Team:SYSU-Software

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         <ul class="nav">
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           <li><a href="https://2012.igem.org/Team:SYSU-Software/Project" >Project<span>Software Projct</span></a></li>
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           <li><a href="https://2012.igem.org/Team:SYSU-Software/Project" >Project<span>Software Project</span></a></li>
           <li><a href="https://2012.igem.org/Team:SYSU-Software/Models">
           <li><a href="https://2012.igem.org/Team:SYSU-Software/Models">
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Models <span>Models&Algorithm</span></a></li>
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Models<span>Models &amp; Algorithm</span></a></li>
           <li><a href="https://2012.igem.org/Team:SYSU-Software/Tutorial">Tutorial<span>Guidance book and videos</span></a></li>
           <li><a href="https://2012.igem.org/Team:SYSU-Software/Tutorial">Tutorial<span>Guidance book and videos</span></a></li>
           <li><a href="https://2012.igem.org/Team:SYSU-Software/Team">Team<span>Instructor and members</span></a></li>
           <li><a href="https://2012.igem.org/Team:SYSU-Software/Team">Team<span>Instructor and members</span></a></li>
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           <li><a href="https://2012.igem.org/Team:SYSU-Software/Notebook">Notebook<span>Schedule of this project</span></a></li>
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           <li><a href="https://2012.igem.org/Team:SYSU-Software/WorldJamboree">
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           <li><a href="https://2012.igem.org/Team:SYSU-Software/Practice">Tips<span>Human practice and safety</span></a></li>
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For Special Awards <span>For World Jamboree awards</span></a><span lang="zh-cn"><span class="style1">
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</span></span></li>
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           <li><a href="https://2012.igem.org/Team:SYSU-Software/Practice">Tips<span>Human practice, safety...</span></a></li>
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               <strong>creative ideas</strong>
               <strong>creative ideas</strong>
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              <strong>best solutions</strong>
 
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              <li class="first"><a href="#tab1">GenomeBrowser</a></li>
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            <li class="first"><a href="#tab0">Overview</a></li>
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              <li style="left: 0px; top: 0px" ><a href="#tab1">Browser</a></li>
               <li><a href="#tab2">Biobrick</a></li>
               <li><a href="#tab2">Biobrick</a></li>
               <li><a href="#tab3">Riboswitch</a></li>
               <li><a href="#tab3">Riboswitch</a></li>
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<li><a href="#tab5">MetaNetwork</a></li>
               <li><a href="#tab6">Simulator</a></li>
               <li><a href="#tab6">Simulator</a></li>
               <li><a href="#tab7">G-Circle</a></li>
               <li><a href="#tab7">G-Circle</a></li>
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              <li><a href="#tab8">Clotho</a></li>
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           </div>
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                <p><img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/7/7c/Cvvxx.png" alt="" width="300px" height="230px" style="float: left ;"/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Synthetic Biology, depending on interdisciplinary knowledge and experience , cooperates wet and dry experiments to create artificial biological systems . Our team has developed a novel software system,
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<a href="https://2012.igem.org/Team:SYSU-Software/Project">BiArkit</a>, to facilitate the design and engineering of specially functional systems. For visualization of genomic data and expression level of functional genes, we develop
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r2"><FONT color="blue">GenomeBrowser</FONT></a> and
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r8"><FONT color="blue">G-Circle</FONT></a>  Besides,
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r3"><FONT color="blue">Biobrick</FONT></a> is localized and transformed into searching kit for users to get comprehensive information conveniently. Further,
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r4"><FONT color="blue">Riboswitch</FONT></a> and
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r5"><FONT color="blue">SiRNA</FONT></a> are designed to compute out potential regulatory parts for engineering systems. For processing data from system level,
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r6"><FONT color="blue">MetaNetwork</FONT></a> can illustrate information of various biological pathways on the graphical and user-friendly interface. And
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r7"><FONT color="blue">Simulator</FONT></a> 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
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<a href="https://2012.igem.org/Team:SYSU-Software/Clotho">Clotho</a> Frame.
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<a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"  style="float: right ;""><b>read more</b></a></p>
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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"/>
               <img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/3/3e/Genome.png" alt="" width="300px" height="230px"/>
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                 <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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.</p>
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                 <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; This
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is the section for sequences information. With this browser, researchers can
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surf for genomes from the typical model organisms. Users can locate the  
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interested genes in terms of the input items, including name, product or  
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coordinate. In addition, new genomes data will be saved on our website as
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downloadable contents.</p>
                    
                    
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                   <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                   <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project#r2" class="link1"><b>read more</b></a></div>
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                 <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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.</p>                   
                 <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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.</p>                   
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                   <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                   <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project#r3" class="link1"><b>read more</b></a></div>
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up-regulation and down-regulation riboswiches can be  
up-regulation and down-regulation riboswiches can be  
provided by this kit.</span></p>
provided by this kit.</span></p>
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                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project#r4" class="link1"><b>read more</b></a></div>
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sequences, it can figure out the potential siRNA  
sequences, it can figure out the potential siRNA  
automatically.</span></p>
automatically.</span></p>
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                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project#r5" class="link1"><b>read more</b></a></div>
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                 <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
                 <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
<span lang="EN-US">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.</span></p>
<span lang="EN-US">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.</span></p>
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                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project#r6" class="link1"><b>read more</b></a></div>
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                 <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
                 <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
<span lang="EN-US">This is the section for generating system  
<span lang="EN-US">This is the section for generating system  
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behavior under the given environmental conditions and  
behavior under the given environmental conditions and  
interpret the coupled reaction activities.</span></p>
interpret the coupled reaction activities.</span></p>
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                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project#r7" class="link1"><b>read more</b></a></div>
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<img class="img-indent" src="http://www.autodeskresearch.com/img/header_projects_clotho.jpg" alt="" width="256" height="230px"  style="float: left ;">
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                <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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.
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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.</span></p>
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                                    <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Clotho" class="link1"><b>read more</b></a></div>
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addition, we have developed it as one app and integrated it into
addition, we have developed it as one app and integrated it into
<i>Clotho</i>.</span></p>
<i>Clotho</i>.</span></p>
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                 <p class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></p>
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                 <p class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project#r8" class="link1"><b>read more</b></a></p>
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                      <h2><span lang="zh-cn">Software</span></h2>
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                        <li  style="text-align: center ;"><h2> <span lang="zh-cn">&nbsp;&nbsp; </span>
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<span class="style2">video</span></h2>
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<td>Version 1.00 <span lang="zh-cn">Sept.2012</span></td><td>Version 1.05<span lang="zh-cn">  
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Oct.2012</span></td>
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<td><iframe width="380" height="320" src="http://www.youtube.com/embed/en_OuQ8Ur_8" frameborder="0" allowfullscreen style="float: left ;margin-right: 10px;"></iframe></td>
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<td><iframe width="380" height="320" src="http://www.youtube.com/embed/vgP_uKks2Cg" frameborder="0" allowfullscreen style="float: left "></iframe></td>
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                      <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
 
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                      <h2><span lang="zh-cn">Notebook</span></h2>
 
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                            <p>Notebook shows you the schedule we developed this project.</p>
 
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                      <h2><span lang="zh-cn">Contact</span> us</h2>
 
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                      <p>Click "read more" to get access to contact us.                    </p>
 
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                      <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Contact" class="link1"><b>read more</b></a></div>
 
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Latest revision as of 04:03, 27 October 2012

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Team:SYSU-Software

      Synthetic Biology, depending on interdisciplinary 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 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. read more

      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.

     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.

      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.

      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.

      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.

      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.

      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.

      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.

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