Team:SYSU-Software/template2/header

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   <div class="skip-content"><a href="#content">Skip to content</a></div>
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     <li class="mainlevel" id="mainlevel_02"><a href="#">Project</a>
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     <ul class="sub_nav_01">
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    <span class="Triangle_con"></span>
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    <li><a href="#">Overview</a></li>
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    <li><a href="#">Genome Browser</a></li>
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    <li><a href="#">Regulator Designer</a></li>
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    <li><a href="#">Network Illustrator</a></li>
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    <li><a href="#">Simulator</a></li>
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     <li class="mainlevel"><a href="#">Tutorial</a>
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    <span class="Triangle_con"></span>
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    <li><a href="#">Overview</a></li>
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    <li><a href="#">Genome Browser</a></li>
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    <li><a href="#">Regulator Designer</a></li>
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    <li><a href="#">Network Illustrator</a></li>
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    <li><a href="#">Simulator</a></li>
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         <h1 id="doctitle" class="pagetitle">Software Tutorial</h1>
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         <h1 id="doctitle" class="pagetitle">Our Project</h1>
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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="#r0"><span class="tocnumber">1</span> <span class="toctext">Project Introduction</span></a></li>
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<li class="toclevel-1"><a href="#r2"><span class="tocnumber"></span> <span class="toctext">Riboswitch</span></a></li>
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<li class="toclevel-1"><a href="#r1"><span class="tocnumber">2</span> <span class="toctext">Section I: Genome Browser</span></a></li>
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<li class="toclevel-1"><a href="#r3"><span class="tocnumber"></span> <span class="toctext">SiRNA</span></a></li>
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<li class="toclevel-1"><a href="#r2"><span class="tocnumber">3</span> <span class="toctext">Section II: Regulator Designer</span></a></li>
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<li class="toclevel-1"><a href="#r4"><span class="tocnumber"></span> <span class="toctext">KEGG Network</span></a></li>
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<li class="toclevel-1"><a href="#r3"><span class="tocnumber">4</span> <span class="toctext">Section III: Network Illustrator</span></a></li>
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<li class="toclevel-1"><a href="#r5"><span class="tocnumber"></span> <span class="toctext">Fba</span></a></li>
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<li class="toclevel-1"><a href="#r4"><span class="tocnumber">5</span> <span class="toctext">Section IV: Simulator</span></a></li>
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<div id="doc-contents">
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<h2 id="r1">Genome Browser</h2>
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<h2 id="r0">Project Introduction</h2>
<div>
<div>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Procedure: File→Open Fasta→Open xml Component</p>
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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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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Parts: In the main display window, the first ribbon is the sequence that the  
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user has inputted, and the third ribbon shows the corresponding gene annotation.  
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You can click any annotation that you want, and then the sequence site will
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automatically jump to the fragment related to it. Between those ribbons is an
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adjustable slider, which can adjust your view location by sliding to the left or
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to the right. Above the sequence are the head and tail of the location that you
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are viewing while the head and tail of the whole sequence are displayed in the
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bottom textbox. What’s more, the textbox contains the length, product, tag of
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the sequence, and links of related papers are also included sometimes. </p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;On the left, there are two useful tools: you can search the fragment that you want by position or name (Position represents the position of its head and Name stands for its tag or key word of its gene annotation); the slider of Zoom is designed for regulating the display frame rate of the sequence.
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</p></div>
</p></div>
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<h2 id="r0">Biobrick</h2>
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<h2 id="r1">Section I: Genome Browser</h2>
<div>
<div>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Procedure: Open your biobrick file(in xml format)</p>
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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;Component Parts: In the main display window, you can view information of existing biobricks. On the left is the list of the files that you have opened.
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</p>
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</div>
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<h2 id="r2">Riboswitch</h2>
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<div>
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<p>Procedure: choose a target type→choose a target name→choose an aptamer→choose a regulation direction (up regulation or down regulation) →GO
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</p><p>Component Parts: On the right is the main operating area and you can choose your target type (your experimental object) and corresponding target name, aptamer and regulation direction. Attention should be paid to the input box named Input your Target. You can search your target name by key words or even several letters of it. It should be useful to you. Click GO and you will see a picture. The designed riboswitch is in the dotted box on the top left corner. Below it is a diagram to show how the riboswitch works. Besides, there is a list on the left box. It records your choices that you have made in created riboswich project, and you need only click Go next time.
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</p></div>
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<h2 id="r3">SiRNA</h2>
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<h2 id="r2">Section II: Regulator Designer</h2>
<div>
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<p>Procedure: Input your DNA sequence</p>
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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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<p>Component Parts: The left textbox is for you to input DNA sequence. There are two ways to input that: you can either input the sequence directly or open a file in FASTA format. If you choose the former, click Direct Input, then input your sequence, and click Go. If you choose the latter, you need only click Open Fasta and choose your FASTA file to open. Two solutions are provided on the right——one is solved by Tom Tuschl’s method and the other is by rational design.  
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<h2 id="r3">Section III: Network Illustrator</h2>
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<h2 id="r4">KEGG Network</h2>
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<div>
<div>
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<p>Procedure: open a file (in xml format)</p>
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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>Component Parts: In the main display window, you will see a network from KEGG website. On the left box displays a list of the files you have opened. Pay attention that you can right click the main display window to open another KEGG xml file or to search any element in the network (choose find element).
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<h2 id="r4">Section IV: Simulator</h2>
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<h2 id="r5">Fba</h2>
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<div>
<div>
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<p>Procedure: Open a file (in xml format)→select your options→Go</p>
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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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<p>Component Parts: There are 5 options for you to select: exhaustive single deletion, reaction deletion, fva solve, preturbation analysis and PHPP analysis. You can select all of them or part of them, or even nothing, then click Go. If you select none of them, you will see a table showed basic information of each reaction. If you select several of them, the corresponding windows will tiled in the resulting window. If you select reaction deletion option, a selection of the reaction you want to wipe off is required, and if there is any change, it will be highlighted in red font.
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               <ul>
               <ul>
                 <li><a href="http://www.sysu.edu.cn">SUN YAT-SEN University</a></li>
                 <li><a href="http://www.sysu.edu.cn">SUN YAT-SEN University</a></li>
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                 <li><a href="http://lifescience.sysu.edu.cn/main/default/index.aspx">SYSU LifeSCience</a></li>
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Latest revision as of 12:41, 22 September 2012

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 无标题 1

Skip to content

Our Project

Contents

Project Introduction

      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.

Section I: Genome Browser

      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.

Section II: Regulator Designer

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.

Section III: Network Illustrator

Relying on the KEGG Pathway database, the Illustrator exports the optimized relevant pathway map of a gene or transcription factor the user interests in.

Section IV: Simulator

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.

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