Team:SYSU-Software/Tutorial

From 2012.igem.org

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     </li>
     </li>
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    <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/WorldJamboree">
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<li class="toclevel-1"><a href="#r6">Simulator</a></li>
<li class="toclevel-1"><a href="#r6">Simulator</a></li>
<li class="toclevel-1"><a href="#r7">G-Circle</a></li>
<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>
</td>
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<div id="doc-contents">
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<h1 id="r1"><a name="_Toc336260397">Genome Browser</a></h1>
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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 class="MsoNormal"><span lang="EN-US">On the left is the logo of
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<b style="mso-bidi-font-weight:normal">BiArkit</b> which is created by 2012
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SYSU-software igem team.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US">In the main display window, there are
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six buttons, G-Circle, Network Illustrator, RiboSwitch, Genome Browser, SiRNA,
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Biobrick, and Simulator, which will take you to corresponding parts once
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clicking.<o:p></o:p></span></p>
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  <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/>
+
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</v:shape></o:wrapblock><br clear="ALL">
+
-
<span lang="EN-US">Procedure: <o:p></o:p>
+
-
</span></p>
+
<p>
<p>
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/0/03/Image0001.png"></p>
+
<o:p></o:p>
-
<p>
+
<i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p>
-
<img src="https://static.igem.org/mediawiki/igem.org/f/f5/Image002.jpg"></p>
+
</span>
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<p>
+
<o:p></o:p>
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<img src="https://static.igem.org/mediawiki/igem.org/1/1e/Image0003.jpg" style="width: 650px;"><br clear="ALL">
+
</p>
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<span lang="EN-US">
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<p>
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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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type="#_x0000_t75">
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</p>
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<v:imagedata src="image003.jpg" o:title=""/>
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<p class="MsoNormal"><span lang="EN-US">In the main display window, the first  
-
</v:shape>In the main display window, the first ribbon is the sequence that the  
+
ribbon is the sequence that the user has inputted, and the third ribbon shows  
-
user has inputted, and the third ribbon shows the corresponding gene annotation.  
+
the corresponding gene annotation. You can click any annotation that you want,  
-
You can click any annotation that you want, and then the sequence site will  
+
and then the sequence site will automatically jump to the fragment related to  
-
automatically jump to the fragment related to it. Between those ribbons is an  
+
it. Between those ribbons is an adjustable slider, which can adjust your view  
-
adjustable slider, which can adjust your view location by sliding to the left or  
+
location by sliding to the left or to the right. Above the sequence are the head  
-
to the right. Above the sequence are the head and tail of the location that you  
+
and tail of the location that you are viewing while the head and tail of the  
-
are viewing while the head and tail of the whole sequence are displayed in the  
+
whole sequence are displayed in the bottom textbox. What’s more, the textbox  
-
bottom textbox. What’s more, the textbox contains the length, product, tag of  
+
contains the length, product, tag of the sequence, and links of related papers  
-
the sequence, and links of related papers are also included sometimes. <o:p></o:p>
+
are also included sometimes. <o:p></o:p></span></p>
-
</span></p>
+
<p class="MsoNormal"><span lang="EN-US">On the left, there are two useful tools:  
-
<p><span lang="EN-US">On the left, there are two useful tools: you can search  
+
you can search the fragment that you want by position, product or name (Position  
-
the fragment that you want by position, product or name (Position represents the  
+
represents the position of its head, Product and Name stand for products and  
-
position of its head, Product and Name stand for products and names of related  
+
names of related genes, both of them support fuzzy search), besides, whether you  
-
genes, both of them support fuzzy search), besides, whether you choose product  
+
choose product or name, a dialog box that contains names of related genes will  
-
or name, a dialog box that contains names of related genes will appear; the  
+
appear; the slider of Zoom is designed for regulating the display frame rate of  
-
slider of Zoom is designed for regulating the display frame rate of the
+
the sequence. <o:p></o:p></span></p>
-
sequence. <o:p></o:p></span></p>
+
<h1><a name="_Toc338881880">
-
<h1 id="r2"><a name="_Toc336260391"><span lang="EN-US">Biobrick</span></a><span lang="EN-US"><o:p></o:p></span></h1>
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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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 +
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 +
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 +
AAAAAAAAAE8KAABjbGlwYm9hcmQvdGhlbWUvdGhlbWUxLnhtbFBLAQItABQABgAIAAAAIQADwKI8
 +
EQQAAN9BAAAeAAAAAAAAAAAAAAAAAGkRAABjbGlwYm9hcmQvZGlhZ3JhbXMvY29sb3JzMS54bWxQ
 +
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 +
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 +
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 +
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 +
LnhtbFBLBQYAAAAACgAKAOYCAABMIAAAAAA=
">
">
-
   <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image004.png" o:title=""/>
+
   &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>
-
  <o:lock v:ext="edit" aspectratio="f"/>
+
-
  <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/>
+
-
</v:shape></o:wrapblock><br clear="ALL">
+
-
<span lang="EN-US">Procedure: <o:p></o:p>
+
</span></p>
</span></p>
-
<p>
+
<p class="MsoNormal">
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/6/6a/Image0004.png"></p>
+
<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>
-
<img src="https://static.igem.org/mediawiki/igem.org/b/b7/Image005.jpg" style="width: 650px;></p>
+
<p class="MsoNormal"><span lang="EN-US">Notice that there is a finder on the  
-
<p><span lang="EN-US">
+
left; you can search biobricks by key words and then a window showing the search
-
<v:shape id="图片_x0020_19"
+
result will pop up. Bellow it is a list of biobrick. Turning to the right, a
-
o:spid="_x0000_i1045" type="#_x0000_t75">
+
schematic diagram that shows components of the biobrick is on the top. And
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image005.jpg" o:title=""/>
+
related information about the biobrick is below it.<o:p></o:p></span></p>
-
</v:shape>In the main display window, you can view the information of existing
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
biobricks, which are all localized and enable you to get rid of loading when you
+
<h1><a name="_Toc338881881">
-
are studying a biobrick. On the left is the list of the files that you have
+
<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>
-
opened. <o:p></o:p></span></p>
+
<p class="MsoNormal"><i style="mso-bidi-font-style:normal"><span lang="EN-US">
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
Procedure</span></i><span lang="EN-US">: <o:p></o:p>
-
<h1 id="r3"><a name="_Toc336260392"><span lang="EN-US">Riboswitch</span></a><span lang="EN-US"><o:p></o:p></span></h1>
+
-
<p><span lang="EN-US">Procedure: <span>
+
-
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-
type="#_x0000_t75"
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">
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<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image006.png" o:title=""
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  croptop="-7957f" cropbottom="-1952f"/>
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<o:lock v:ext="edit" aspectratio="f"/>
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</v:shape></span><o:p></o:p>
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</span></p>
</span></p>
-
<p>
+
<p class="MsoNormal">
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/3/3e/Image006.png" style="width: 630px;></p>
+
<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>
-
<img src="https://static.igem.org/mediawiki/igem.org/5/5c/Image0007.jpg" style="width: 650px;></p>
+
<p class="MsoNormal"><span lang="EN-US">On the right is the main operating area  
-
<p>
+
and you can choose your target type (your experimental object) and corresponding  
-
<v:shape id="图片_x0020_12"
+
target name, aptamer and regulation direction. Attention should be paid to the  
-
o:spid="_x0000_i1042" type="#_x0000_t75">
+
input box named Input your Target. You can search your target name by key words  
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image008.jpg" o:title=""/>
+
or even several letters of it. It should be useful to you. Click
-
</v:shape>
+
<b style="mso-bidi-font-weight:normal">GO</b> and you will see a picture. The  
-
<img src="https://static.igem.org/mediawiki/igem.org/0/06/Image008.jpg" style="width: 650px;></p>
+
-
<p><span lang="EN-US">
+
-
<v:shape id="图片_x0020_12"
+
-
o:spid="_x0000_i1042" type="#_x0000_t75">
+
-
</v:shape>
+
-
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  
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  
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,  
box. It records your choices that you have made in created riboswich project,  
-
and you need only click GO next time.<o:p></o:p></span></p>
+
and you need only click <b style="mso-bidi-font-weight:normal">GO</b> next time.<o:p></o:p></span></p>
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
<h1 id="r4"><a name="_Toc336260393"><span lang="EN-US">SiRNA</span></a><span lang="EN-US"><o:p></o:p></span></h1>
+
<h1><a name="_Toc338881882">
-
<p><o:wrapblock>
+
<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>
-
<v:shape id="图示_x0020_6" o:spid="_x0000_s1028"
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<p class="MsoNormal">
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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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jw3TnBJxLaH3xNPxCNTs8UQfT9bHE9lUqYL2BL0VdvOfQ+iuUJQZ7DGnmdXtJLUuFUhQqkVjVVFa
+
-
nwvPFxeEsStMKcihgboBHBE72AJBxQaueAeZ8+KerVdPUIJnZ8nY51zIVZ2hEXC5zawvsamruzbp
+
-
B4VLn/5j1bY2QHZYXRSu9x/rPavaOnMa2PDxjmUzPyBtdzK57H1YQXiAKnZSSn7mGh8qcF59opUo
+
-
uwNq9qZLOTxMcvUAeYH0gXBOl+4XysAcmwlmoRHYfc0LlsG9kjJRrnXpWyJnRyvfVbLHmV/IzMlC
+
-
ZgK49p7Yi2tZN5bsVaPJ1c2CGP6xgccVx4sOogKjc5bLHOvrrvP5adtLbzBfUHvYnf5fMfj7j9/+
+
-
+vP3l2JwcMo5CsXoek97yvyJ+/H5AySaTAZn7gUSxeM4DvFvXyGDJIqn8EBxr5DJWZwMXbiPkUJ7
+
-
aw93eMY5aXh1XvwDAAD//wMAUEsBAi0AFAAGAAgAAAAhAGAmNyhcAQAAdgQAABMAAAAAAAAAAAAA
+
-
AAAAAAAAAFtDb250ZW50X1R5cGVzXS54bWxQSwECLQAUAAYACAAAACEAOP0h/9YAAACUAQAACwAA
+
-
AAAAAAAAAAAAAACNAQAAX3JlbHMvLnJlbHNQSwECLQAUAAYACAAAACEAYoicwhcGAADbEgAAFgAA
+
-
AAAAAAAAAAAAAACMAgAAZHJzL2RpYWdyYW1zL2RhdGExLnhtbFBLAQItABQABgAIAAAAIQDpLGRF
+
-
JwEAAGcCAAAOAAAAAAAAAAAAAAAAANcIAABkcnMvZTJvRG9jLnhtbFBLAQItABQABgAIAAAAIQDS
+
-
M9z5HQEAAGYDAAAZAAAAAAAAAAAAAAAAACoKAABkcnMvX3JlbHMvZTJvRG9jLnhtbC5yZWxzUEsB
+
-
Ai0AFAAGAAgAAAAhAMFYqO3hAAAACQEAAA8AAAAAAAAAAAAAAAAAfgsAAGRycy9kb3ducmV2Lnht
+
-
bFBLAQItABQABgAIAAAAIQADwKI8EQQAAN9BAAAYAAAAAAAAAAAAAAAAAIwMAABkcnMvZGlhZ3Jh
+
-
bXMvY29sb3JzMS54bWxQSwECLQAUAAYACAAAACEAa5uWFBgEAAANUQAAHAAAAAAAAAAAAAAAAADT
+
-
EAAAZHJzL2RpYWdyYW1zL3F1aWNrU3R5bGUxLnhtbFBLAQItABQABgAIAAAAIQArnMf85QQAAPYR
+
-
AAAYAAAAAAAAAAAAAAAAACUVAABkcnMvZGlhZ3JhbXMvbGF5b3V0MS54bWxQSwECLQAUAAYACAAA
+
-
ACEAaBsu41UEAADxCgAAGQAAAAAAAAAAAAAAAABAGgAAZHJzL2RpYWdyYW1zL2RyYXdpbmcxLnht
+
-
bFBLBQYAAAAACgAKAJsCAADMHgAAAAA=
+
-
">
+
-
  <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image009.png" o:title=""/>
+
-
  <o:lock v:ext="edit" aspectratio="f"/>
+
-
  <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/>
+
-
</v:shape></o:wrapblock><br clear="ALL">
+
-
<span lang="EN-US">Procedure: <o:p></o:p>
+
</span></p>
</span></p>
-
<p>
+
<p class="MsoNormal">
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/c/c1/Image009.png"></p>
+
<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>
-
<img src="https://static.igem.org/mediawiki/igem.org/5/5d/Image0010.jpg" style="width: 650px;></p>
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
<p><span lang="EN-US">
+
<h1><a name="_Toc338881883">
-
<v:shape id="图片_x0020_5"
+
<span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r5">Network Illustrator</span></a><o:p></o:p></h1>
-
o:spid="_x0000_i1041" type="#_x0000_t75">
+
<p class="MsoNormal">
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image010.jpg" o:title=""/>
+
<i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p>
-
</v:shape>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</span><span>——</span><span lang="EN-US">one
+
-
is solved by Tom Tuschl’s method and the other is by rational design. <o:p></o:p>
+
</span></p>
</span></p>
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
<p>
-
<h1 id="r5"><a name="_Toc336260394"><span lang="EN-US">MetaNetwork</span></a><span lang="EN-US"><o:p></o:p></span></h1>
+
<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><o:wrapblock>
+
<p class="MsoNormal"><span lang="EN-US">In the main display window, you will see
-
<v:shape id="图示_x0020_7" o:spid="_x0000_s1029"
+
a network from KEGG website. On the left, there is a finder; you can search
-
  type="#_x0000_t75" o:gfxdata="UEsDBBQABgAIAAAAIQBgJjcoXAEAAHYEAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbLSUy07DMBRE
+
elements in the network and a window that shows the search result will pop up.
-
90j8Q+QtStx2gRBq0kVTVggQlA+4sm9Sq34E20mbv8dJU1U8Ctl06cfMHF2PPF/slYwatE4YnZJp
+
Bellow it is a box containing a list of files that you have opened. Pay
-
MiERama40GVK3tcP8R2JnAfNQRqNKWnRkUV2fTVftxW6KKi1S8nG++qeUsc2qMAlpkIdTgpjFfiw
+
attention that you can right click the main display window to open another KEGG
-
tCWtgG2hRDqbTG4pM9qj9rHvPEg2z7GAWvpotQ/bBxKL0pFoebjYZaUEqkoKBj6Q0kbzbynxkJAE
+
xml file or to search any element in the network (choose
-
ZX/HbUTlbgIGob8mdCfnAwbdcxiNFRyjF7D+CVTAoNw6ijOTG5b87dFBKhebohAMk9y6Va86Mp3z
+
<b style="mso-bidi-font-weight:normal">find element</b>).<o:p></o:p></span></p>
-
5gJKC8pRDh6mIzK+jnvI44bVKgw54RZ24TWVTAbjPNiOZpDQmtpfgOKxNx7N8VELtn3zrcQLsPS+
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
o1GYkca6C2Ase+PRHMPDjgE5tfBnGw71+DfV7LTFZkQbT1mh8XmQvWJzdKf9r5F9AgAA//8DAFBL
+
<h1><a name="_Toc338881884">
-
AwQUAAYACAAAACEAOP0h/9YAAACUAQAACwAAAF9yZWxzLy5yZWxzpJDBasMwDIbvg72D0X1xmsMY
+
<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>
-
o04vo9Br6R7A2IpjGltGMtn69jODwTJ621G/0PeJf3/4TItakSVSNrDrelCYHfmYg4H3y/HpBZRU
+
<p class="MsoNormal"><i style="mso-bidi-font-style:normal"><span lang="EN-US">
-
m71dKKOBGwocxseH/RkXW9uRzLGIapQsBuZay6vW4mZMVjoqmNtmIk62tpGDLtZdbUA99P2z5t8M
+
Procedure</span></i><span lang="EN-US">:  
-
GDdMdfIG+OQHUJdbaeY/7BQdk9BUO0dJ0zRFd4+qPX3kM66NYjlgNeBZvkPGtWvPgb7v3f3TG9iW
+
-
Oboj24Rv5LZ+HKhlP3q96XL8AgAA//8DAFBLAwQUAAYACAAAACEA0JokxwkGAADDEgAAFgAAAGRy
+
-
cy9kaWFncmFtcy9kYXRhMS54bWzcWM1u3DYQvhfoOxA6tSiYpf6lRdaBflsDbhLETnooioIrcXfV
+
-
Uj8htbE3Qc499Figpz5C0Tfo27R5jg4p7Xrt2MjGQYOiPsjaofRp5uPHmSHvP7ioOXrBhKzaZmaY
+
-
94iBWFO0ZdUsZ8bTsxwHBpI9bUrK24bNjA2TxoOjTz+5Xy7raUl7+nVbMo4ApZFTsM2MVd9308lE
+
-
FitWU3mv7VgDo4tW1LSHn2I5KQU9B/yaTyxCvElZ0aWgtTGC0DtA1LRqjCPtU9efyH57i2rl3XE5
+
-
M145qZ1bdh5jEmYWdkic4Si3YxyGcWinnuOGcfTaQP2mgyjLttjCiVPWI96egV3hrEUzratCtLJd
+
-
9PeKtp60i0VVsPEfFb0Kyp0EE0437bqfdKItmJSmASAJ7RXGaDLQc/n+sM/XVfGj7DecTWRVd5w5
+
-
CmdEHiwGKu4AXLS8FXJCi4I1vfm9pVBG2NFmoG7FSwEyMSYDw7J7LOB2osTQ3cR6HpPMsp0Ux5Zi
+
-
PcocHHuJhQnJHD/NstD3yOsrVOtPnM2Mb9/8+tOb337/DtxYyx4MVz56dJ9OLxaiVv9hAtAFjBMS
+
-
GmgzM4jyjk7ZRY8KsFvEc0LiAQ6MucQJLFc9MLkE6ITsv2RtjdTNzBDtuimfsKIHv+iUvtB6otNl
+
-
iRpagzho+YOBFjUHob6gHMF3if4kII4Pw90WU0GAusu84hyJtv+m6lenK6pERjT+Um7xJepauTVL
+
-
sZwnXCD4wsxw8sCMU/34as0eQbzaPAYqaX/dxNf1dRPl3YpeN8oVLdkA5qo4BuYAEFb1YDbtvfBG
+
-
pzR5S6lDG50O9FPK8tEdD5WHd3Zcz94wEx/fc+cWz93RDjq6TjmYdorhVYOoytOmBzlHvYNkQTmD
+
-
FLMV5FZ6amZ4o65Nq6Q4LIDBwhYLEPuoQkhZTJyuynM052vxhAKW8hKgy0otDkuzDT8gDbh6BIZu
+
-
0vUVNhUCYKjvax0O2rJviXPngxbanns6z6icM2QfSDh0Om/LjU5CEKDsT3ViVPZOXeBBuDwWiGue
+
-
WIOfngJJL4EyiEP7I1te6dWpHpUbuVt0UKLK9hzSNpU9GGdGrv/G3HHlNU57mApVOha0gJWdUF7N
+
-
RTWIktG9kS/qBjM6DBTy2kAhR3DwWHnTH6niiShaVJyhz+ATqlgPlfRzlcCAALjqZ1lTPqaCPtnF
+
-
+nKFk4cGorw/+Y/E/vcfP//15y/viv0yEB0cTKOedRXqrVXGjRyYT9PDcWgl2LFjD4deFuE0cUCi
+
-
uRUnJN7V9o6KM0EbCQXhohlaAz/LoR/wseemOXaCwASgLMO2ZdlpYnqpl/pXihSsHuWLUuJ4+24p
+
-
XsY1ivHmCRoW5kFR+44buUmUYzPwHAyROlj9BredNI9I6pups4taVvP/R9RRZmUksnNs+VGIHZ/4
+
-
ELXpYJKGxIws288ycxd1J6BdHZtB3cgpQyRlWxynh/eE6qWHuvSrK+Q7ZdCZJmkgJao8oqUJ1hPd
+
-
9D2jAqqjskGeHBUCg9VL9hV00pzJIf+xCwpNhprxm14fjdB+XlHb7asgIXlmQjeLiQ98OGZs4zg2
+
-
fex7ThS6cQhje6sA/Nn5rVrcq8wc1rfplwZmGmi094g5mUPbomzQ9+7YOi6hHXuLPnPnxtv0zdec
+
-
sz5r6Byq2tiQvC9hituPsDzHedFlVH0Sksv+/d5OJMvsnCQhwTHMCGSr0MMBSVLsQWMcOHmWmhb0
+
-
xONORJH3aAE1SxTvs40pmdRbjVcHLheAfySg1qs6D69u79XXP2zXM6of2NhjwDko4d455gPFe1vM
+
-
Y33QdB9YWbbZVb9zWF6+kZjEjQIrtFxQhZtiJyEujn07Amn4ISF+nNmZdas0Dgx7J40D88VtNP07
+
-
0ohS2w8UA7mZQSl3kwQHsRtiPwviCDbsgeVfFjUlT+h69tfHgXr/L5GgM8d+upgvR3Gcr1rY5g/p
+
-
H7azY4uuNrZrUb11THLjscR41qIOJYLdSQsgyu7y9CYDwPEAR3YfAIvEcNYijkvXQHXVPGPQNt/5
+
-
PAgCh+4Woh0L5JYBzdfu6OnoHwAAAP//AwBQSwMEFAAGAAgAAAAhAPuUGacnAQAAZwIAAA4AAABk
+
-
cnMvZTJvRG9jLnhtbKSSTUsDMRCG74L/IeRu066lbkN3eylCT170B8RkshvIl5PU1X/v9AOpJ0Fv
+
-
78zAw8ObbLYfwbN3wOJS7PhiNucMok7GxaHjL8+Pdy1npapolE8ROv4JhW/725vNlCU0aUzeADKC
+
-
xCKn3PGx1iyFKHqEoMosZYh0tAmDqjTiIAyqiejBi2Y+X4kpocmYNJRC2935yPsT31rQ9cnaApX5
+
-
ji+b1UPDWSXPtmlJDI+7Zr3g7LXjq3axXnPRb5QcUOXR6YuW+oNVUC6SxDdqp6piB3R/QBmnyCcQ
+
-
zQxBIvi9KRczWvwDeIFQCb+Xnqx1GnZJHwLEem6eVFSlZy+jy4XKlIZscG+oTpQ+nTLVjfKtnPL9
+
-
MetzXh6LFj/quZ4pX/+P/gsAAP//AwBQSwMEFAAGAAgAAAAhANIz3PkdAQAAZgMAABkAAABkcnMv
+
-
X3JlbHMvZTJvRG9jLnhtbC5yZWxztJNdT8MgFIbvTfwPhHtLOz9jRndhY7LEG3X+gBNKWzLgVGBq
+
-
/7246WITVr3ZJTzhPU9yXuaLD6PJm3ReoeW0yHJKpBVYK9ty+rK6P7uhxAewNWi0ktNBerooT0/m
+
-
T1JDiI98p3pPYor1nHYh9LeMedFJAz7DXtpIGnQGQjy6lvUg1tBKNsvzK+Z+Z9BylEmWNaduWZ9T
+
-
shr6OPnvbGwaJWSFYmOkDYkRrFbQOjCPGyXWz2HQMoaDa2Xg9Bt59rqHRRblKUt7zY7g9QADbkLC
+
-
SW/BpE9xBJ8KAiRs6ng96XJ5wMUo4dBjEzKBhu3W9bWm63ETftZUOXiPPUwZ7MikxMUBiUQp/12c
+
-
O9TofEJIbMHeh41+R/kJAAD//wMAUEsDBBQABgAIAAAAIQAZiIvr3AAAAAkBAAAPAAAAZHJzL2Rv
+
-
d25yZXYueG1sTI9BTsMwEEX3SNzBGiR2rd0EpTTEqRAClWXScoBJPCQRsR3Fbhtuz7CC5eg//Xm/
+
-
2C92FBeaw+Cdhs1agSDXejO4TsPH6W31CCJEdAZH70jDNwXYl7c3BebGX11Nl2PsBJe4kKOGPsYp
+
-
lzK0PVkMaz+R4+zTzxYjn3MnzYxXLrejTJTKpMXB8YceJ3rpqf06nq2G18NJvVfYNFVa1xXVKh5C
+
-
3Gl9f7c8P4GItMQ/GH71WR1Kdmr82ZkgRg2rbMukhoeMJ3GepkkComEw3W1AloX8v6D8AQAA//8D
+
-
AFBLAwQUAAYACAAAACEAA8CiPBEEAADfQQAAGAAAAGRycy9kaWFncmFtcy9jb2xvcnMxLnhtbOyc
+
-
XU/bMBSG7yftP0S+H2kZIFYREB+rhITQpLHryU2cNMJxMtuF8u9nO5/toKWxuzTF3JQmyrHz5Pj1
+
-
8fFJzy7mCXaeEGVxSjwwPBgABxE/DWISeeDXw/jLKXAYhySAOCXIAy+IgYvzz5/OgigZ+SlOKbtB
+
-
oSOsEDYSxzww5TwbuS7zpyiB7CDNEBFnw5QmkIuvNHIDCp+F/QS7h4PBiRvEMKIwAYUR2MJEAmMC
+
-
nBmJ/8zQbeCBGSWjJPZpytKQH/hp4qZhGPuo+ICUy6aP3VM3vwUX+j4ifPj7EJyrO+Mxx8h5gtgD
+
-
wM0PBYj5i0d8yO8Yz8+K/x3+kglChSngZDQWRIeiIWnCVcAaVzD+gtHdBDsEJuIykgZoULQexhhf
+
-
YyqMOwniUw9QlCHIxVk4UlyROJv3pWytbKG+NO8Xjsk7LWE+rPpZXZUbQWGIfJ7bKWjw+V1puToy
+
-
rrpdHfq+eKWCUN54brv8VmCAOI7IvWAx7JLFMtXueEi36BTFbrgF7t4ndgPEEyK6KKSKQJxNYa4g
+
-
xwPxp0Z+Q1wKveq7msjRU0p6fS8fTlQlhq9d6ulujB2J4chiCKPbJPqBoa8zsUgR4THhfdGQtWO+
+
-
6aJ8XocyeZTC5+0iGUv635DVOOmJdehXVgbGMbN48kAhYYc3GgHpom6cbCX2KKP397fVXXwfRj8t
+
-
VrXUrdaMtfZWhzYW34nFWqz7K4YmsJYSMNSRANEjlQeoA/JNUxXlAC8t6Q7ftcEBn9e5ESPBgQ8x
+
-
TmcyoyPTQjWJtT1ZvvX60rYQF1Vy1Wqwf5ghY9wm1YDEoDFnl8Osva81YxFdL6oEbeNJQWKw2QDl
+
-
DTYboDDYbADIIL2e2rhe7LVUwjKu9jHWTsdNYTMSGDQfR6datRxo6Mp2tyg71bv9QtmpZu4Tyh1Z
+
-
RKnU0RQGxXb3qpTM1jXA+DqrltPhzU7I6YehvROKu0T7dEW6sd++vROivNe0w+jS91ssomWEKME0
+
-
dty/rXDD9mvs/z41Bo+mk2IpGVvKSwVeximrCivry7I8sS6jM06Z00tZyWaM85HVjDzBvVQvOLGC
+
-
sW3BYCmOAx1h1s8f939uUxA1JcFy9IDieKUx6C1ED6hYdpyKLcjne7364rci22Zx2HanLt0ebH3d
+
-
Zzy0KAM4+wBVGUH/HqCKWezT6+nTU+LZoqjAJgLkC03l9FuG8a8G9Qpxi3StRbwZ4hY5Wot4M8Qt
+
-
ErMW8bsRizLPada+iE7GjvVLDNuNU0vh61+4Ejxe6WNm9Q7jql2YHqW/5TAtH6qR0g9ODXCu3bmq
+
-
5FzYe9gTJzcOX9Thm1OSVXvo7T28ec/9UxGKnh7mm0v1K5Oh+ZdV5RJ9KY/wViNbB69XAqHWVPlv
+
-
GoifZTj/CwAA//8DAFBLAwQUAAYACAAAACEAa5uWFBgEAAANUQAAHAAAAGRycy9kaWFncmFtcy9x
+
-
dWlja1N0eWxlMS54bWzsnNtO2zAYgO8n7R0i34+UwyZUERAHISEhhBh7ANdxEgvHDrYL5e1nO2na
+
-
jVZzoVGdzDclSfs7sT//R+ycnM1KGr1gIQlnCdjfG4EIM8RTwvIE/Hq8/nYMIqkgSyHlDCfgDUtw
+
-
dvr1y0mal2Op3ii+wlmkG2FyrC8loFCqGsexRAUuodzjFWb624yLEip9KvI4FfBVN1/S+GA0+hGn
+
-
BOYClqBpBH6giRISBqIpI89TfJMmYCrYuCRIcMkztYd4GfMsIwg3f6BQ5tbf4+P4eUrQk+1GLElZ
+
-
UXwETm3XFFEURy+QJgDE9aUUS/TnFQTVrVT1t/o4Um+VHqK6IRBVgugRHR2NRqaF2AzYsoBEmOHD
+
-
9PQE6sslFlALSJUALlTB9YhUBUHXgjNlpOGYkrxQDySPBNFkVCEwvlcgSonQZ+0N2kZbPLcTGjHd
+
-
fgIYT/Go6V77u+5uXh2mzcCp2b1oDu1Q2+6wBz1vSDpLgHkmOJZI5JNLKiLdHz0JdR/158R8msHT
+
-
/TcC5ocZobSVPXSSbUSMNM4yjFQrf+Ak3wrZ+2skrXxJGBdNG3rCY9MBO2mo2m8ePKt/38yAZgDs
+
-
bLDHmk89geZnDS3K7jSvfd22Rdn9ZHHmZZ4p8KqN30K7XjDzltguNczt3h/QMDX7pIZBbVK9RRaU
+
-
bBFhLJTMuDAfTaLbJP/fXJihZRysbw4s0FqnWyacCrQW4Z2/4aHRrXmuEoL5OpHwl1aW35T5PYVo
+
-
cN7LLU7pOgEzKWKb8S4fr8uubOwXmDQpdRt9b1OPNmYyCUpiChudVSk2BiLJ5FFAJg+uQszdl7JR
+
-
lv8M1DpVo7r4td1i3yRQq6u6nRm/LqjN7eO+l/bRLTJbXZNwy5DXR3Vu8m3YYeA0ZfI6AqnL6hs7
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">
+
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  <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image011.png" o:title=""/>
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  <o:lock v:ext="edit" aspectratio="f"/>
+
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  <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/>
+
-
</v:shape></o:wrapblock><br clear="ALL">
+
-
<span lang="EN-US">Procedure:<span> </span><o:p></o:p>
+
</span></p>
</span></p>
-
<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>
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/7/79/Image011.png"></p>
+
<p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/a/ae/Tutorial_%2814%29.png" o:title="main"/></p>
-
<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>
-
<img src="https://static.igem.org/mediawiki/igem.org/6/6f/Image0012.jpg" style="width: 650px;></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><span lang="EN-US">
+
<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>
-
<v:shape id="图片_x0020_13"
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<p class="MsoNormal">
-
o:spid="_x0000_i1040" type="#_x0000_t75">
+
<o:wrapblock>
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image012.jpg" o:title=""/>
+
<v:shape id="图片_x0020_15" o:spid="_x0000_s2052"
-
</v:shape>In the main display window, you will see a network from KEGG website.  
+
  type="#_x0000_t75" style='position:absolute;left:0;text-align:left;
-
On the left box displays a list of the files you have opened. Pay attention that
+
  margin-left:0;margin-top:3.9pt;width:414.7pt;height:319.2pt;z-index:251666432;
-
you can right click the main display window to open another KEGG xml file or to  
+
  visibility:visible;mso-wrap-style:square;mso-width-percent:0;
-
search any element in the network (choose find element).<o:p></o:p></span></p>
+
  mso-height-percent:0;mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
  mso-wrap-distance-right:9pt;mso-wrap-distance-bottom:0;
-
<h1 id="r6"><a name="_Toc336260395"><span lang="EN-US">Simulator</span></a><span lang="EN-US"><o:p></o:p></span></h1>
+
  mso-position-horizontal:absolute;mso-position-horizontal-relative:text;
-
<p><span lang="EN-US">Procedure: <span>
+
  mso-position-vertical:absolute;mso-position-vertical-relative:text;
-
<v:shape id="图示_x0020_3" o:spid="_x0000_i1039"
+
  mso-width-percent:0;mso-height-percent:0;mso-width-relative:margin;
-
type="#_x0000_t75"
+
  mso-height-relative:margin'>
-
o:gfxdata="UEsDBBQABgAIAAAAIQBgJjcoXAEAAHYEAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbLSUy07DMBRE
+
  &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
-
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+
deletion, reaction deletion, Fva analysis, <span style="mso-no-proof:yes">
-
tCWtgG2hRDqbTG4pM9qj9rHvPEg2z7GAWvpotQ/bBxKL0pFoebjYZaUEqkoKBj6Q0kbzbynxkJAE
+
Perturbation analysis</span> and <span style="mso-no-proof:yes">PhPP analysis</span>.
-
ZX/HbUTlbgIGob8mdCfnAwbdcxiNFRyjF7D+CVTAoNw6ijOTG5b87dFBKhebohAMk9y6Va86Mp3z
+
They with FBA solve will be introduced in detail. You can select all of them or
-
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+
part of them, or even nothing, then click <b style="mso-bidi-font-weight:normal">
-
o1GYkca6C2Ase+PRHMPDjgE5tfBnGw71+DfV7LTFZkQbT1mh8XmQvWJzdKf9r5F9AgAA//8DAFBL
+
Go</b>. If you select none of them, you will see a table showed basic
-
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+
information of each reaction. If you select several of them, the corresponding
-
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+
windows will tiled in the resulting window. If you select reaction deletion
-
m71dKKOBGwocxseH/RkXW9uRzLGIapQsBuZay6vW4mZMVjoqmNtmIk62tpGDLtZdbUA99P2z5t8M
+
option, a selection of the reaction you want to wipe off is required, and if
-
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+
there is any change, it will be highlighted in red font.<o:p></o:p></span></p>
-
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+
<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">
-
cy9kaWFncmFtcy9kYXRhMS54bWzsXN2O47YVvi/QdxB81aLgmiIpiRxkNiBFMVlgk11kN2mBoig0
+
<![if !supportLists]>
-
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+
<span lang="EN-US" style="mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
-
vAxeFXUzqxb7o/ARHQXFYlJNZ4uj/dHXLx2Ro6Bp88U0L6tFsT86K5rRp49//atPpkfzvWne5l9U
+
mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin">
-
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+
<span style="mso-list:Ignore">1.<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-
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+
</span></span></span><![endif]><span lang="EN-US">FBA_solve<o:p></o:p></span></p>
-
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+
<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">
-
wiRp3vo5lnU1KZpmFHzb3Hzab09mk7807VlZjJvZfFkWws/Tz7waGQWTW0w8qcqqbsb5ZFIs2vDP
+
<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>
-
zM/ST9uPjYLlcTmtYSaj8UrDzfJ53b+FzvO9g2p61o3ke2XTvuhW6ceX/qVYTJ/ndf7V8zooc29e
+
<p class="MsoNormal">Above<span lang="EN-US"> column displays names of the
-
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+
reactions while the right one displays the flux amount of each reaction<o:p></o:p></span></p>
-
2chOgJf7oz/++I+//vjPf/1pWxC/xtPDeu7/YlOD0/0RZzIaBWf7I+p/CBFO22CC8ZCrkEcxVITv
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
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+
<p class="MsoNormal"><span lang="EN-US">2. exanstive single deletion<o:p></o:p></span></p>
-
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+
<p class="MsoNormal"><span lang="EN-US">Calculate the flux amount of the
-
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+
objective reaction when each other reaction is deleted one by one.<o:p></o:p></span></p>
-
cgxtLKacLYLueIUxPJN/JmgmeVnAEa13bG16Xr5y4V8XlTfFlZGuRorDw2Ky8q04HidtUb84nr4O
+
<p class="MsoNormal">
-
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+
<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>
-
s2PCD/O9euOWVm4oOPB+Lpj5127fq3LWnc/uw1mzOXYIZdPqNdx73rQY3B+57p/eHzTbj5V5i83w
+
<p class="MsoNormal"><span lang="EN-US">Left column display names of the
-
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+
reactions <o:p></o:p></span></p>
-
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+
<p class="MsoNormal"><span lang="EN-US">The right one displays the flux amount
-
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+
of objective reaction the user has chosen, when each other reaction is deleted
-
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+
one by one.<o:p>&nbsp;</o:p></span></p>
-
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<span lang="EN-US" style="mso-no-proof:yes">
-
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+
<v:shape id="图片_x0020_24"
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+
o:spid="_x0000_i1045" type="#_x0000_t75" alt="说明: super optimal dels.bmp"
-
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style='width:117.6pt;height:40.2pt;visibility:visible;mso-wrap-style:square'><p><span lang="EN-US" style="mso-no-proof:yes">
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<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"
-
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+
  croptop="3449f" cropbottom="34000f"/></span></p></v:shape>
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</span><p class="MsoNormal"><span lang="EN-US">when rolling down the screen, you can
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see the reaction-names related to lethal deletions, sub optimal deletions and
-
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super optimaldeletions<span style="mso-no-proof:yes">.<o:p></o:p></span></span></p>
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<p class="MsoNormal">
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<o:p><img src="https://static.igem.org/mediawiki/igem.org/b/b7/Tutorial_%2823%29.png" o:title=""/></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">This graph shows how many lethal
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knockouts in each reaction subsystem. The information of the reaction subsystem
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can be attained in SBML <o:p></o:p>
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-
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-
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-
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-
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-
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+
-
">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image013.png" o:title=""/>
+
-
<o:lock v:ext="edit" aspectratio="f"/>
+
-
</v:shape><v:shape id="图片_x0020_16" o:spid="_x0000_i1038" type="#_x0000_t75">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image014.jpg" o:title=""/>
+
-
</v:shape></span><o:p></o:p>
+
</span></p>
</span></p>
-
<p>
+
<p class="MsoNormal">
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/9/9e/Image013.png" style="width: 650px;></p>
+
<o:p><img src="https://static.igem.org/mediawiki/igem.org/1/19/Tutorial_%2824%29.png" o:title=""/></o:p></p>
-
<p>
+
<p class="MsoNormal"><span lang="EN-US">This hist graph shows the frequency of  
-
<img src="https://static.igem.org/mediawiki/igem.org/0/07/Image014.jpg"></p>
+
reaction which has different quantified effect showed in the X-axis opon  
-
<p>
+
objective reaction.<o:p></o:p></span></p>
-
<img src="https://static.igem.org/mediawiki/igem.org/5/5b/Image015.png" style="width: 650px;></p>
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
<p><span lang="EN-US">
+
<p class="MsoNormal"><span lang="EN-US">3. reaction deletion<o:p></o:p></span></p>
-
<v:shape id="图片_x0020_15"
+
<p class="MsoNormal">
-
o:spid="_x0000_i1037" type="#_x0000_t75">
+
<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>
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image015.png" o:title=""/>
+
<p class="MsoNormal"><span lang="EN-US">Middle column displays the flux amount  
-
</v:shape>There are 5 options for you to select: exhaustive single deletion,
+
of the wild type while the right column displays the mutant type, which is  
-
reaction deletion, Fva analysis, <span>Perturbation analysis</span> and <span>
+
calculated based on the deletion of one chosen reaction.<o:p></o:p></span></p>
-
PhPP analysis</span>. They with FBA solve will be introduced in detail. You can
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
select all of them or part of them, or even nothing, then click Go. If you
+
<p class="MsoNormal"><span lang="EN-US">4. FVA analysis<o:p></o:p></span></p>
-
select none of them, you will see a table showed basic information of each
+
<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>
-
reaction. If you select several of them, the corresponding windows will tiled in
+
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">5.Perturbation
-
the resulting window. If you select reaction deletion option, a selection of the
+
analysis:<o:p></o:p></span></p>
-
reaction you want to wipe off is required, and if there is any change, it will
+
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">
-
be highlighted in red font.<o:p></o:p></span></p>
+
-
<p><span lang="EN-US">1.FBA_solve<span><v:shape id="图片_x0020_28"
+
-
o:spid="_x0000_i1036" type="#_x0000_t75" alt="说明: fba_sove.bmp">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image016.png" o:title="fba_sove"/>
+
-
</v:shape></span><o:p></o:p>
+
-
</span></p>
+
-
<p>
+
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/b/ba/Image016.png" style="width: 650px;></p>
+
-
<p><span lang="EN-US">Left column displays names of the reactions while the
+
-
right one displays the flux amount of each reaction<o:p></o:p></span></p>
+
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
-
<p><span lang="EN-US">2. exanstive single deletion<o:p></o:p></span></p>
+
-
<p><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><span lang="EN-US">
+
-
<v:shape id="图片_x0020_27"
+
-
o:spid="_x0000_i1035" type="#_x0000_t75" alt="说明: exaustive single deletion.bmp">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image017.png" o:title="exaustive single deletion"/>
+
-
</v:shape><o:p></o:p></span></p>
+
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span><img src="https://static.igem.org/mediawiki/igem.org/b/b2/Image017.png" style="width: 650px;></p>
+
-
<p><span lang="EN-US">Left column display names of the reactions <o:p></o:p>
+
-
</span></p>
+
-
<p><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></o:p></span></p>
+
-
<p>
+
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/d/d3/Image018.png"></p>
+
-
<p>
+
-
<img src="https://static.igem.org/mediawiki/igem.org/d/dc/Image019.png"></p>
+
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span><img src="https://static.igem.org/mediawiki/igem.org/7/71/Image020.png"></p>
+
-
<p><span lang="EN-US">
+
-
<v:shape id="图片_x0020_26"
+
-
o:spid="_x0000_i1034" type="#_x0000_t75" alt="说明: lethal deletions.bmp">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image018.png" o:title="lethal deletions"/>
+
-
</v:shape>.<span><v:shape
+
-
id="图片_x0020_25" o:spid="_x0000_i1033" type="#_x0000_t75" alt="说明: sub optimal dels.bmp">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image019.png" o:title="sub optimal dels"/>
+
-
</v:shape></span>when rolling down the screen, you can see the
+
-
reaction-names related to lethal deletions, sub optimal deletions and super
+
-
optimaldeletions<span>.<o:p></o:p></span></span></p>
+
-
<p>
+
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/f/f1/Image021.png"></p>
+
-
<p><span lang="EN-US">
+
-
<v:shape id="图片_x0020_23"
+
-
o:spid="_x0000_i1031" type="#_x0000_t75" alt="说明: reaction subsystem">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image021.png" o:title="reaction subsystem"
+
-
  croptop="3988f" cropbottom="3190f"/>
+
-
</v:shape><o:p></o:p></span></p>
+
-
<p><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>
+
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/2/28/Image022.png"></p>
+
-
<p><span lang="EN-US">
+
-
<v:shape id="图片_x0020_22"
+
-
o:spid="_x0000_i1030" type="#_x0000_t75" alt="说明: single%20knock">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image022.png" o:title="single%20knock"
+
-
  croptop="1456f" cropbottom="3311f"/>
+
-
</v:shape><o:p></o:p></span></p>
+
-
<p><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><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
-
<p><span lang="EN-US">3. reaction deletion<o:p></o:p></span></p>
+
-
<p>
+
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/8/81/Image023.png" style="width: 650px;></p>
+
-
<p>
+
-
<v:shape id="图片_x0020_21"
+
-
  o:spid="_x0000_i1029" type="#_x0000_t75" alt="说明: reacion deletions.bmp">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image023.png" o:title="reacion deletions"/>
+
-
</v:shape><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><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
-
<p><span lang="EN-US">4. FVA analysis<o:p></o:p></span></p>
+
-
<p>
+
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/0/0d/Image024.png" style="width: 650px;></p>
+
-
<p>
+
-
<v:shape id="图片_x0020_20"
+
-
  o:spid="_x0000_i1028" type="#_x0000_t75" alt="说明: fva.bmp">
+
-
<v:imagedata src="file:///I:\msohtmlclip1\01\clip_image024.png" o:title="fva"/>
+
-
</v:shape><span lang="EN-US">This analysis exams the robustness of the whole metabolic
+
-
network by calculating flux value which can be reached in reality. In other
+
-
words, this function works out the upper and lower limit of the flux of each
+
-
reaction, as you can see in the column name </span><span>‘</span><span lang="EN-US">lower
+
-
flux limit </span><span>’</span><span lang="EN-US">and </span><span>‘</span><span lang="EN-US">upper
+
-
flux limit</span><span>’</span><span lang="EN-US">.<o:p></o:p></span></p>
+
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
-
<p><span lang="EN-US">5.Perturbation analysis:</span></p>
+
-
<p><img src="https://static.igem.org/mediawiki/igem.org/0/05/Image025.png"></p>
+
-
<p><span lang="EN-US">
+
<v:shape id="图片_x0020_11"
<v:shape id="图片_x0020_11"
-
  o:spid="_x0000_i1027" type="#_x0000_t75" alt="说明: perturbation">
+
  o:spid="_x0000_i1041" type="#_x0000_t75" style='width:414pt;height:411pt;
-
  <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image025.png" o:title="perturbation"/>
+
visibility:visible;mso-wrap-style:square'>
-
</v:shape><o:p></o:p></span></p>
+
  &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><span lang="EN-US">X-axis refers to the continuously increasing flux value of  
+
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">X-axis refers  
-
the chosen reaction.<o:p></o:p></span></p>
+
to the continuously increasing flux value of the chosen reaction.<o:p></o:p></span></p>
-
<p><span lang="EN-US">Y-axis refers to the flux value of the objective reaction  
+
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">Y-axis refers  
-
according to the variation of the flux value of chosen reaction in the X-axis<o:p></o:p></span></p>
+
to the flux value of the objective reaction according to the variation of the  
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
flux value of chosen reaction in the X-axis<o:p></o:p></span></p>
-
<p><span lang="EN-US"><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><span lang="EN-US">6.PhPP analysis <o:p></o: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>
</span></p>
-
<p>
+
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">
-
<o:p></o:p><img src="https://static.igem.org/mediawiki/igem.org/8/8d/Image026.png"></p>
+
-
<p><span lang="EN-US">
+
<v:shape id="图片_x0020_10"
<v:shape id="图片_x0020_10"
-
  o:spid="_x0000_i1026" type="#_x0000_t75" alt="说明: PHPP">
+
  o:spid="_x0000_i1040" type="#_x0000_t75" style='width:409.2pt;height:433.8pt;
-
  <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image026.png" o:title="PHPP"/>
+
visibility:visible;mso-wrap-style:square'>
-
</v:shape><o:p></o:p></span></p>
+
  &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><span lang="EN-US">The value marked on the contour represents the flux value  
+
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">The value  
-
of the objective reaction based on the variation of two chosen reactions The  
+
marked on the contour represents the flux value of the objective reaction based  
-
color of the graph changes according to the altitude, namely, the objective flux  
+
on the variation of two chosen reactions The color of the graph changes  
-
value.</span></p>
+
according to the altitude, namely, the objective flux value.<o:p></o:p></span></p>
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
<h1><a name="_Toc338881885">
-
<h1 id="r7"><a name="_Toc336260396"><span lang="EN-US">G-Circle</span></a><span lang="EN-US"><o:p></o:p></span></h1>
+
<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><o:wrapblock>
+
<p class="MsoNormal">
-
<v:shape id="图示_x0020_9" o:spid="_x0000_s1030"
+
<o:wrapblock>
-
   type="#_x0000_t75" o:gfxdata="UEsDBBQABgAIAAAAIQBgJjcoXAEAAHYEAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbLSUy07DMBRE
+
<v:shape id="图示_x0020_9" o:spid="_x0000_s2050"
-
90j8Q+QtStx2gRBq0kVTVggQlA+4sm9Sq34E20mbv8dJU1U8Ctl06cfMHF2PPF/slYwatE4YnZJp
+
   type="#_x0000_t75" style='position:absolute;left:0;text-align:left;
-
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">
">
-
   <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image027.png" o:title=""
+
   &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">
-
  croptop="-3052f"/>
+
<i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">:</span></p>
-
  <o:lock v:ext="edit" aspectratio="f"/>
+
<p class="MsoNormal">
-
  <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/>
+
&nbsp;<img src="https://static.igem.org/mediawiki/igem.org/a/ab/Tutorial_%2829%29.png" o:title=""
-
</v:shape></o:wrapblock><br clear="ALL">
+
  croptop="-3052f"/></p>
-
<span lang="EN-US">Procedure: <o:p></o:p>
+
<p class="MsoNormal">
-
</span></p>
+
&nbsp;<img src="https://static.igem.org/mediawiki/igem.org/1/1d/Tutorial_%2830%29.png" style="width: 650px;" o:title=""/></p>
-
<p>
+
<p class="MsoNormal"><span lang="EN-US">&nbsp;<o:p></o:p></span></p>
-
<o:p></o:p>
+
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">
-
<img src="https://static.igem.org/mediawiki/igem.org/9/94/Image027.png"></p>
+
-
<p>
+
-
<img src="https://static.igem.org/mediawiki/igem.org/9/98/Image028.jpg" style="width: 650px;></p>
+
-
<p><span lang="EN-US">
+
<v:shape id="图片_x0020_18"
<v:shape id="图片_x0020_18"
-
  o:spid="_x0000_i1025" type="#_x0000_t75">
+
  o:spid="_x0000_i1039" type="#_x0000_t75" style='width:442.2pt;height:249pt;
-
  <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image028.jpg" o:title=""/>
+
  visibility:visible;mso-wrap-style:square'>
-
</v:shape>You can open several file so that you can compare the difference of  
+
&nbsp;</v:shape></span><span lang="EN-US">You can open several file so that you can  
-
these genomes. Each genome have 2 circles in this picture: the outer one is the  
+
compare the difference of these genomes. Each genome have 2 circles in the
-
genes of the genome, the inner is the expression level of corresponding genes  
+
picture: the outer one is the genes of the genome, the inner is the expression  
-
under two different conditions. By the way, right click different sites in the  
+
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,  
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 zoom
+
you can move to anywhere you want to enlarge and see more details in the  
-
window.<o:p></o:p></span></p>
+
amplifier window.<o:p></o:p></span></p>
-
<p><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
+
<p class="MsoNormal"><span lang="EN-US"><o:p>&nbsp;</o:p></span></p>
-
</div>
+
<h1><a name="_Toc338881886"><span lang="EN-US" id="r8">Clotho</span></a><span lang="EN-US"><o:p></o:p></span></h1>
-
              </div><!--end entry-->
+
<p class="MsoNormal"><span lang="EN-US">All above seven parts have been
-
          </div><!--end content-->
+
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>
 +
<p style="mso-char-indent-count: 0; mso-list: l1 level1 lfo1; text-justify: inter-ideograph;" class="style1">
 +
<![if !supportLists]>
 +
<span lang="EN-US" style="font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings"><span style="mso-list:Ignore"><span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;
 +
</span></span></span><![endif]></p>
 +
<p style="mso-char-indent-count: 0; mso-list: l1 level1 lfo1; text-justify: inter-ideograph;" class="style2">
 +
<span lang="EN-US"><strong>Home</strong><o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_14"
 +
o:spid="_x0000_i1038" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\截图with注释\Home-clotho.png"
 +
style='width:412.8pt;height:278.4pt;visibility:visible;mso-wrap-style:square'>
 +
<img src="https://static.igem.org/mediawiki/igem.org/9/9a/Home.png"  style="width: 650px;" o:title="Home-clotho"/>
 +
</v:shape></span><span lang="EN-US"><o:p></o:p></span></p>
 +
<p style="mso-char-indent-count: 0; mso-list: l1 level1 lfo1; text-justify: inter-ideograph;" class="style1">
 +
<![if !supportLists]>
 +
<span lang="EN-US" style="font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings"><span style="mso-list:Ignore"><span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;
 +
</span></span></span><![endif]></p>
 +
<p style="mso-char-indent-count: 0; mso-list: l1 level1 lfo1; text-justify: inter-ideograph;" class="style1">
 +
<o:p></o:p></p>
 +
<p style="mso-char-indent-count: 0; mso-list: l1 level1 lfo1; text-justify: inter-ideograph;" class="style1">
 +
<span lang="EN-US" class="style3"><strong>Genome Browser</strong><o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_30"
 +
o:spid="_x0000_i1037" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\genomebrowser2.png"
 +
style='width:414.6pt;height:319.2pt;visibility:visible;mso-wrap-style:square'>
 +
<img src="https://static.igem.org/mediawiki/igem.org/5/54/Genomebrowser2.png" style="width: 650px;"  o:title="genomebrowser2"/>
 +
</v:shape></span><span lang="EN-US"><o:p></o:p></span></p>
 +
<p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">
 +
<v:shape id="图片_x0020_31"
 +
o:spid="_x0000_i1036" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\genomebrowser.png"
 +
style='width:412.8pt;height:259.2pt;visibility:visible;mso-wrap-style:square'>
 +
&nbsp;</v:shape></span><span lang="EN-US"><o:p></o:p></span></p>
 +
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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"