Team:SYSU-Software/Project

From 2012.igem.org

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<li class="toclevel-1"><a href="#r0"><span class="tocnumber"></span> <span class="toctext">Project Introduction</span></a></li>
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<li class="toclevel-1"><a href="#r0"><span class="tocnumber"></span> <span class="toctext"> Introduction</span></a></li>
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<li class="toclevel-1"><a href="#r1"><span class="tocnumber"></span> <span class="toctext">Section I: Genome Browser</span></a></li>
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<li class="toclevel-1"><a href="#r2">Genome Browser</a></li>
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<li class="toclevel-1"><a href="#r2"><span class="tocnumber"></span> <span class="toctext">Section II: Regulator Designer</span></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="#r3"><span class="tocnumber"></span> <span class="toctext">Section III: Network Illustrator</span></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="#r4"><span class="tocnumber"></span> <span class="toctext">Section IV: Simulator</span></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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<div id="doc-contents">
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<h2 id="r0">Project Introduction</h2>
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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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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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.</p>
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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:
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</div>
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11.0pt;font-family:&quot;Georgia&quot;,&quot;serif&quot;">Faced with the
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<h2 id="r1">Section I: Genome Browser</h2>
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emergency of bio-information in recent years, we are motivated to consider how
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<div>
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to exploit them and integrate them into biological researches. In order to
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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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design and engineer artificial organisms, Synthetic Biology has much more
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</div>
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requirements to the understanding of the information comprehensively as its
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<h2 id="r2">Section II: Regulator Designer</h2>
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final goal is to assemble and construct the systems under the standard criteria.  
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<div>
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BiArkit, a multifunctional tool box, assists synthetic biology researchers to  
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<p>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>
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further comprehend bio-information from sequences and parts to the whole
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</div>
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systems. Besides, it provides medium for users to generate desired information
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<h2 id="r3">Section III: Network Illustrator</h2>
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in experiments. <o:p></o:p></span></p>
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<div>
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<h2><span lang="EN-US" id="r2">GenomeBrowser<o:p></o:p></span></h2>
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<p>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 class="MsoNormal">
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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:
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<h2 id="r4">Section IV: Simulator</h2>
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11.0pt;font-family:&quot;Georgia&quot;,&quot;serif&quot;">This is the section
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<div>
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for sequences information. With this browser, researchers can surf for genomes
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<p>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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from the typical model organisms. Users can locate the interested genes in terms
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</div>
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of the input items, including name, product or coordinate. In addition, new
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genomes data will be saved on our website as downloadable contents. <o:p></o:p>
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</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">
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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:
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11.0pt;font-family:&quot;Georgia&quot;,&quot;serif&quot;">This is the section
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for parts information. It can facilitate researchers to search features and  
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functions of Biobricks documented in the <i style="mso-bidi-font-style:normal">
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Registry of Standard Biological Parts</i>. All of the relevant operations can be
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completed without connecting with the Internet.<o:p></o:p></span></p>
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<h2><span lang="EN-US" id="r4">Riboswitch<o:p></o:p></span></h2>
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<p class="MsoNormal">
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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:
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11.0pt;font-family:&quot;Georgia&quot;,&quot;serif&quot;">This is the section
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for generating parts information. It can assist researchers to design the  
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sequences and structures of potential riboswitches according to their inputs and  
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choices of aptamers. Both of the up-regulation and down-regulation riboswiches
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can be provided by this kit. </span><b style="mso-bidi-font-weight:normal">
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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:11.0pt"><o:p></o:p>
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</span></b></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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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:
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11.0pt;font-family:&quot;Georgia&quot;,&quot;serif&quot;">This is the section
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for generating parts information. It can design another regulator in engineering
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biological systems – siRNA. According to the input sequences, it can figure out
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the potential siRNA automatically.<span style="mso-spacerun:yes">&nbsp;&nbsp;
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</span><o:p></o:p></span></p>
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<h2><span lang="EN-US" id="r6">MetaNewtwork<o:p></o:p></span></h2>
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<p class="MsoNormal">
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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:
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11.0pt;font-family:&quot;Georgia&quot;,&quot;serif&quot;">This is the section
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for system information. Given the friendly interface, researchers can explore
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and acquire their interested gene’s relevant pathways and networks in one map.
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Users can even drag every graphic element in the maps to check the information
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conveniently and effectively.<o:p></o:p></span></p>
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<h2><span lang="EN-US" id="r7">Simulator<o:p></o:p></span></h2>
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<p class="MsoNormal">
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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:
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11.0pt;font-family:&quot;Georgia&quot;,&quot;serif&quot;">This is the section
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for generating system information. Based on the reconstruction of genome-scale
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models, researcher can use this kit to edit the existent models according to
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their needs. Then, they can choose different combination of analysis to predict
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effect from a intended loss-of –function mutation, find necessary and basic
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genes maintaining the whole system, predict phenotypic behavior under the given
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environmental conditions and interpret the coupled reaction activities. <o:p></o:p>
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</span></p>
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<h2><span lang="EN-US" id="r8">G-Circle<o:p></o:p></span></h2>
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<p class="MsoNormal">
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<span lang="EN-US" style="font-size:12.0pt;mso-bidi-font-size:
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11.0pt;font-family:&quot;Georgia&quot;,&quot;serif&quot;">This is the section
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for sequence information. It can illustrate the given genome and the expression
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level of genes within it under different environment in one graph. In addition,
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we have developed it as one app and integrated it into
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<i style="mso-bidi-font-style:
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normal">Clotho</i>.<span style="mso-spacerun:yes">&nbsp;&nbsp; </span><o:p></o:p>
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</span></p>
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Revision as of 12:00, 24 September 2012

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Our Project

Contents

Introduction

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.

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.  

MetaNewtwork

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.  

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