Team:SYSU-Software/Tutorial

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{{:Team:SYSU-Software/menu}}
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<a href="/" class="sysu-title"></a>
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<a href="https://2012.igem.org/Team:SYSU-Software" class="sysu-title"></a>
        
        
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     </li>
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    <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Practice">Practice</a><!--input an em tag as a space,IE is gread need-->
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     <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Notebook">Notebook</a></li>  
     <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Notebook">Notebook</a></li>  
        
        
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    <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Practice">
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Tips</a><!--input an em tag as a space,IE is gread need-->
      
      
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   <div id="content">                  <div class="entry page clear">
   <div id="content">                  <div class="entry page clear">
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         <h1 id="doctitle" class="pagetitle">Software Tutorial</h1>
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         <h1 id="doctitle" class="pagetitle">Tutorial</h1>
<table class="doc-toc">
<table class="doc-toc">
<tbody>
<tbody>
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</div>
<ul id="toc-ul">
<ul id="toc-ul">
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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="#r1">Genome Browser</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="#r2">Biobrick</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="#r3">Riboswitch</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="#r4">SiRNA</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="#r5">Meta Network</a></li>
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<li class="toclevel-1"><a href="#r6">Simulator</a></li>
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<li class="toclevel-1"><a href="#r7">G-Circle</a></li>
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<li class="toclevel-1"><a href="#r8">Clotho</a></li>
</ul>
</ul>
</td>
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<div id="doc-contents">
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              </div>
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<h2 id="r1">Genome Browser</h2>
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<span></span>
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<div>
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<h1><a name="_Toc338881878">
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Procedure: File→Open Fasta→Open xml Component</p>
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<span lang="EN-US" style="font-size:14.0pt;line-height:240%">Home<o:p></o:p></span></a></h1>
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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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<p><span style="mso-bookmark:_Toc338881878">
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user has inputted, and the third ribbon shows the corresponding gene annotation.
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<span lang="EN-US" style="font-size:14.0pt;line-height:240%;mso-no-proof:yes"><v:shape id="图片_x0020_29" o:spid="_x0000_i1060" type="#_x0000_t75"
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You can click any annotation that you want, and then the sequence site will
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style='width:400.2pt;height:314.4pt;visibility:visible;mso-wrap-style:square'>
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automatically jump to the fragment related to it. Between those ribbons is an
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<img src="https://static.igem.org/mediawiki/igem.org/e/ef/Tutorial_%281%29.png" style="width: 650px;" o:title=""/ ></span></span></v:shape><o:p></o:p></p>
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adjustable slider, which can adjust your view location by sliding to the left or
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<p class="MsoNormal"><span lang="EN-US">On the left is the logo of
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to the right. Above the sequence are the head and tail of the location that you
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<b style="mso-bidi-font-weight:normal">BiArkit</b> which is created by 2012
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are viewing while the head and tail of the whole sequence are displayed in the
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SYSU-software igem team.<o:p></o:p></span></p>
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bottom textbox. What’s more, the textbox contains the length, product, tag of
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<p class="MsoNormal"><span lang="EN-US">In the main display window, there are  
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the sequence, and links of related papers are also included sometimes. </p>
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six buttons, G-Circle, Network Illustrator, RiboSwitch, Genome Browser, SiRNA,  
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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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Biobrick, and Simulator, which will take you to corresponding parts once
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</p></div>
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clicking.<o:p></o:p></span></p>
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<h2 id="r0">Biobrick</h2>
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<h1><a name="_Toc338881879">
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<div>
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<span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r1">Genome Browser</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"> <o:p></o:p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Procedure: Open your biobrick file(in xml format)</p>
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</span></h1>
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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>
 +
<o:p></o:p>
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<i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p>
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</span>
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<o:p></o:p>
</p>
</p>
-
</div>
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<p>
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<h2 id="r2">Riboswitch</h2>
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<o:p><img src="https://static.igem.org/mediawiki/igem.org/c/cd/Tutorial_%282%29.png"  "o:title=""/></o:p><o:p><img src="https://static.igem.org/mediawiki/igem.org/2/20/Tutorial_%283%29.png" o:title=""  style="width: 650px;"/></o:p><o:p></o:p>
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<div>
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</p>
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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 class="MsoNormal"><span lang="EN-US">In the main display window, the first
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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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ribbon is the sequence that the user has inputted, and the third ribbon shows
-
</p></div>
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the corresponding gene annotation. You can click any annotation that you want,
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<h2 id="r3">SiRNA</h2>
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and then the sequence site will automatically jump to the fragment related to
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<div>
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it. Between those ribbons is an adjustable slider, which can adjust your view
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<p>Procedure: Input your DNA sequence</p>
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location by sliding to the left or to the right. Above the sequence are the head
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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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and tail of the location that you are viewing while the head and tail of the
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</p></div>
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whole sequence are displayed in the bottom textbox. What’s more, the textbox
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<h2 id="r4">KEGG Network</h2>
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contains the length, product, tag of the sequence, and links of related papers
-
<div>
+
are also included sometimes. <o:p></o:p></span></p>
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<p>Procedure: open a file (in xml format)</p>
+
<p class="MsoNormal"><span lang="EN-US">On the left, there are two useful tools:
-
<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).
+
you can search the fragment that you want by position, product or name (Position
-
</p></div>
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represents the position of its head, Product and Name stand for products and
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<h2 id="r5">Fba</h2>
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names of related genes, both of them support fuzzy search), besides, whether you
-
<div>
+
choose product or name, a dialog box that contains names of related genes will
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<p>Procedure: Open a file (in xml format)→select your options→Go</p>
+
appear; the slider of Zoom is designed for regulating the display frame rate of
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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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the sequence. <o:p></o:p></span></p>
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</p></div>
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<h1><a name="_Toc338881880">
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<span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r2">Biobrick</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1>
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 +
">
 +
  &nbsp;<o:lock v:ext="edit" aspectratio="f"/><w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/></v:shape></o:wrapblock><i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p>
 +
</span></p>
 +
<p class="MsoNormal">
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/4/46/Tutorial_%284%29.png" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/0/08/Tutorial_%286%29.png" style="width: 650px;" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/5/58/Tutorial_%285%29.png" style="width: 650px;" o:title="Biobrick"/></o:p>
 +
</p>
 +
<p class="MsoNormal"><span lang="EN-US">Notice that there is a finder on the
 +
left; you can search biobricks by key words and then a window showing the search
 +
result will pop up. Bellow it is a list of biobrick. Turning to the right, a
 +
schematic diagram that shows components of the biobrick is on the top. And
 +
related information about the biobrick is below it.<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<h1><a name="_Toc338881881">
 +
<span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r3">RiboSwitch</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1>
 +
<p class="MsoNormal"><i style="mso-bidi-font-style:normal"><span lang="EN-US">
 +
Procedure</span></i><span lang="EN-US">: <o:p></o:p>
 +
</span></p>
 +
<p class="MsoNormal">
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/7/71/Tutorial_%287%29.png" style="width: 650px;" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/9/92/Tutorial_%288%29.png" style="width: 650px;" o:title="Biobrick"/></o:p>
 +
</p>
 +
<p class="MsoNormal"><span lang="EN-US">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
 +
<b style="mso-bidi-font-weight:normal">GO</b> 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 <b style="mso-bidi-font-weight:normal">GO</b> next time.<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<h1><a name="_Toc338881882">
 +
<span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r4">SiRNA</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1>
 +
<p class="MsoNormal">
 +
<i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p>
 +
</span></p>
 +
<p class="MsoNormal">
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/1/18/Tutorial_%289%29.png" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/1/10/Tutorial_%2810%29.png" style="width: 650px;"  o:title=""/></o:p>
 +
</p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<h1><a name="_Toc338881883">
 +
<span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r5">Network Illustrator</span></a><o:p></o:p></h1>
 +
<p class="MsoNormal">
 +
<i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p>
 +
</span></p>
 +
<p>
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/7/72/Tutorial_%2811%29.png" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/c/ce/Tutorial_%2812%29.png" style="width: 650px;"  o:title=""/></o:p></p>
 +
<p class="MsoNormal"><span lang="EN-US">In the main display window, you will see  
 +
a network from KEGG website. On the left, there is a finder; you can search
 +
elements in the network and a window that shows the search result will pop up.
 +
Bellow it is a box containing a list of files that 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
 +
<b style="mso-bidi-font-weight:normal">find element</b>).<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<h1><a name="_Toc338881884">
 +
<span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r5">Simulator</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1>
 +
<p class="MsoNormal"><i style="mso-bidi-font-style:normal"><span lang="EN-US">
 +
Procedure</span></i><span lang="EN-US">:  
 +
</span></p>
 +
<p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/f/f7/Tutorial_%2813%29.png" style="width: 650px;"  o:title=""/></p>
 +
<p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/a/ae/Tutorial_%2814%29.png" o:title="main"/></p>
 +
<p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/b/be/Tutorial_%2815%29.png" style="width: 650px;"  o:title=""/></p>
 +
<p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/e/e9/Tutorial_%2816%29.png" style="width: 650px;"  o:title=""/></p>
 +
<p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/d/da/Tutorial_%2817%29.png" style="width: 650px;"  o:title=""/>&nbsp;</p>
 +
<p class="MsoNormal">
 +
<o:wrapblock>
 +
<v:shape id="图片_x0020_15" o:spid="_x0000_s2052"
 +
  type="#_x0000_t75" style='position:absolute;left:0;text-align:left;
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  mso-wrap-distance-right:9pt;mso-wrap-distance-bottom:0;
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  mso-position-vertical:absolute;mso-position-vertical-relative:text;
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  mso-width-percent:0;mso-height-percent:0;mso-width-relative:margin;
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  mso-height-relative:margin'>
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  &nbsp;<w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/></v:shape></o:wrapblock><br style="mso-ignore:vglayout" clear="ALL">
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<span lang="EN-US">There are 5 options for you to select: exhaustive single  
 +
deletion, reaction deletion, Fva analysis, <span style="mso-no-proof:yes">
 +
Perturbation analysis</span> and <span style="mso-no-proof:yes">PhPP analysis</span>.
 +
They with FBA solve will be introduced in detail. You can select all of them or  
 +
part of them, or even nothing, then click <b style="mso-bidi-font-weight:normal">
 +
Go</b>. 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.<o:p></o:p></span></p>
 +
<p style="mso-para-margin-top: .5gd; mso-para-margin-right: 0cm; mso-para-margin-bottom: 0cm; mso-para-margin-left: 18.0pt; mso-para-margin-bottom: .0001pt; mso-char-indent-count: 0; mso-list: l0 level1 lfo2; text-justify: inter-ideograph;" class="style1">
 +
<![if !supportLists]>
 +
<span lang="EN-US" style="mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
 +
mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin">
 +
<span style="mso-list:Ignore">1.<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
</span></span></span><![endif]><span lang="EN-US">FBA_solve<o:p></o:p></span></p>
 +
<p style="mso-para-margin-top: .5gd; mso-para-margin-right: 0cm; mso-para-margin-bottom: 0cm; mso-para-margin-left: 18.0pt; mso-para-margin-bottom: .0001pt; mso-char-indent-count: 0; mso-list: l0 level1 lfo2; text-justify: inter-ideograph;" class="style1">
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/b/b6/Tutorial_%2818%29.png" style="width: 650px;"  o:title=""/></o:p></p>
 +
<p class="MsoNormal">Above<span lang="EN-US"> column displays names of the
 +
reactions while the right one displays the flux amount of each reaction<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US">2. exanstive single deletion<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US">Calculate the flux amount of the
 +
objective reaction when each other reaction is deleted one by one.<o:p></o:p></span></p>
 +
<p class="MsoNormal">
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/4/47/Tutorial_%2819%29.png" style="width: 650px;"  o:title=""/></o:p></p>
 +
<p class="MsoNormal"><span lang="EN-US">Left column display names of the
 +
reactions <o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US">The right one displays the flux amount
 +
of objective reaction the user has chosen, when each other reaction is deleted
 +
one by one.<o:p>&nbsp;</o:p></span></p>
 +
<span lang="EN-US" style="mso-no-proof:yes">
 +
<v:shape id="图片_x0020_24"
 +
o:spid="_x0000_i1045" type="#_x0000_t75" alt="说明: super optimal dels.bmp"
 +
style='width:117.6pt;height:40.2pt;visibility:visible;mso-wrap-style:square'><p><span lang="EN-US" style="mso-no-proof:yes">
 +
<img src="https://static.igem.org/mediawiki/igem.org/5/5b/Tutorial_%2820%29.png" o:title="lethal deletions" height="284"/><img src="https://static.igem.org/mediawiki/igem.org/d/d3/Tutorial_%2821%29.png" o:title="sub optimal dels"/><img src="https://static.igem.org/mediawiki/igem.org/3/3b/Tutorial_%2822%29.png" o:title="super optimal dels"
 +
  croptop="3449f" cropbottom="34000f"/></span></p></v:shape>
 +
</span><p class="MsoNormal"><span lang="EN-US">when rolling down the screen, you can
 +
see the reaction-names related to lethal deletions, sub optimal deletions and
 +
super optimaldeletions<span style="mso-no-proof:yes">.<o:p></o:p></span></span></p>
 +
<p class="MsoNormal">
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/b/b7/Tutorial_%2823%29.png" o:title=""/></o:p></p>
 +
<p class="MsoNormal"><span lang="EN-US">This graph shows how many lethal
 +
knockouts in each reaction subsystem. The information of the reaction subsystem
 +
can be attained in SBML <o:p></o:p>
 +
</span></p>
 +
<p class="MsoNormal">
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/1/19/Tutorial_%2824%29.png" o:title=""/></o:p></p>
 +
<p class="MsoNormal"><span lang="EN-US">This hist graph shows the frequency of
 +
reaction which has different quantified effect showed in the X-axis opon
 +
objective reaction.<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US">3. reaction deletion<o:p></o:p></span></p>
 +
<p class="MsoNormal">
 +
<o:p><img src="https://static.igem.org/mediawiki/igem.org/4/48/Tutorial_%2825%29.png" style="width: 650px;"  o:title=""/></o:p></p>
 +
<p class="MsoNormal"><span lang="EN-US">Middle column displays the flux amount
 +
of the wild type while the right column displays the mutant type, which is
 +
calculated based on the deletion of one chosen reaction.<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US">4. FVA analysis<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><o:p>&nbsp;<img src="https://static.igem.org/mediawiki/igem.org/a/a9/Tutorial_%2826%29.png" style="width: 650px;"  o:title=""/></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">5.Perturbation
 +
analysis:<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">
 +
<v:shape id="图片_x0020_11"
 +
o:spid="_x0000_i1041" type="#_x0000_t75" style='width:414pt;height:411pt;
 +
visibility:visible;mso-wrap-style:square'>
 +
&nbsp;</v:shape><o:p><img src="https://static.igem.org/mediawiki/igem.org/c/ce/Tutorial_%2827%29.png" o:title=""/></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">X-axis refers
 +
to the continuously increasing flux value of the chosen reaction.<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">Y-axis refers
 +
to the flux value of the objective reaction according to the variation of the
 +
flux value of chosen reaction in the X-axis<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><o:p>&nbsp;</o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><o:p>&nbsp;</o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">6.PhPP analysis <o:p></o:p>
 +
</span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">
 +
<v:shape id="图片_x0020_10"
 +
o:spid="_x0000_i1040" type="#_x0000_t75" style='width:409.2pt;height:433.8pt;
 +
visibility:visible;mso-wrap-style:square'>
 +
&nbsp;</v:shape><o:p><img src="https://static.igem.org/mediawiki/igem.org/7/78/Tutorial_%2828%29.png" o:title=""/></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">The value
 +
marked on the contour represents the flux value of the objective reaction based
 +
on the variation of two chosen reactions The color of the graph changes
 +
according to the altitude, namely, the objective flux value.<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<h1><a name="_Toc338881885">
 +
<span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r7">G-Circle</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1>
 +
<p class="MsoNormal">
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<o:wrapblock>
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">
 +
  &nbsp;<o:lock v:ext="edit" aspectratio="f"/><w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/></v:shape></o:wrapblock><br style="mso-ignore:vglayout" clear="ALL">
 +
<i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">:</span></p>
 +
<p class="MsoNormal">
 +
&nbsp;<img src="https://static.igem.org/mediawiki/igem.org/a/ab/Tutorial_%2829%29.png" o:title=""
 +
  croptop="-3052f"/></p>
 +
<p class="MsoNormal">
 +
&nbsp;<img src="https://static.igem.org/mediawiki/igem.org/1/1d/Tutorial_%2830%29.png"  style="width: 650px;" o:title=""/></p>
 +
<p class="MsoNormal"><span lang="EN-US">&nbsp;<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">
 +
<v:shape id="图片_x0020_18"
 +
o:spid="_x0000_i1039" type="#_x0000_t75" style='width:442.2pt;height:249pt;
 +
visibility:visible;mso-wrap-style:square'>
 +
&nbsp;</v:shape></span><span lang="EN-US">You can open several file so that you can
 +
compare the difference of these genomes. Each genome have 2 circles in the
 +
picture: the outer one is the genes of the genome, the inner is the expression
 +
level of corresponding genes. By the way, right click different sites in the
 +
small panoramic window or left click and drag the picture in the zoom window,
 +
you can move to anywhere you want to enlarge and see more details in the
 +
amplifier window.<o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
 +
<h1><a name="_Toc338881886"><span lang="EN-US" id="r8">Clotho</span></a><span lang="EN-US"><o:p></o:p></span></h1>
 +
<p class="MsoNormal"><span lang="EN-US">All above seven parts have been
 +
developed into <b style="mso-bidi-font-weight:normal">
 +
<i style="mso-bidi-font-style:normal">Clotho</i></b> apps and have been updated
 +
into <b style="mso-bidi-font-weight:normal">
 +
<i style="mso-bidi-font-style:normal">Clotho, </i></b>which has met the
 +
requirements for gold medal of IGEM.<o:p></o:p></span></p>
 +
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Latest revision as of 23:56, 26 October 2012

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无标题 1
 

Tutorial

Contents

Home

On the left is the logo of BiArkit which is created by 2012 SYSU-software igem team.

In the main display window, there are six buttons, G-Circle, Network Illustrator, RiboSwitch, Genome Browser, SiRNA, Biobrick, and Simulator, which will take you to corresponding parts once clicking.

Genome Browser

Procedure:

In the main display window, the first ribbon is the sequence that the user has inputted, and the third ribbon shows the corresponding gene annotation. You can click any annotation that you want, and then the sequence site will automatically jump to the fragment related to it. Between those ribbons is an adjustable slider, which can adjust your view location by sliding to the left or to the right. Above the sequence are the head and tail of the location that you are viewing while the head and tail of the whole sequence are displayed in the bottom textbox. What’s more, the textbox contains the length, product, tag of the sequence, and links of related papers are also included sometimes.

On the left, there are two useful tools: you can search the fragment that you want by position, product or name (Position represents the position of its head, Product and Name stand for products and names of related genes, both of them support fuzzy search), besides, whether you choose product or name, a dialog box that contains names of related genes will appear; the slider of Zoom is designed for regulating the display frame rate of the sequence.

Biobrick

 Procedure:

Notice that there is a finder on the left; you can search biobricks by key words and then a window showing the search result will pop up. Bellow it is a list of biobrick. Turning to the right, a schematic diagram that shows components of the biobrick is on the top. And related information about the biobrick is below it.

 

RiboSwitch

Procedure:

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.

 

SiRNA

Procedure:

 

Network Illustrator

Procedure:

In the main display window, you will see a network from KEGG website. On the left, there is a finder; you can search elements in the network and a window that shows the search result will pop up. Bellow it is a box containing a list of files that 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).

 

Simulator

Procedure:

 

 
There are 5 options for you to select: exhaustive single deletion, reaction deletion, Fva analysis, Perturbation analysis and PhPP analysis. They with FBA solve will be introduced in detail. 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.

1.      FBA_solve

Above column displays names of the reactions while the right one displays the flux amount of each reaction

 

2. exanstive single deletion

Calculate the flux amount of the objective reaction when each other reaction is deleted one by one.

Left column display names of the reactions

The right one displays the flux amount of objective reaction the user has chosen, when each other reaction is deleted one by one. 

when rolling down the screen, you can see the reaction-names related to lethal deletions, sub optimal deletions and super optimaldeletions.

This graph shows how many lethal knockouts in each reaction subsystem. The information of the reaction subsystem can be attained in SBML

This hist graph shows the frequency of reaction which has different quantified effect showed in the X-axis opon objective reaction.

 

3. reaction deletion

Middle column displays the flux amount of the wild type while the right column displays the mutant type, which is calculated based on the deletion of one chosen reaction.

 

4. FVA analysis

 

5.Perturbation analysis:

 

X-axis refers to the continuously increasing flux value of the chosen reaction.

Y-axis refers to the flux value of the objective reaction according to the variation of the flux value of chosen reaction in the X-axis

 

 

6.PhPP analysis

 

The value marked on the contour represents the flux value of the objective reaction based on the variation of two chosen reactions The color of the graph changes according to the altitude, namely, the objective flux value.

 

G-Circle

 
Procedure:

 

 

 

 You can open several file so that you can compare the difference of these genomes. Each genome have 2 circles in the picture: the outer one is the genes of the genome, the inner is the expression level of corresponding genes. By the way, right click different sites in the small panoramic window or left click and drag the picture in the zoom window, you can move to anywhere you want to enlarge and see more details in the amplifier window.

 

Clotho

All above seven parts have been developed into Clotho apps and have been updated into Clotho, which has met the requirements for gold medal of IGEM.

 

Home

 

Genome Browser

 

  Biobrick

 

  RiboSwitch

SiRNA

 

Network Illustrator

 

  Simulator 

 

  G-Circle

 

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