Team:SYSU-Software/template2/header

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   <div class="skip-content"><a href="#content">Skip to content</a></div>
   <div class="skip-content"><a href="#content">Skip to content</a></div>
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<ul id="toc-ul">
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<li class="toclevel-1"><a href="#r0"><span class="tocnumber">1</span> <span class="toctext">List Window</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="#r1"><span class="tocnumber">2</span> <span class="toctext">Columns</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="#r2"><span class="tocnumber">3</span> <span class="toctext">Using the Calendar</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="#r3"><span class="tocnumber">4</span> <span class="toctext">Editing Reminders</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="#r4"><span class="tocnumber">5</span> <span class="toctext">Filtering</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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<li class="toclevel-1"><a href="#r5"><span class="tocnumber">6</span> <span class="toctext">Views and Criteria</span></a></li>
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<div id="doc-contents">
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<h2 id="r0">List Window</h2>
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<h2 id="r0">Project Introduction</h2>
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<p>The List dialog is one of the main places to allow you to view and manage the reminders. To bring up the list dialog, you can double-click on the ribbon icon, or right-click on it and select <code>[View Reminders ..</code>] from the context menu. The list dialog has tabs for your Reminders, ToDo's, as well as any custom lists that you set up. The main dialog displays all of your reminders along with any attributes in the various list columns.</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>
</p></div>
</p></div>
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<h2 id="r1">Columns</h2>
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<h2 id="r1">Section I: Genome Browser</h2>
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<h2 id="r2">Using the Calendar</h2>
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<div>
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<h2 id="r3">Editing Reminders</h2>
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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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<h2 id="r4">Filtering</h2>
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</p></div>
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<h2 id="r5">Views and Criteria</h2>
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<h2 id="r2">Section II: Regulator Designer</h2>
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<div>
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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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</div>
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<h2 id="r3">Section III: Network Illustrator</h2>
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<div>
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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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</div>
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<h2 id="r4">Section IV: Simulator</h2>
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<div>
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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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<h5>Getting Started </h5>
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<h5>IGEM-SYSU-Software </h5>
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<a href="/documentation/">Main Page</a>
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<a href="/videos/">Main Page</a>
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<a href="/documentation-install">Installing Reminderfox</a>
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<a href="/documentation/">Album</a>
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<a href="/videos/">How-To Videos</a>
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<a href="/documentation-install">Video</a>
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documentation-user-guide-main-reminderfox-window">Main ReminderFox Window</a>
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documentation-user-guide-main-reminderfox-window">Download</a>
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<a href="/documentation-userguide-reminders">Reminders</a>
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<a href="/documentation-userguide-reminders">Tutorial</a>
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<a href="/documentation-user-guide-todos">ToDo's</a>
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<a href="/documentation-user-guide-todos">Video</a>
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<a href="/documentation-user-guide-options-and-preferences">Options and Preferences</a>
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<a href="/documentation-user-guide-sharing-reminders">Sharing Reminders</a>
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<a href="/documentation-user-guide-notifications">Email</a>
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<a href="">Questions</a>
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<a href="">Troubleshooting</a>
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<a href="/documentation-faq-uninstalling">Uninstalling</a>
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<a href="">Uninstalling</a>
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                               <h2>Links</h2>
                               <h2>Links</h2>
               <ul>
               <ul>
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                 <li><a href="http://www.twitter.com/reminderfox">ReminderFox on Twitter</a></li>
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                 <li><a href="http://www.sysu.edu.cn">SUN YAT-SEN University</a></li>
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                 <li><a href="https://addons.mozilla.org/en-US/firefox/addon/1191/">Mozilla Add-ons Page</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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       <h2>Facebook</h2>
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<iframe src="http://www.facebook.com/plugins/likebox.php?id=319600074107&amp;width=292&amp;connections=0&amp;stream=false&amp;header=false&amp;height=62" scrolling="no" frameborder="0" style="border:none; overflow:hidden; width:292px; height:62px;" allowTransparency="true"></iframe>
 
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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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