Team:SYSU-Software

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                 <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Faced with the emergency of bio-information in recent years, we are motivated to consider how to exploit them and integrate them into biological researches. In order to design and engineer artificial organisms, Synthetic Biology has much more requirements to the understanding of the information comprehensively as its final goal is to assemble and construct the systems under the standard criteria. BiArkit, a multifunctional tool box, assists synthetic biology researchers to further comprehend bio-information from sequences and parts to the whole systems. Besides, it provides medium for users to generate desired information in experiments.</p>
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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 interdisplinary knowledge and experience , cooperate 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">GenomeBrowser</a> and
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r8">G-Circle</a> which has been added to the Clotho frame for researchers. Besides,
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r3">Biobrick</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">Riboswitch</a> and  
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r5">SiRNA</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">MetaNetwork</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">Simulator</a> is intended for modificating and simulating genome-scale metabolic models, which involves many kinds of analysis to predict possible results of conditional changes in experiments.
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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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                       <h2><span lang="zh-cn">Software</span></h2>
                       <h2><span lang="zh-cn">Software</span></h2>
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                         <li><span lang="zh-cn"><a href="https://2012.igem.org/Team:SYSU-Software/Download">Download</a> &nbsp;&nbsp;&nbsp;
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                         <li><span lang="zh-cn"><a href="#">Download</a> &nbsp;&nbsp;&nbsp;
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                         <li><a href="https://2012.igem.org/Team:SYSU-Software/Tutorial">Tutorial</a></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/Faq">FAQs</li>
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                         <li><a href="#">FAQs</li>
                          
                          
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                       <div class="wrapper"><a href="#" class="link1"><b>read more</b></a></div>
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                             <p>Notebook shows you the schedule we developed this project.</p>
                             <p>Notebook shows you the schedule we developed this project.</p>
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                             <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Notebook" class="link1"><b>read more</b></a></div>
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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>
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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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Revision as of 17:22, 26 September 2012

Team:SYSU-Software

      Synthetic Biology, depending on interdisplinary knowledge and experience , cooperate 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 which has been added to the Clotho frame 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 modificating and simulating genome-scale metabolic models, which involves many kinds of analysis to predict possible results of conditional changes in experiments. read more

      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.

     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.

      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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Notebook

  • Notebook shows you the schedule we developed this project.

Contact us

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