Team:UESTC

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Hi! We are 2013 iGEM Competition Software Team UESTC

(University of Electronic Science and Technology of China)

Blueprint

No matter who you are, a scientist proficient in synthetic biology or a greenhand who only cares about output, Blueprint is your best choice. Two major parts are provided: Interactive part & Automatic part. In the first part, you are free to get what you want linking any parts we provide. But you have to make sense, of course. In the second part, the only thing you need to do is to determine the inducer and the output. Then, you can sit back and wait for our software to provide you with the optimized circuit. Wow!

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Transpeeder

The satisfying amino acid or nucleic acid sequences that the user submitted will be compared to the chosen CD sequences by ClustalW, the sequence which has highest similarity with SD sequences are defined as the slow-translating sequence, on the contrary, the one which has lowest similarity with SD sequences are defined as the fast-translating sequence.

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iBricks

iBricks is an iphone game concerning synthetic biology. In this game, what you need to do is to synthesize protein to compound a cell. You are provided with several basic parts to synthesize protein. Once you accomplish combining these parts into a circuit, you will enter into transcription process, during which phage will continuously attack your circuit. To protect it, you can press on these phages to kill them. You can also utilize several tools to eliminate phages with higher efficiency. After successfully synthesizing the protein, you can get new parts that increase the possibility of successfully synthesizing proteins. With several synthesized proteins, you can accomplish the goal of synthesizing a complete cell.

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Hello

This is the voice from UESTC, Chengdu, China. We are proud to announce that we have achieved two first here: It‘s the first time that our university take part in iGEM. What’s more, we are also the first team from the southwest region of China participating in the software competition. Wow! We come from University of electronic science and technology of China, which is renowned as China's cradle for the national electronic industry. Also, our universty is situated at Chengdu, the city of over a thousand-year-old cultural history in 'the land of abundance' What's more, we are from the hometown of PANDAs!

Student Members

  • Hi, I am the leader of our team and the director of iBricks. Being as a junior student majoring in Biomedical Engineering, I have great interest in data mining in social network and programming software on mobile devices. I did all the scoring algorithm of Blueprint in our team.

    Muruo Liu

  • Hi, I am a junior student from school of life science and technology, majoring in Biomedical Engineering and minoring in English. For my great organizational capability, I am the director of Blueprint. I am in charge of the statistics of parts in the registry and database established for Blueprint.

    Xiaonan Guo

  • Hi, I am a junior student majoring in Biomedical Engineering. I am fond of photography and sports, especially basketball. I did part of parts statistics and the realization of Transpeeder by Java.

    Yingping Han

  • Hi, I am a junior student majoring in Biomedical Engineering with strong learning ability. I like running, reading and traveling around. I did part of parts statistics and kept the minutes of our discussion in our way to MIT. My life motto is nothing is impossible to a willing heart.

    Jurong Zhao

  • Hi, I am a junior student majoring in Biomedical Engineering with great interest in programming. I chose programming on IOS system as the main attack. iBricks is my first experience in video games. Programming Blueprint on iphone is relatively easy to me. My maxim is where there is a will, there is a way.

    Wenpin Xiang

  • Hi, I am a sophomore majoring in Theoretical Physics from school of physical electronics. I am regarded as a hard-working student with easy-going personality. Making great videos is what I am always pursuing. Besides this, I also participated in parts statistics work for our projects.

    Guodong Zhu

  • Hi, I am a freshman from School of Information and Software Engineering, also a fantastic guy with passion and great imagination. Wiki is rather a great challenge for me, but I really enjoy this process, learning and progressing. The realization of Blueprint is also my work. I expected to show you a grand map of parts distributed in 2013 by iGEM.

    Yang Xue

Advisors

  • Hi, I am a graduate student majoring in biochemistry and molecular biology, responsible for giving advice on some of the arts designing work in our team, including T-shirts and wiki design.

    Shangnian Wang

  • Hi, I am a doctoral student in CEFG.Current Research interests: codon usage, bioinformatic database. I did algorithm of visualization of Blueprint and Transpeeder.

    Yuannong Ye

Instructors

  • Dr Jian Huang is a professor in the University of Electronic Science and Technology of China. He holds M.D. degree with experience in medicine, basic immunology and bioinformatics from the West China University of Medical Sciences and the Kyoto University. His studies focus on the molecular aspects of antigens, antibodies and peptide aptamers. His work has resulted in the development of a few immunological databases and web programs which have become to be important tools and data resources for both computationalbiologists and experimental biologists, especially those using phage display technology.

    For more information, please visit his homepage http://immunet.cn/hlab

    Jian Huang

  • Dr Lin is an associate professor of the Center of Bioinformatics in the School of Life Science and Technology interested in proteomics bioinformatics and system biology.

    For more information, please visit http://lin.uestc.edu.cn/

    Hao Lin

  • Dr. Xianlong Wang is an associate professor of computational chemistry and biology at the Center of Bioinformatics, the University of Electronic Science and Technology of China. He is interested in modelling both small molecules and biological macromolecules and developing new algorithms.

    Xianlong Wang

Contact us

Shahe Campus:No.4, Section 2, North Jianshe Road, 610054
Qingshuihe Campus:No.2006, Xiyuan Ave, West Hi-Tech Zone, 611731
School street view Powered by SOSO Map

List of Content

Diaries in May

Friday May 3, 2013

The university tryouts which has lasted for nearly a month ended, and the name list of the selected members of the school team has been determined. Launching ceremony of the iGEM event this year was staged today and the people present are Dezhong Yao, Dean of School of Life; Qiong Zhang, vice secretary of the Communist Party Committee of School of Life; Jian Huang, supervisor of the software team; Xuelian Zheng, supervisor of the Wetware team and all members of the UESTC iGEM team. The leaders conveyed the great attention and expectations from the university.

Saturday May 4, 2013

It is the first meeting that was convened by the software team. Apart from the team members, the people who attended were the supervisors and the advisors. We discussed the schedule and main tasks at this stage and the team leader emphasized the discipline required during the preparations for iGEM. In May, we plan to do massive reading of academic papers on synthetic biology and each member is required to share the ideas that he or she has got from reading these papers, and then the team will discuss the ideas and make a decision on a general direction of our project. In June, the team is to do the intensive reading on the major direction and conceive frame of the project and assign tasks to each team member. In July and August, all members are to dedicate their time to the work distributed to him or her. In late August and September, the project will be under optimizing and improving, and the team will make preparations for the presentation to be held in Hong Kong.

Friday May 10, 2013

We shared six papers in this meeting, the paper “Synthetic biology: New engineering rules for an emerging discipline” introduced some new engineering rules on synthetic biology; the paper “Engineering microbial consortia: a new frontier in synthetic biology” discussed the relationships between commensalism, amensalism symbiosis, mutualism, and parasitism from the perspective of synthetic biology; the paper “Protein promiscuity and its implications for biotechnology” introduced the application of protein engineering in synthetic biology; the paper “Synthetic biology: Applications come of age” summarized the challenges and opportunities of synthetic biology; the paper “Synthetic biology projects in vitro” introduced in vitro synthesis of bioengineering and artificial life as well as the idea of minimal gene design method. After the discussion we had a deeper understanding of the idea of synthetic biology.

Sunday May 12, 2013

In this meeting we discussed eight reviews read by the team members during the past several days. The contents of the reviews are in the areas of gene switch which is based on the research of protein isomerism; mammalian cell structure design using the idea of engineering of small molecules; synonymous codon bias; application of catalytic efficiency of light in synthetic biology reactions and RNA functions. The software Notebook done by other team for past competition was also introduced. Considering what we have already discussed before, we decided to focus more on the projects from the past iGEM teams. Now the topic that interests us is codon optimization based on selection bias, but it calls for further discussion.

Friday May 17, 2013

In this meeting we discussed four papers and some software. “SynBioSS: the synthetic biology modeling suite” is a synthetic gene structure modeling and simulation software in which different parts could be set in a complete network, but it highly recommends a wider and more comprehensive knowledge on synthetic biology, molecular biology and computers. Another paper talked about how antibiotics kill bacteria, and what we can learn from it is the possibility to create a piece of software to simulate this process, which, of course,will provide great convenience to synthetic biology researchers. Yang Xue introduced SBOL to the team, which is an open language for synthetic biology. “Engineering of synthetic intercellular communication systems” summarized how to accomplish cell communication systems in cells in synthetic biology. The software Bioguide introduced by Jurong Zhao focused on the categories for pathway generation and database search. After the discussion, we all agreed that the project we plan to do should be fully considered with the user needs and provide convenience to synthetic biology researchers.

Sunday May 19, 2013

This discussion is mainly on software and biobricks as well as the CLOTHO platform. We talked about the ideas of the software finished by the team Wellesley_HCT_2012, UTP_Software_2012 and USTC_Software_2012 and their advantages, disadvantages and use value, which are inspiring to our own projects.

Wednesday May 22, 2013

We talked about the software MGEC finished by the team Edinburgh _2008, which was designed for biologists to establish genetic engineering circuit model more easily based on modeling and data analysis. Another piece of software we discussed is BioBrick Manager_2010 which is mainly designed to connect Biobrick parts, and then to save as XML file. We also analyzed their disadvantages that need to be improved.

Friday May 24, 2013

In this meeting, we discussed some pieces of software of the iGEM competitions before. For examples, Synthetic Biology Simulation Software: measuring the efficiency of the terminator; Digital Synthetic Gene Circuit Software (which can not perform large-scale optimization), then we thought about what we can do about it. USTC 2012 Software: Anti-circuit design was also introduced.. This time, we discussed a relatively new paper on anti-SD sequence, and the question that whether we can create a piece of software on codon optimization. So after the meeting, we should research this literature intensively to understand how to use the anti-SD sequence to achieve codon optimization and whether someone has already done similar software. Then we should study the corresponding data on RBS site, and grasp the information from compared sequences. More details will be finalized in next meeting.

Sunday May 26, 2013

Today, we continued to discuss some software. Such as Tinker Cell which is a synthetic biology CAD software, in which analysis and biological networks are visualized by third-party C or C + + as well as python modules. And CAD tools, databases, a rule of network Design and a language Kera, GenoCAD, and network concepts were also introduced by different team members. Finally, we summarized the software discussed and drew some conclusions for our projects.

Friday May 29, 2013

CLOTHO platform is a way that can be considered for making software. Also we discussed M4B (with its network structures, including a relatively new scoring rules for parts), and Synbioss. And we studied the python scripting language. This time, a new idea was proposed by Xiaonan Guo, which is to make a phone-based game in order to popularize synthetic biology and concept of biobricks. People can learn some knowledge on synthetic biology in their leisure time. The proposal interested us a lot and we need to check more information. Before we began to realize this idea, there are a lot of tasks to be done.

Wednesday May 31, 2013

For the implementation of the idea we discussed last time, we also need to do a lot of work, and in which deep research is essential. We learned a lot from the game--USTC 2010 IGAME, such as the interface design, understanding a good sense from the perspective of a player. We also discussed AMDL (automatic modeling database language), the smallest gene design software. Last but not the least, we made the plan for the refinement of the game idea proposed last Friday, and discussed the direction and so on. Projects are in progress.

Diaries in June

Sunday June 2, 2013

We continued to discuss some software we’ve collected, including Plasmid Automatic Design Software. And from its idea and approaches we can think about how to combine our game and the concept of synthetic biology. Other pieces of software we discussed are BioBricks jtools, which is a small set of utilities; Biomortar, EvoGents, focusing on how to make gene circuits stable based on genetic algorithms; and Agent Based System. Then, we determined agenda for the next meeting. In addition, the coach told us that Gil-- MIT judger -- would come to communicate with us in our college.

Tuesday June 4, 2013

Software we discussed are: Lachesis, a visualization tool based on parametric models. We talked about a literature which introduced how to choose a route from massive biobrick parts by scoring and the feasibility of the parts in the database. Biodesign is a program which automatically connects the selected parts, but it only supports IOS Systems. ABCD which was made by the USTC in 2009 can automatically generate the designed circuit. We also discussed Gil’s trip and our presentations.

Friday June 7, 2013

This main content of the meeting was the discussion on the codon optimization based on anti-SD sequence, then combined with the previous paper, we summarized a lot comments after researching. We confirmed our second project, codon optimization software, and some preliminary concepts have been conceived. Also we discussed the database to be established for the game.

Sunday June 9, 2013

Gil arrived at our college and gave us a good view of his own research and iGEM competition’s concepts as well as its requirements and rules.All iGEM team members of our university are present on the presentation. During the meeting, we asked a lot of questions and Gil answered all of them patiently.

Monday June 10, 2013

Our team held a meeting with the co-chair of the iGEM software track. We introduced our team and the progress that we have made to Gil, and he gave us some feedbacks and comments which really inspired us. Hope to see him again at MIT!

Friday June 14, 2013

After this term’s preparations, we strongly felt that it’s the right time for us to make our plan a concrete one. So we divided our projects, distributed the work and all of us are being dedicated to learning and working.

Thursday June 20, 2013

More details were settled, mainly focused on the requirements and the programming languages.

Diaries in July

Saturday July 10, 2013

Mr. Lu, who is responsible for the logistical preparations for our team, held a meeting with us. It mainly focused on the disciplinary issues for the coming intensified training during the whole summer. He also pointed out that we need to take note of the deadlines.

Tuesday July 16, 2013

Our head coach, Prof. Huang, held a meeting with some leaders of our college. And then he conveyed their expectations that we should enjoy the competition process and try to make awesome software. At the same time, he also suggested that we can collaborate with the other team of our university and have a better understanding about what is needed in experiments.

Thursday July 18, 2013

Today’s meeting is a plenary one held for the software and Wetware team of our university. Students from two teams gave some presentations on our ongoing projects and we all learned a lot from each other. Also, we focused on how we can reach some consensus on the collaboration issues.

Thursday July 25, 2013

It’s been a week since we last held a meeting and we are indeed confronting some obstacles in collecting parts information. So today it was a great chance for us to solve these problems and set up basic principles and unified standards on how to extract information on the parts registry.

Sunday July 28, 2013

We gathered and made a report on what we’ve done for the whole July. We determined the name of each project, outlined the framework of next month’s work plan and made some arrangements and work distributions.

Diaries in August

Saturday August 10, 2013

In this meeting, each member introduced the work which he/she was mainly responsible for. It contributed to gave us a better understanding of the progress of our three projects. And then, we made some comments and suggestions on the projects for our future work.

Wednesday August 21, 2013

For nearly two months’ hard work, our projects have been almost completed by now. Now we are still engaged in improving day by day. So, today, we held this meeting mainly to make some decisions for the competition in Hong Kong. On the one hand, we discussed the project's progress and improvements. On the other hand, we confirmed the namelist that who will make presentation for our team in Hongkong.

Table of Contents
Voice Notes

Medal Fufillment

This part is empty now!

Human Practice

In order to popularize the concept of synthetic biology and iGEM, as well as communicate with high school students, on July 27th we carried out some activities with students of the High School Attached to Sichuan University in cooperation with UESTC wetware team.

To make this campaign more fascinating and inspiring, we made good preparations for this human practice. Elaborate posters and videos were released in advance; thoughtful presentations were carefully prepared; and at last, a deliberate plan came to be true.

First, we gave them a lecture named Promises to my dream University. Silong Jiang, who is from wetware team made a short introduction of UESTC, and then Shangnian Wang, who is from we software team led us to the world of synthetic biology. Apart from giving us a general idea of synthetic biology, he also presented us some appealing examples from previous iGEM teams. Colorful bacteria, banana smelling E.Coli, man-made life and synthetic world aroused the young student’s great interest in synthetic biology and iGEM.

Second, together with students of the high school, we were divided into 6 groups for games which would help us have a deeper understanding of synthetic biology and iGEM. In spite of the generation gap, all of us really enjoyed this short but beautiful period.

At last, we took some photos as permanent mementos.

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