYSU-Software/HP/Silver
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.
