Team:SYSU-Software/Project

From 2012.igem.org

(Difference between revisions)
(Undo revision 144304 by Nie1234567 (talk))
Line 1: Line 1:
 +
{{:Team:SYSU-Software/menu}}
 +
<html xmlns="http://www.w3.org/1999/xhtml">
-
<!-- *** What falls between these lines is the Alert Box! You can remove it from your pages once you have read and understood the alert *** -->
+
<head>
 +
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 +
<title>无标题 1</title>
 +
<link href="https://2012.igem.org/Team:SYSU-Software/template2/style.css?action=raw&ctype=text/css" rel="stylesheet" type="text/css" />
 +
<script language="javascript" type="text/javascript" src="https://2012.igem.org/Team:SYSU-Software/template2/js/jquery-1.4.2.js?action=raw&ctype=text/javascript"></script>
 +
<script language="javascript" type="text/javascript" src="https://2012.igem.org/Team:SYSU-Software/template2/js/menu.js?action=raw&ctype=text/javascript"></script>
 +
 
 +
</head>
 +
 
 +
<body>
 +
<body class=""
 +
style="
 +
  text-align:center;
 +
  width:970px;
 +
  margin:0 auto;>
 +
  <div class="skip-content"></div>
 +
  &nbsp;<div id="header" class="clear" style="background-color: #545454">
 +
    <div class="wrapper">
 +
<a href="/" class="sysu-title"></a>
 +
     
 +
      <!--end navigation-->
 +
    </div><!--end wrapper-->
 +
</div><!--end header-->
 +
<div class="content-background">
 +
<div id="blank" ><br/></div>
 +
<div class="wrapper">
 +
 
 +
<div id="menu">
 +
<ul id="nav">     
 +
    <li class="mainlevel" id="mainlevel_01"><a href="#">Home</a>
 +
   
 +
    </li>
 +
   
 +
    <li class="mainlevel" id="mainlevel_02"><a href="#">Project</a>
 +
   
 +
    </li>
 +
     
 +
    <li class="mainlevel"><a href="#">Team</a>
 +
   
 +
    </li>
 +
       
 +
    <li class="mainlevel"><a href="#">Safety</a><!--input an em tag as a space,IE is gread need-->
 +
   
 +
    </li>
 +
   
 +
    <li class="mainlevel"><a href="#">Tutorial</a>
 +
   
 +
    </li>
 +
   
 +
    <li class="mainlevel"><a href="#">Notebook</a></li>
 +
     
 +
   
 +
   
 +
</ul>
-
<html>
 
-
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #fe2b33;">
 
-
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;">
 
-
This is a template page. READ THESE INSTRUCTIONS.
 
</div>
</div>
-
<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;">
+
  <img src=" https://static.igem.org/mediawiki/2012/6/6d/Little-boy.png" id="little-boy"></img>
-
You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
+
 
 +
 
 +
  <div id="content">                  <div class="entry page clear">
 +
        <h1 id="doctitle" class="pagetitle">Our Project</h1>
 +
<table class="doc-toc">
 +
<tbody>
 +
<tr>
 +
<td>
 +
<div id="toctitle">
 +
<h2>Contents</h2>
</div>
</div>
-
<div id="warning" style="text-align: center; font-weight: bold; font-size: small; color: #f6f6f6; padding: 5px;">
+
<ul id="toc-ul">
-
You <strong>MUST</strong> have all of the pages listed in the menu below with the names specified.  PLEASE keep all of your pages within your teams namespace.
+
<li class="toclevel-1"><a href="#r0"><span class="tocnumber"></span> <span class="toctext">Project Introduction</span></a></li>
 +
<li class="toclevel-1"><a href="#r1"><span class="tocnumber"></span> <span class="toctext">Section I: Genome Browser</span></a></li>
 +
<li class="toclevel-1"><a href="#r2"><span class="tocnumber"></span> <span class="toctext">Section II: Regulator Designer</span></a></li>
 +
<li class="toclevel-1"><a href="#r3"><span class="tocnumber"></span> <span class="toctext">Section III: Network Illustrator</span></a></li>
 +
<li class="toclevel-1"><a href="#r4"><span class="tocnumber"></span> <span class="toctext">Section IV: Simulator</span></a></li>
 +
</ul>
 +
</td>
 +
</tr>
 +
</tbody>
 +
</table>
 +
<div id="doc-contents">
 +
<h2 id="r0">Project Introduction</h2>
 +
<div>
 +
<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>
 +
<h2 id="r1">Section I: Genome Browser</h2>
 +
<div>
 +
<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></div>
 +
<h2 id="r2">Section II: Regulator Designer</h2>
 +
<div>
 +
<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>
</div>
</div>
 +
<h2 id="r3">Section III: Network Illustrator</h2>
 +
<div>
 +
<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>
</div>
</div>
-
</html>
+
<h2 id="r4">Section IV: Simulator</h2>
 +
<div>
 +
<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>
 +
</div>
 +
</div>
 +
              </div><!--end entry-->
 +
          </div><!--end content-->
 +
 +
  <div id="sidebar">
 +
      <div id="doc-nav">
 +
<div>
 +
<h5>IGEM-SYSU-Software </h5>
 +
<div>
 +
<ul>
 +
<li>
 +
<a href="/videos/">Main Page</a>
 +
</li>
 +
<li>
 +
<a href="/documentation/">Album</a>
 +
</li>
 +
<li>
 +
<a href="/documentation-install">Video</a>
 +
</li>
 +
 +
</ul>
 +
</div>
 +
</div>
-
<!-- *** End of the alert box *** -->
+
<div>
 +
<h5>User Guide</h5>
 +
<div>
 +
<ul>
 +
<li>
 +
<a href="/
 +
documentation-user-guide-main-reminderfox-window">Download</a>
 +
</li>
 +
<li>
 +
<a href="/documentation-userguide-reminders">Tutorial</a>
 +
</li>
 +
<li>
 +
<a href="/documentation-user-guide-todos">Video</a>
 +
</li>
 +
                    <li>
 +
<a href="/documentation-user-guide-options-and-preferences">Options and Preferences</a>
 +
</li>
 +
<li>
 +
<a href="/documentation-user-guide-notifications">Email</a>
 +
</li>
 +
 +
</ul>
 +
</div>
 +
</div>
-
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
+
<div>
-
!align="center"|[[Team:SYSU-Software|Home]]
+
<h5>FAQ </h5>
-
!align="center"|[[Team:SYSU-Software/Team|Team]]
+
<div>
-
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=SYSU-Software Official Team Profile]
+
<ul>
-
!align="center"|[[Team:SYSU-Software/Project|Project]]
+
<li>
-
!align="center"|[[Team:SYSU-Software/Parts|Parts Submitted to the Registry]]
+
<a href="">Questions</a>
-
!align="center"|[[Team:SYSU-Software/Modeling|Modeling]]
+
</li>
-
!align="center"|[[Team:SYSU-Software/Notebook|Notebook]]
+
<li>
-
!align="center"|[[Team:SYSU-Software/Safety|Safety]]
+
<a href="">Troubleshooting</a>
-
!align="center"|[[Team:SYSU-Software/Attributions|Attributions]]
+
</li>
-
|}
+
<li>
 +
<a href="">Uninstalling</a>
 +
</li>
 +
<li>
 +
<a href="">Contact Us</a>
 +
</li>
 +
</ul>
 +
</div>
 +
</div>
 +
<div>
 +
<h5>E-mail Integration</h5>
 +
<div>
 +
<ul>
 +
<li>
 +
<a href="/documentation-email-messages">Messages</a>
 +
</li>
 +
<li>
 +
<a href="/documentation-email-invitations">Invitations</a>
 +
</li>
 +
</ul>
 +
</div>
 +
</div>
 +
</div>
 +
  </div><!--end sidebar-->
 +
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script>
 +
<script type="text/javascript">
 +
var name = "#doc-nav";
 +
var menuYloc = null;
 +
 +
$(document).ready(function(){
 +
menuYloc = parseInt($(name).css("top").substring(0,$(name).css("top").indexOf("px")))
 +
$(window).scroll(function () {
 +
offset = menuYloc+$(document).scrollTop()+"px";
 +
$(name).animate({top:offset},{duration:500,queue:false});
 +
});
 +
});
-
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.
+
</script>
-
== Project Details==
+
</div></div><!--end wrapper-->
 +
</div><!--end content-background-->
 +
<!--end footer-->
 +
<script type="text/javascript">
 +
  var _gaq = _gaq || [];
 +
  _gaq.push(['_setAccount', 'UA-15948744-2']);
 +
  _gaq.push(['_trackPageview']);
 +
  (function() {
 +
    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
 +
    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
 +
    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
 +
  })();
 +
</script></body><div id="footer">
 +
  <div class="wrapper clear">
 +
    <div id="footer-about" class="footer-column">
 +
      <h2>About</h2>
 +
                  <ul>
 +
<li>
 +
<a href="/developers">Developers</a>
 +
</li>
 +
<li>
 +
<a href="/help/">Contact Us</a>
 +
</li>
 +
</ul>
 +
            </div>
 +
    <div id="footer-flickr" class="footer-column">
 +
                              <h2>Links</h2>
 +
              <ul>
 +
                <li><a href="http://www.sysu.edu.cn">SUN YAT-SEN University</a></li>
 +
                <li><a href="http://lifescience.sysu.edu.cn/main/default/index.aspx">SYSU LifeSCience</a></li>
 +
              </ul>
 +
         
 +
                    </div>
 +
    <div id="footer-search" class="footer-column">
 +
      <h2>Facebook</h2>
-
=== Section I:  ===
+
    </div>
-
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.
+
    <div id="copyright">
 +
    </div><!--end copyright-->
 +
  </div><!--end wrapper-->
 +
</div>
 +
</body>
-
=== Section II  ===
 
-
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:  ===
+
</html>
-
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 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.
+
-
 
+
-
== Results ==
+

Revision as of 03:36, 23 September 2012

无标题 1
 

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.

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