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        <h1 id="doctitle" class="pagetitle">Our Project</h1>
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<table class="doc-toc">
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<tbody>
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<td>
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<div id="toctitle">
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<h2>Contents</h2>
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<li class="toclevel-1"><a href="#r0"><span class="tocnumber"></span> <span class="toctext"> Introduction</span></a></li>
 +
<li class="toclevel-1"><a href="#r2">Genome Browser</a></li>
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<li class="toclevel-1"><a href="#r3">Biobrick</a></li>
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<li class="toclevel-1"><a href="#r4">Riboswitch</a></li>
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<li class="toclevel-1"><a href="#r5">SiRNA</a></li>
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<li class="toclevel-1"><a href="#r6">Meta Network</a></li>
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<li class="toclevel-1"><a href="#r7">Simulator</a></li>
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<li class="toclevel-1"><a href="#r8">G-Circle</a></li>
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<li class="toclevel-1"><a href="https://2012.igem.org/Team:SYSU-Software/Clotho">Clotho</a></li>
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<h2><span lang="EN-US"  id="r1">Introduction<o:p></o:p></span></h2>
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<p class="MsoNormal">
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              <img class="style1" src="https://static.igem.org/mediawiki/igem.org/7/7c/Cvvxx.png" alt="" width="300px" height="230px" style="float: left ;"/><span lang="EN-US" style="mso-bidi-font-size:10.5pt"> Synthetic Biology, depending on interdisplinary knowledge and experience , cooperates wet and dry experiments to create artificial biological systems . Our team has developed a novel software system, BiArkit, to facilitate the design and engineering of specially functional systems. For visualization of genomic data and expression level of functional genes, we develop GenomeBrowser and G-Circle for researchers. Besides, Biobrick is localized and transformed into searching kit for users to get comprehensive information conveniently. Further, Riboswitch and SiRNA are designed to compute out potential regulatory parts for engineering systems. For processing data from system level, MetaNetwork can illustrate information of various biological pathways on the graphical and user-friendly interface. And Simulator is intended for modifying and simulating genome-scale metabolic models, which involves many kinds of analyses to predict possible results of conditional changes in experiments. All the functional modules have been successfully added to the Clotho Frame. </span></p>
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<h2><span lang="EN-US" id="r2">GenomeBrowser</span></h2>
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<p class="MsoNormal">
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              <img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/3/3e/Genome.png" alt="" width="300px" height="230px" style="float: left ;"/><span lang="EN-US" style="mso-bidi-font-size:10.5pt">This
 +
is the section for sequences information. With this browser, researchers can
 +
surf for genomes from the typical model organisms. Users can locate the
 +
interested genes in terms of the input items, including name, product or
 +
coordinate. In addition, new genomes data will be saved on our website as
 +
downloadable contents. <o:p></o:p></span></p>
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<h2><span lang="EN-US" id="r3">Biobrick<o:p></o:p></span></h2>
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<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
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<p class="MsoNormal">
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              <img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/4/4f/Biobrick.png" alt="" width="300px" height="230px" style="float: left ;"/><span lang="EN-US" style="mso-bidi-font-size:10.5pt">This
 +
is the section for parts information. It can facilitate researchers to search
 +
features and functions of Biobricks documented in the Registry of Standard
 +
Biological Parts. All of the relevant operations can be completed without
 +
connecting with the Internet.<o:p></o:p></span></p>
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<p class="MsoNormal">
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              <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;</p></p>
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<h2><span lang="EN-US" id="r4">Riboswitch<o:p></o:p></span></h2>
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<p>
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</p>
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<p class="MsoNormal">
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              <img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/a/ad/Riboswitch.png" alt="" width="300px" height="230px" style="float: left ;"><span lang="EN-US" style="mso-bidi-font-size:10.5pt">This
 +
is the section for generating parts information. It can assist researchers to
 +
design the sequences and structures of potential riboswitches according to their
 +
inputs and choices of aptamers. Both of the up-regulation and down-regulation
 +
riboswiches can be provided by this kit. <o:p></o:p>
 +
</span></p>
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<p class="MsoNormal">
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              <p>&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;</p></p>
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<h2><span lang="EN-US" id="r5">SiRNA<o:p></o:p></span></h2>
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<p class="MsoNormal">
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              <img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/f/f9/Sirna.png" alt="" width="300px" height="230px" style="float: left ;"/><span lang="EN-US" style="mso-bidi-font-size:10.5pt">This
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is the section for generating parts information. It can design another regulator
 +
in engineering biological systems – siRNA. According to the input sequences, it
 +
can figure out the potential siRNA automatically.<span style="mso-spacerun:yes">&nbsp;&nbsp;</span></span></p>
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<p class="MsoNormal">
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              &nbsp;</p>
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<p class="MsoNormal">
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              <span lang="EN-US" style="mso-bidi-font-size:10.5pt">
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<span style="mso-spacerun:yes">&nbsp;</span><o:p></o:p></span></p>
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<h2><span lang="EN-US" id="r6">MetaNetwork<o:p></o:p></span></h2>
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<p>
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<o:p></o:p></p>
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<p class="MsoNormal">
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              <img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/b/b2/Designer.png" alt="" width="300px" height="230px" style="float: left ;"/><span lang="EN-US" style="mso-bidi-font-size:10.5pt">This
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is the section for system information. Given the friendly interface, researchers
 +
can explore and acquire their interested gene’s relevant pathways and networks
 +
in one map. Users can even drag every graphic element in the maps to check the
 +
information conveniently and effectively.</span></p>
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<p class="MsoNormal">
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              &nbsp;</p>
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<p class="MsoNormal">
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              &nbsp;</p>
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<h2><span lang="EN-US" id="r7">Simulator<o:p></o:p></span></h2>
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<p>
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<o:p></o:p></p>
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<p class="MsoNormal">
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              <img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/6/6b/Simulator.png" alt="" width="300px" height="230px" style="float: left ;"/><span lang="EN-US" style="mso-bidi-font-size:10.5pt">This
 +
is the section for generating system information. Based on the reconstruction of  
 +
genome-scale models, researcher can use this kit to edit the existent models
 +
according to their needs. Then, they can choose different combination of
 +
analysis to predict effect from a intended loss-of –function mutation, find
 +
necessary and basic genes maintaining the whole system, predict phenotypic
 +
behavior under the given environmental conditions and interpret the coupled
 +
reaction activities. <o:p></o:p></span></p>
 +
<h2><span lang="EN-US" id="r8">G-Circle<o:p></o:p></span></h2>
 +
<p class="MsoNormal">
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            <img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/4/43/G-circle.png" alt="" width="300px" height="230px" style="float: left ;"/><span lang="EN-US" style="mso-bidi-font-size:10.5pt">This
 +
is the section for sequence information. It can illustrate the given genome and
 +
the expression level of genes within it under different environment in one
 +
graph. In addition, we have developed it as one app and integrated it into
 +
Clotho.<span style="mso-spacerun:yes">&nbsp;&nbsp;</span></span></p>
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<p class="MsoNormal">
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            <span lang="EN-US" style="mso-bidi-font-size:10.5pt">
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<span style="mso-spacerun:yes">&nbsp;</span></span></p>
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<h2>Clotho</h2>
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<p><a href="https://2012.igem.org/Team:SYSU-Software/Clotho">
 +
<img class="style1" src="http://www.autodeskresearch.com/img/header_projects_clotho.jpg" alt="" width="256" height="230px" style="float: left ;"></a>Clotho assists researchers to engineer synthetic biological systems and manage the data which is used to create them. It has been developed as the App environment that anyone can create and share new tools in it. These tools facilitate synthetic biologists to arrange their researches under the computer-based and automated- designed environment. Thus, to advanced develop the Clotho frame, we have successfully transfer the seven parts of our software, BiArkit, into Apps. Users can choose to employ our software through the Clotho media.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
<a href="https://2012.igem.org/Team:SYSU-Software/Clotho">Click to get detailed
 +
introduction</a></p>
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<h5>IGEM-SYSU-Software </h5>
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!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=SYSU-Software Official Team Profile]
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!align="center"|[[Team:SYSU-Software/Project|Project]]
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We are developing a multifunctional toolbox biArkit, which integrates different modules together and help researchers approach information they need. Firstly, we consider the Genome Browser, which visualizes the genomes of several microorganisms, locates the genes on the genome and make it easy to study the characteristics of the genome. Secondly, we develop a Regulator Designer, to help the design of regulatory elements, mainly non-coding RNA, a thriving method applied in biological research. Thirdly, to meet the need of systems and synthetics researches, we optimize the methods of scanning and output of the existing database of pathways.  Fourthly, to analyze the dynamic change in various metabolic networks, we present a simulator that help the researchers analyze the network in silico, in method of flux balance analysis (FBA). Further, to make it more convenient, the software is localized; that is to say, all functions mentioned above can be achieved without linkage to Internet.
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=== Section I:  ===
 
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With this Genome Browser, users are able to search Biobricks, plasmids and genomes of model microorganisms; at the same time, gene annotations and information of GenBank are presented. The primary protein sequence is also presented according to the DNA sequences. Aside from searching sequences, users can also input or modify the sequences, insert annotation and build target plasmids they need.
 
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=== Section II  ===
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</html>
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This part of the software focus on the design of regulatory elements of metabolic networks, mainly non-coding RNAs including SiRNA and Riboswitch. When a certain gene or protein is given, the Designer would generate the elements. What’s more, the primary and secondary structure can be predicted and presented in the Designer. The function of structure prediction can be also applied in other non-coding RNAs, for instance, microRNAs.
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=== Section III:  ===
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=== Section IV:  ===
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== Results ==
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Latest revision as of 03:15, 27 October 2012

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无标题 1
 

Our Project

Contents

Introduction

Synthetic Biology, depending on interdisplinary knowledge and experience , cooperates wet and dry experiments to create artificial biological systems . Our team has developed a novel software system, BiArkit, to facilitate the design and engineering of specially functional systems. For visualization of genomic data and expression level of functional genes, we develop GenomeBrowser and G-Circle for researchers. Besides, Biobrick is localized and transformed into searching kit for users to get comprehensive information conveniently. Further, Riboswitch and SiRNA are designed to compute out potential regulatory parts for engineering systems. For processing data from system level, MetaNetwork can illustrate information of various biological pathways on the graphical and user-friendly interface. And Simulator is intended for modifying and simulating genome-scale metabolic models, which involves many kinds of analyses to predict possible results of conditional changes in experiments. All the functional modules have been successfully added to the Clotho Frame.

GenomeBrowser

This is the section for sequences information. With this browser, researchers can surf for genomes from the typical model organisms. Users can locate the interested genes in terms of the input items, including name, product or coordinate. In addition, new genomes data will be saved on our website as downloadable contents.

Biobrick

 

This is the section for parts information. It can facilitate researchers to search features and functions of Biobricks documented in the Registry of Standard Biological Parts. All of the relevant operations can be completed without connecting with the Internet.

         

Riboswitch

This is the section for generating parts information. It can assist researchers to design the sequences and structures of potential riboswitches according to their inputs and choices of aptamers. Both of the up-regulation and down-regulation riboswiches can be provided by this kit.

      

SiRNA

This is the section for generating parts information. It can design another regulator in engineering biological systems – siRNA. According to the input sequences, it can figure out the potential siRNA automatically.  

 

 

MetaNetwork

This is the section for system information. Given the friendly interface, researchers can explore and acquire their interested gene’s relevant pathways and networks in one map. Users can even drag every graphic element in the maps to check the information conveniently and effectively.

 

 

Simulator

This is the section for generating system information. Based on the reconstruction of genome-scale models, researcher can use this kit to edit the existent models according to their needs. Then, they can choose different combination of analysis to predict effect from a intended loss-of –function mutation, find necessary and basic genes maintaining the whole system, predict phenotypic behavior under the given environmental conditions and interpret the coupled reaction activities.

G-Circle

This is the section for sequence information. It can illustrate the given genome and the expression level of genes within it under different environment in one graph. In addition, we have developed it as one app and integrated it into Clotho.  

 

Clotho

Clotho assists researchers to engineer synthetic biological systems and manage the data which is used to create them. It has been developed as the App environment that anyone can create and share new tools in it. These tools facilitate synthetic biologists to arrange their researches under the computer-based and automated- designed environment. Thus, to advanced develop the Clotho frame, we have successfully transfer the seven parts of our software, BiArkit, into Apps. Users can choose to employ our software through the Clotho media.            Click to get detailed introduction

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