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Revision as of 13:23, 18 October 2019
HUMAN PRACTICE
XIANG MING HIGH SCHOOL
In the early stage of the team, we represented for 2019 Tongji_Software team to give an introduction of Alpha Ant, the project of 2018 Tongji_Software, to the high school students of Xiang Ming High School.
We aimed at making those who are going to enter university have a general idea of iGEM and synthetic biology by making project presentations. Meanwhile, we encouraged them to take part in the iGEM competition, because they can learn many interesting
and useful things by engaging themselves to the whole process of iGEM. Through this presentation, we found that those high school students showed great interests in iGEM and synthetic biology, and they also had some fresh ideas about synthetic
biology and the project. For example, they asked whether there are connections between synthetic pathway of biology and organic synthesis of chemistry, and they were interested in the possibility of using machines or robots to simulate
the biology pathways in reality.
This presentation, for our team, is the first human practice activity, and the role of this human practices is a review and conclusion of Alpha Ant, so as to have a clearer understanding of the whole project process and a deeper understanding
of iGEM. Through this human practice, we realized the importance of biology simulation and the necessity of using computers to simulate bacteria to achieve the goal of reducing costs
NEW YORK UNIVERSITY SHANGHAI
After presenting the brief idea of our project, we got a useful suggestion that we should point out where do we get the scoring matrix
CHINA PHARMACEUTICAL UNIVERSITY
Through this meetup, we got some suggestions from teachers. The most impressive one is that because of the limitation of time, we may not able to make every part to be perfect, but we can lay emphasis on a certain aspect and make this aspect to be as good as possible. With this suggestion, we adjusted our plan about our software, and finally decided that enzyme is the most important part in our project.
EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY
In order to further investigate the project, with the help of our PI Fei Jian, we contacted the teacher of microbiology in East China University of Science and Technology. We introduced our project to the teacher, who was also interested in iGEM and our project content, so we had a very deep communication with the teacher. The suggestions from the teacher are as follows.
Firstly, compared with making all enzymes into one single bacterium, making the flora seems to be more practical and feasible. We can put each step of the reaction in a pathway into a single flora, instead of just putting in a bacterium to complete the whole pathway, which makes us reconsider the synthesis environment of a pathway.
Secondly, we should consider the influence of the external environment, because the expression of some enzymes is relatively dependent on the condition of the external environment. Therefore, cofactors of enzyme are added to the selection of enzymes as an influencing factor.
Thirdly, enzyme kinetics was also considered as the screening method for enzyme selection.
GENEWIZ
In order to verify whether our software is useful, we paid a visit to GENEWIZ and want to get some useful suggestions. GENEWIZ is a company that involved in many biology fields like gene synthesis, protein optimization and synthetic biology, and some of our team members are users of GENEWIZ, so we chose it as the first company to visit and we thought we may get some answers we want.
In this human practices, we first give a brief introduction about the functions that the software had already had and what we want to do, therefore, we pointed out that enzyme selection and optimization are the key points of our project,
and we would like to know how to make our results more reliable and more practical.
On enzyme selection, firstly, they suggested that we can widely read articles about protocols to realize certain pathway, and conclude their methods to select enzymes. Secondly, they told us that the selected enzyme’s physical and
chemical character must be very stable, which means it can work as widely as possible. Thirdly, we should take the whole process and the final result into consideration, because enzyme selection is not a separated job and every
best step does not necessarily lead to an overall best.
On enzyme optimization, they honestly told us that each enzyme optimization was able to be a project, so it was hard to find a general method for all enzymes, but we can consult some teachers major in biochemistry, maybe they had some
ideas about it. Although we didn’t get a specific method from GENEWIZ, they gave us some suggestions about scoring those enzymes. From gene synthesizing, their production department gave us some deduction items, the most typical of
which was some sequences in certain species like E. coli were difficult to synthesize in the productive process.
PRESENTATION IN TONGJI UNIVERSITY
The second presentation mainly introduced the status of bioinformatics in life science, the functions of bioinformatics in iGEM and how to use the knowledge of bioinformatics to construct a software about synthetic biology in iGEM. This
presentation made us have a new understanding of bioinformatics, and understand the application of bioinformatics in synthetic biology. Meanwhile, in the process of preparing, we also organized the construction of software，to prepare
for the later construction of software.
Firstly, we raised questions and divided these questions into parts, then we read related literature and discussed about the solutions, and in the process of finding solutions, we collected and cleared up useful data, built models
to solve it, and we set up visual platform to make abstract problems more concrete. The interesting combination of codes in bioinformatics attracted students to join in the study of bioinformatics. The participation of software teams
in iGEM competition also makes them see the wide application of bioinformatics and more motivated for them to learn.
At the same time, in this presentation, we raised a question to the students about how to do the sequence alignment, and some of them thought that we can do the alignment from the beginning or the end of the sequences. Although
the students didn’t take many aspects into consideration, their different opinions on the same question inspired us to continue to try different algorithms, continuously optimize.