Team:USTC Software/Main


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<span class="head">iGEM USTC_Software</span><br>
<span class="head">iGEM USTC_Software</span><br>

Revision as of 13:27, 17 July 2010

  • iGEM USTC_Software

    Welcome to the Team USTC_Software wiki for iGEM 2010 !

    We are a team of both undergraduate and graduate students along with many advisors. This is the second year that USTC has sent a software team to iGEM.
    From left to right: Soimort Yao, Kun Jiang, Jue Wang, Zhen Wang, Chen Liao, Shangyu Luo, Zhengda He.
    Missing on the photo: Zhaoyi Li,Yubo Qi,Luojun Wang.

    Best Software Tool.PNG

    iGaME: Synthetic Biology for Gamers

    To promote public awareness of synthetic biology and introduce its basic ideas to the laymen, our team is devoted to the development of an experimental video game which aims at instructing non-biologists to design and improve biological systems. Following the games-with-a-purpose paradigm in which players help solve scientific problems, we apply the human brain's puzzle-solving abilities to the complex designs of biological systems. While most of developed simulation tools are designed for experts to model the reaction networks from scratch, our game integrates a modeling environment in which users only need to submit their assembling of parts for our program to discover and generate the biological model automatically. With a mass of data for the use of modeling, we propose the Standard Biological Parts Automatic Modeling Database Language, which enables descriptions of complicated biological processes. Additionally, previous iGEM project models will be featured to demonstrate the availability of our idea.

    USTC Software igame.jpg

    Recommendations For Our Site

    • New Database Language

    A new language called MoDeL (Standard Biological Part Automatic Modeling Database Language) is proposed for automatic modeling of biological system. Due to introducing of novel concepts of species and reaction templates, which are two main components in MoDeL, interactions between species need not to be completely provided and thus making automation possible. [Learn More]

    • Demos of Automatic Modeling

    To show results of our program, some classical genetic regulatory networks are provided as demos, including toggle switch, repressilator as well as quorum-sensing oscillator. Each selected demo, representing a certain pattern of reaction network in biological process, is carefully designed to cover all our features as much as possible. [Learn More]

    • Human Practice

    We started a long term human practice, “the C project”, since this summer to explore the approaches of promotion of synthetic biology. “the C project”, as we call, consists of three parts: Curriculum, Communication and Community. All three parts are carefully designed and organized. [Learn More]

  • Idea

    One-Minute Introduction

    You are about to begin an exciting journey of the main ideas in MoDeL. For each picture, start from the green flag, follow the arrows, and finally you will reach the destination! Read on from the first step or click one of the three steps!

    Chain-Node Model -> Template Modeling -> Automatic Modeling Database Language

    Ustcs Go.jpg

    Chain-Node Model

    Ustcs WIKI widescreen 1.jpg

    Ustcs WIKI widescreen 2.jpg

    Ustcs WIKI widescreen 3.jpg

    Ustcs WIKI widescreen 4.jpg

    Ustcs WIKI widescreen 5.jpg

    Back Up

    Template Modeling

    Ustcs WIKI widescreen 6.jpg

    Ustcs WIKI widescreen 7.jpg

    Back Up

    Automatic Modeling Database Language

    Ustcs WIKI widescreen 8.jpg

    Back Up

    Ustcs Finish.jpg

    Read More on MoDeL Here! Read More on Our Project Here!

  • Project

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  • Notebook

    Monthly Notebook

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    Daily Notebook

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  • Downloads
    pLux-LuxR repression system Toggle-Switch
    USTCs luxr gfp assembly.PNG
    USTCs Toggle assembly.PNG
    USTCs Oscillator assembling.PNG
  • Resources


    On this page we provide the information of downloading the executable files and source files of our project, and the documentation to introduce the source code build steps and system prerequisites.


    Executable files can be download at SourcForge
    Project source code is available at gitHub

    Source Code OverView

    We use C++ as our programming language, cmake to manage our project, git to reversion control, yacc and lex to build our model file input assistant tool, Qt4 to build the GUI, Oracle dbxml as our Database manager system. Other wise, several 3-rd party open source software or tools are used in our iGame source code. Libsbml is used to deal with sbml file operations. Qwt and Qwtplot3D are used for simulation data visual system. At the early stage of our project SBML Ode Solver and Sundials were our main ode solver to produce the simulation data from our sbml model file, because the latest SBML Ode Solver is 1.6.0, developed in 2005, which is out of date and fail to support the newest sbml Level 2 Version 4 standard. We succeed in updating the SBML Ode Solver 1.6.0 to support SBML L2V4, but some unfixed bugs was found, so we turn to a better ode solver copasi, which moreover can flexibly display the ode solver output data and modify parameter to adjust the simulation output data curve. Obviously, those open source library and tools convenient to our design and implementation and help us to focus on our core working.

    Build instruction


    To sum up, iGame should be complied and run in computers with following tools and libraries:

    • C++ development environment. In Linux should be GNU C++ Tool Chain And in windows MingW Tool Chain.
    • Qt4 develop and run-time environment. Qt4.7 is requirement. Editor or IDE like QtCreator or Vim is also needed.
    • CMake, to configure the project and generate the Makefile. CMake 2.8 or later version is a requirement
    • dbxml, The Berkeley xml native database, is available at
    • copasi, copasi 4.6 is a requirement. the source code and executable binary file can be downloaded at, and one can follow those instruction to build it from source code. What should be noticed is that copasi also has prerequisites, including LAPACK/CLAPACK for Maths, Qwt and Qwtplot3D for plotting, expat to parser xml, raptor The latest version of this RDF parsing library, and libsbml for deal with SBML operations.
    • libsbml, Version 3.4.1 is required. Not only it is the dependence of copasi, but also the dependence of igame core code.
    And libsbml should be built with configure option "./configure --enable-layout=yes --enable-compression=no --with-expat"
    • Bison & Flex
    To compile our code, bison and flex is required. They are used to build a expression parser in igame/core/str_cacu path. To get the those software and more detailed information, please visit Bison site and Flex site.

    • git, to download our source code by command our source code can be downloaded in github, git is helpful to download.
    • git clone git://


    We use cmake to manage the build progress, cmake can generate cross-platform Makefile, we intend to make our project could be built in different operating system. Until now, only Linux operating system is tested. Windows and Mac should be supported soon. Download all source code, run cmake-gui to configure the project. Pay attention to the configure information.There should be "missing ***" messages when Cmake fail to find the dependent libraries. To fix those messages, one need to assign the path of related libraries by Cmake GUI. When Makefiles are successfully generated, execute the Make command to build.

  • Human Practice

    As a tutor game aimed at improving the understanding and facilitating IGEM and synthetic biology, iGAME itself is exactly a great way of human practice. With iGAME, people do not feel any distance to synthetic biology any more. Actually, it is time for everyone to join this trend to be as cool as Sheldon’s new biologist girlfriend. However, we do not stop here. We paid great effort to the safety issue and we have been dedicated to improving the knowledge of synthesis biology from classes and tried to share the part we contribute to the worldwide. We innovatively plot a new way of spreading the spirits of IGEM by starting our own community and we will never stop sharing and communicating.

    --Luojun Wang, author of USTC_SOFTWARE human practice

    USTC Software hp author.jpg

    Human Practice,"the C project"

    Although we do software, we also keep eyes on promotion of synthetic biology and sharing our own program. Therefore, we started a long term human practice, “the C project”, since this summer.“the C project”, as we call, consists of three parts: Curriculum, Communication and Community.


    As a IGEM team, we try to let people as many as possible to know what synthetic biology is. Therefore, advisors of our team, Haiyan Liu and Jiong Hong, have established a set of synthesis biology curriculum this summer. We have done many works related to human practice on the curriculum.

    1. Jiong Hong (in the right picture), advisor of our team, gave lectures introducing safety and ethnics issues of synthetic biology.
    2. Luojun Wang (in the head picture), members of our team, gave lectures promoting iGAME.
    3. A survey* on how students know about synthetic biology and their interests for tutor game was made.(*the survey statistics comes from a sample of 240 students. Numbers of undergraduates, masters and PhDs are 160, 60 and 20)
    USTC Software hp guy1.jpg

    Analysis of the results of the survey The first chart shows students' favorite game types for iGAME, and the second chart shows their knowledge of IGEM project.

    USTC Software hp chart.png
    USTC Software hp chart2.png

    The Circos Map
    We tried many methods to plot our survey more straightforwardly and clearly before we finally chose Circos Circos is biological software used to plot genome elements and relationship. Here, we innovatively used Circos to demonstrate our survey.(as in the right picture) Circos is somehow like pie chart yet it can present multi information as all the statistics are proportional and clear on the graph.

    In the graph, there are three circles. The inner circle stands for their knowledge of synthetic biology, and middle circle stands for their interests of iGame. Deeper the color is, the more they know of synthetic biology or the more they are interested in iGame. For example, light pink means they know little about synthetic biology and deep green means they are very interested of the coming tutor games. The outer circle, however, stands for their major;light green for biology major and light orange for other majors. As the graph shows, synthetic biology is still new to them as the majority have little idea of it, for which is what we will continue our project in the future. However, we are delighted to see that their interests of tutor game are fairly strong.

    Referring to the possible game types, adventure and strategy games are students’ favorite, while some of them prefer stimulation and action games. In our program, we tried our best to listen to their voice and develop a game which is both educational and appealing.

    USTC Software hp chart1.png


    We’d like to share what we have achieved with the world, so we did and will do a great deal to communicate with others and learn. For example, we collaborate closely with USTC wet team to learn what biology majors think of iGame and improve. Several seminars have been hold to make sure our program can really help the promotion of both synthesis biology and our tutor game. In addition, further transnational communication is not absent, like we had a deep talk with Dr. Joy Yueyue Zhang*(*BIOS Centre, London School of Economics and Politics Science) on how our program can change the development of both IGEM and make biology a better subject.

    Yet we do not stop here. We have sent emails to other teams for further communications and asked for their opions on how we can improve iGame. What is more, all our codes are shared on github[1](in the right picture). With fixes and new features putting forward every day,any one in any corner of the world can learn and keep update of our work, not just from the surface, but from codes and essense of our work. This is really a great way of communication, for we do not have to say too much to put our achieves across to those who really want to know our work, which really works. Great contributions have been given through github and we get a lot of advices and opinions as well.

    USTC Software hp london.jpg


    To better promote synthesis and the spirit of IGEM, we decided to establish a community together with IGEM USTC team. For the community, we have set regular classes and lectures for both synthesis biology and IGEM. We also open our laboratory to our community members and teach them basic skills of biology experiment(as in the right picture), like PCR. Of course, this is the main field we will update our progress on in the future.

    USTC Software hp yz.jpg

    More information of our community and other human practice of USTC IGEM team, please click2010 USTC IGEM humanpractice!

  • Team



    This year 10 students start USTC_Software igem team. Chen Liao, Zheng Wang, Kun Jiang, XiaoMo Yao, Jue Wang, Luojun Wang, Yubo Qi, Zhaoyi Li, Zhengda He, Shangyu Luo. There are only 8 of us in the picture, when the picture was taken the only female team member, Jue Wang was in Beijing for her TOEFL exam. And Shangyu Luo had been to HongKong for studying in The University of Hong Kong as exchange student. What a pity! But they will join us at igem 2010 Jamboree!

    USTC has two IGEM teams this year, One wet lab team and our software team, all students majoring in biology was attracted to the wet lab team. Our team consists of students of other departments, such as Mathematics, Physics, Computer Science and so on. Thanks to our Instructors, Hao Jiang, Zhaofeng Luo. With their professional instruction, we are guided to decide the project plan, design and implementation.

    About iGEM@USTC

    The iGEM Team of USTC are the combination of the exact tradition of USTC and the exact vitality of the young. Rigorous daily schoolwork has provided the team members with a solid foundation of basic knowledge, and an innovative spirit enables us to stand on the frontier of the modern science.

    In 2007, Jian Zhan, Bo Ding, Rui Ma, Xiaoyu Ma, Yun Zhao, Ziqing Liu and Xiaofeng Su, guided by Prof. Haiyan Liu, Prof. Jiarui Wu and Prof. Zhonghuai Hou, won the "Best Foundational Technology Prize" and a Gold Medal, with the project "Extensible Logic Circuit in Bacteria".

    In 2008, Xunyao Wu, He Shen, Genxin Liu, Jia Liu, Binjie Xu, Yanting Xue, Yu Chen, Zhen Xu, Bo Ding and Jian Zhan, guided by Prof. Haiyan Liu, won a Silver Medal, with the project "Artificial Multi-cellular Self-organization System".

    In 2009, Hao Jiang, Li Xing, Hao Wu, Zongxiao He, Danqian Liu, Chao Li, Jiayi Dou, Hanyu Lu, Hao Zhou and Bing Wu, guided by Zhaofeng Luo, Jian Zhan, Jiong Hong and Xiaoxiao Ma, won a Gold Medal, with the project "E. coli Automatic Directed Evolution Machine (E.ADEM)".

    In 2009 we also formed a software team for the first time. Wei Pan, Yuwei Cui, Jiahao Li, Yu He and Xiaomo Yao, guided by Bo Ding, also won a Gold Medal, with the Project "Automatic Biological Circuit Design (ABCD)".

    Since last year we have accumulated some experience from the project of Automatic Biological Circuit Design (ABCD), we expect to develop a synthetic biology game this time. The game aims at teaching non-biologists how to design biological systems so that players can compete to improve their designs in order to help biologists create the best engineered machines!

    For more information, go to USTC iGEM Forum.

    About USTC

    • Message from the President

    A university is the important assurance of maintaining belief, developing science and culture. It is a significant symbol of the level of civilization achieved by a nation.

    • USTC Today

    The University of Science and Technology of China is a new type of university established by the Chinese Academy of Sciences (CAS) after the founding of People's Republic of China. The establishment of the University is aimed at fostering high-level personnel of science and technology absolutely necessary for the development of the national economy, national defense construction, and education in science and technology. The University was founded in Beijing in September of 1958. Mr. Guo Moruo is the first president of the University......

    • History of USTC

    "Pooling the entire strength of the CAS for the development of USTC and combining the institutes of the CAS with the departments at USTC" "Studying hard and excelling in both integrity and specialty"USTC was established in Beijing in September, 1958 under the presidential leadership of Guo Moruo. The establishment was hailed as "a major event in the history of Chinese science and education"......

    To get more information, please visit in English and in Chinese.

    Team Cooperation

    Helps and acknowledges


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