Team:USTC Software/home

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==Welcome to the Team USTC_Software wiki for iGEM 2010 !==
==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.
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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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横着放一张照片。
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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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==='''iGaME: Synthetic Biology for Gamers'''===
==='''iGaME: Synthetic Biology for Gamers'''===
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[[Image:USTC_Software_igame.jpg|250px|right]]
 
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To promote public awareness of synthetic biology and introduce its basic ideas to the laymen, our team 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 attempt to 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 Modeling Database Language, which enables descriptions of complicated biological processes. Furthermore, previous iGEM project models will be featured to demonstrate the availability of our idea.
 
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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]]
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==='''Recommendations For Our Site'''===
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==='''Recommondations For Our Site'''===
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*'''New Database Language'''<BR>
*'''New Database Language'''<BR>
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A new language called '''MoDeL'''(System Biology Part 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.<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:PKU_Beijing/Human/Survey|'''[Learn More]''']].
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[[Team:USTC_Software/MoDeL|'''[Learn More]''']]
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<br>
*'''Demos of Automatic Modeling'''<BR>
*'''Demos of Automatic Modeling'''<BR>
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Our original AND Gate is from Voigt Lab. We make it into standard parts and use a combination of promoter, which leads to several AND Gates that has different properties. The most wonderful thing in the summer holiday that we achieved a greatly improved AND Gate.<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:PKU_Beijing/Parts_Characterization/BBa_K228258|'''[Learn More]''']].
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[[Team:USTC_Software/downloads|'''[Learn More]''']]
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<br>
*'''Human Practice'''<BR>
*'''Human Practice'''<BR>
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The most difficult work in the construction of a multi-Module system is assembly. After we have accomplished all the individual modules from Jul to Sept, we made a breakthrough during the National Day (we did experiments during the holiday). That is the first stage assembly is accomplished.<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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[[Team:PKU_Beijing/Project/Assemble|'''[Learn More]''']].
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[[Team:USTC_Software/human_practice|'''[Learn More]''']]
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==Sponsors==
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<a href="http://www.ustcif.org/default.php/">
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<a href="http://www.teach.ustc.edu.cn/">
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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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<img src="https://static.igem.org/mediawiki/2009/4/42/Sponsor2.png" style="width:200px; height: 50px">
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<!--> <font size = "2"; style="font-family:Georgia">'''School of Life Sicences, USTC'''</font><-->
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<a href="http://ustcaf.org/">
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<!--> <font size = "2"; style="font-family:Georgia">'''USTCAF'''</font><-->
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<a href="http://math.ustc.edu.cn/Ch/">
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<img src="https://static.igem.org/mediawiki/2010/8/87/USTC_Software_ma_logo.jpg" style="width:150px; height: 50px">
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<a href="http://cs.ustc.edu.cn/">
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<!--> <font size = "2"; style="font-family:Georgia align:left">'''School of Computer Sicence, USTC'''</font><-->
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<a href="http://gradschool.ustc.edu.cn/">
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<!--> <font size = "2"; style="font-family:Georgia">'''Graduate School, USTC'''</font><-->
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<a href="http://physics.ustc.edu.cn/">
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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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<!--> <font size = "2"; style="font-family:Georgia">'''School of Physics, USTC'''</font><-->
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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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