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!align="center"|[[Team:SYSU-Software/Project|Project]]
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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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<tr>
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<td>
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<div id="toctitle">
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<h2>Contents</h2>
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</div>
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<ul id="toc-ul">
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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>
 +
<li class="toclevel-1"><a href="#r3">Biobrick</a></li>
 +
<li class="toclevel-1"><a href="#r4">Riboswitch</a></li>
 +
<li class="toclevel-1"><a href="#r5">SiRNA</a></li>
 +
<li class="toclevel-1"><a href="#r6">Meta Network</a></li>
 +
<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">
 +
              <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>
 +
<h2><span lang="EN-US" id="r2">GenomeBrowser</span></h2>
 +
<p class="MsoNormal">
 +
              <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>
 +
<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>
 +
</p>
 +
<p class="MsoNormal">
 +
              <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>
 +
<p class="MsoNormal">
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              <p>&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;</p></p>
 +
<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>
 +
<p class="MsoNormal">
 +
              &nbsp;</p>
 +
<p class="MsoNormal">
 +
              &nbsp;</p>
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<h2><span lang="EN-US" id="r7">Simulator<o:p></o:p></span></h2>
 +
<p>
 +
<o:p></o:p></p>
 +
<p class="MsoNormal">
 +
              <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">
 +
            <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">
 +
<span style="mso-spacerun:yes">&nbsp;</span></span></p>
 +
<h2>Clotho</h2>
 +
<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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<a href="https://2012.igem.org/Team:SYSU-Software">Main Page</a>
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== '''Overall project''' ==
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<h5>User Guide</h5>
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Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)
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<h5>FAQ </h5>
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<a href="https://2012.igem.org/Team:SYSU-Software/Contact">Contact Us</a>
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We have inclination to develop a multifunctional toolbox “Blablabla”, that integrates different modules together and help researchers approach information they need. Firstly, we consider the Genome Viewer, which visualizes the E coli genome, locates the genes on the genome and make it easy to study the characteristics of the genome. Secondly, to meet the need of protein-protein interaction researches, we optimize the methods of scanning and output of the existing database, and also supplement the biological information by building novel database. Thirdly, we develop a Riboswitch Designer, to help the design of riboswitch, a thriving method applied in biological research, by building an optimized algorithm. Further, to make it more versatile, more functions may be developed or supplemented, facilitating the researches on biology.
 
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=== The Experiments ===
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=== Part 3 ===
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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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