Team:USTC Software/home

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==Welcome to the Team USTC_Software wiki for iGEM 2010 !==
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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.<br/>
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From left to right: Soimort Yao, Kun Jiang, Jue Wang, Zhen Wang, Chen Liao, Shangyu Luo, Zhengda He.
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<br/>
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Missing on the photo: Zhaoyi Li,Yubo Qi,Luojun Wang.
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[[image:Best Software Tool.PNG|730px|center]]
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==Welcome to USTC_Software 2010 !==
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==='''iGaME: Synthetic Biology for Gamers'''===
==='''iGaME: Synthetic Biology for Gamers'''===
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The USTC_Software 2010 team attempts to take synthetic biology modeling a step further by introducing new methods for automatic modeling of biological systems. Just as automation implies, users are only required to submit their assembling of parts for our program to discover and generate the biological model automatically. Being the first-ever team trying to develop a synthetic biology automatic modeling tool, we emphasize on genetic regulatory network at the first year and develop our software tool, '''iGame''', which will assist in the design of genetic function modules for biological systems in synthetic biology.
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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.
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[[Image:USTC_Software_igame.jpg|250px|center]]
[[Image:USTC_Software_igame.jpg|250px|center]]
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===Source Code===
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==='''Recommendations For Our Site'''===
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The source code of our project is available now at [http://github.com/jkdirac/igame igame] in github.
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*'''New Database Language'''<BR>
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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.
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[[Team:USTC_Software/MoDeL|'''[Learn More]''']]
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==Sponsors==
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<!--> <font size = "2"; style="font-family:Georgia align:left">'''Teaching Affair Office, USTC'''</font><-->
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<a href="http://biox.ustc.edu.cn/">
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<!--> <font size = "2"; style="font-family:Georgia">'''School of Life Sicences, USTC'''</font><-->
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<a href="http://math.ustc.edu.cn/Ch/">
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*'''Demos of Automatic Modeling'''<BR>
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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.
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[[Team:USTC_Software/downloads|'''[Learn More]''']]
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<img src="https://static.igem.org/mediawiki/2009/b/b8/Sponsor4.png" style="width: 200px; height: 50px">
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<!--> <font size = "2"; style="font-family:Georgia">'''Graduate School, USTC'''</font><-->
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*'''Human Practice'''<BR>
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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.
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<a href="http://physics.ustc.edu.cn/">
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[[Team:USTC_Software/human_practice|'''[Learn More]''']]
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<img src="https://static.igem.org/mediawiki/2010/1/16/USTC_Software_ph_logo.jpg" style="width: 200px; height: 50px">
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Latest revision as of 03:29, 21 November 2010

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]

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