Team:SYSU-Software

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<title>Team:SYSU-Software</title>
<title>Team:SYSU-Software</title>
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         <div id="logopic"><a href="#"><img src="https://static.igem.org/mediawiki/igem.org/c/c9/Logo.png"  alt=""  width="320px"  height="145px"/></a>  
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           <div class="wrapper">
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             <ul class="tabs">
             <ul class="tabs">
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               <li class="first"><a href="#tab1">Genome Browser</a></li>
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               <li class="first"><a href="#tab1">GenomeBrowser</a></li>
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               <li><a href="#tab2">Regulator&nbsp;Designer</a></li>
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               <li><a href="#tab2">Biobrick</a></li>
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               <li><a href="#tab3">Network&nbsp;Illustrator</a></li>
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               <li><a href="#tab3">Riboswitch</a></li>
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               <li><a href="#tab4">Simulator</a></li>
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               <li><a href="#tab4">SiRNA</a></li>
 +
<li><a href="#tab5">MetaNewtwork</a></li>
 +
              <li><a href="#tab6">Simulator</a></li>
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              <li><a href="#tab7">G-Circle</a></li>
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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>
                 <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>
                    
                    
-
                   <div class="wrapper"><a href="#" 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" class="link1"><b>read more</b></a></div>
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               <img class="img-indent" src="https://static.igem.org/mediawiki/2012/7/71/Designer.jpg" alt="" width="300px" height="230px"/>
               <img class="img-indent" src="https://static.igem.org/mediawiki/2012/7/71/Designer.jpg" alt="" width="300px" height="230px"/>
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                 <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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.</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="#" class="link1"><b>read more</b></a></div>
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               <img class="img-indent" src="https://static.igem.org/mediawiki/2012/8/8f/Illustrator.jpg" alt="" width="300px" height="230px" />
               <img class="img-indent" src="https://static.igem.org/mediawiki/2012/8/8f/Illustrator.jpg" alt="" width="300px" height="230px" />
                 <div class="extra-wrap">
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                 <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Relying on the KEGG Pathway database, the Illustrator exports the optimized relevant pathway map of a gene or transcription factor the user interests in. </p>
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                 <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
-
                                     <div class="wrapper"><a href="#" class="link1"><b>read more</b></a></div>
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<span lang="EN-US">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.</span></p>
 +
                                     <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
                 </div>
                 </div>
               </div>
               </div>
             </div>
             </div>
             <div id="tab4" class="tab_content">
             <div id="tab4" class="tab_content">
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            <div class="wrapper">
 +
              <img class="img-indent" src="https://static.igem.org/mediawiki/2012/8/8f/Illustrator.jpg" alt="" width="300px" height="230px" />
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                <div class="extra-wrap">
 +
                <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
 +
<span lang="EN-US">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.</span></p>
 +
                                    <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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              <img class="img-indent" src="https://static.igem.org/mediawiki/2012/8/8f/Illustrator.jpg" alt="" width="300px" height="230px" />
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                <div class="extra-wrap">
 +
                <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>
 +
                                    <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>
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              </div>
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            <div class="wrapper">
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              <img class="img-indent" src="https://static.igem.org/mediawiki/2012/8/8f/Illustrator.jpg" alt="" width="300px" height="230px" />
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                <div class="extra-wrap">
 +
                <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
 +
<span lang="EN-US">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.</span></p>
 +
                                    <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
 +
                </div>
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              </div>
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            </div>
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            <div id="tab7" class="tab_content">
             <div class="wrapper">
             <div class="wrapper">
             <img class="img-indent" src="https://static.igem.org/mediawiki/2012/5/55/Simulator.jpg" alt="" width="300px" height="230px" />
             <img class="img-indent" src="https://static.igem.org/mediawiki/2012/5/55/Simulator.jpg" alt="" width="300px" height="230px" />
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               <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Simulator is a tool to analyze target metabolic network in method of flux balance analysis (FBA). The Simulator would help researchers rebuild the metabolic network and search key genes in the network, in order to simplify the synthesis design. Relying on the KEGG Pathway database, a novel rFBA model is formed when regulation-relevant conditions are added into the primitive FBA model, which would help the researchers observe the dynamic change in the metabolic system. Moreover, unlike the mainstream of FBA, the analysis of the Simulator is not based on Matlab and is more convenient for researchers to use.</p>
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               <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
-
                 <p class="wrapper"><a href="#" class="link1"><b>read more</b></a></p>
+
<span lang="EN-US">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
 +
<i>Clotho</i>.</span></p>
 +
                 <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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                       <h2><span lang="zh-cn">Software</span></h2>
                       <h2><span lang="zh-cn">Software</span></h2>
                       <ul class="list1">
                       <ul class="list1">
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                         <li><span lang="zh-cn"><a href="#">Download</a> &nbsp;&nbsp;&nbsp;
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                         <li><span lang="zh-cn"><a href="https://2012.igem.org/Team:SYSU-Software/Download">Download</a> &nbsp;&nbsp;&nbsp;
</span></li>
</span></li>
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                         <li><a href="#">Tutorial</a></li>
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                         <li><a href="https://2012.igem.org/Team:SYSU-Software/Tutorial">Tutorial</a></li>
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                         <li><span lang="zh-cn"><a href="#">Video</a></span></li>
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                         <li><span lang="zh-cn"><a href="https://2012.igem.org/Team:SYSU-Software/Video">Video</a></span></li>
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                         <li><a href="#">FAQs</li>
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                         <li><a href="https://2012.igem.org/Team:SYSU-Software/Faq">FAQs</li>
                          
                          
                       </ul>
                       </ul>
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                       <div class="wrapper"><a href="#" 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" class="link1"><b>read more</b></a></div>
                     </div>
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                           <div class="extra-wrap">
                           <div class="extra-wrap">
                             <p>Notebook shows you the schedule we developed this project.</p>
                             <p>Notebook shows you the schedule we developed this project.</p>
-
                             <div class="wrapper"><a href="#" class="link1"><b>read more</b></a></div>
+
                             <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Notebook" class="link1"><b>read more</b></a></div>
                           </div>
                           </div>
                         </li>
                         </li>
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                       <h2><span lang="zh-cn">Contact</span> us</h2>
                       <h2><span lang="zh-cn">Contact</span> us</h2>
                       <p>Click "read more" to get access to contact us.                    </p>
                       <p>Click "read more" to get access to contact us.                    </p>
-
                       <div class="wrapper"><a href="#" class="link1"><b>read more</b></a></div>
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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>
                     </div>
                     </div>
                   </div>
                   </div>
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Revision as of 04:12, 25 September 2012

Team:SYSU-Software

      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.

read more

     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.

read more

      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.

read more

      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.

read more

      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.

read more

      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.

read more

      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.

read more

Software

read more

Notebook

  • Notebook shows you the schedule we developed this project.

    read more

Contact us

Click "read more" to get access to contact us.

read more

Retrieved from "http://2012.igem.org/Team:SYSU-Software"