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| | {{:Team:SYSU-Software/menu}} | | {{:Team:SYSU-Software/menu}} |
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| | </li> | | </li> |
| | + | <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/WorldJamboree"> |
| | + | World-Jamboree</a><!--input an em tag as a space,IE is gread need--> |
| | + | |
| | + | </li> |
| | + | |
| | | | |
| | </ul> | | </ul> |
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| | | | |
| | <div id="content"> <div class="entry page clear"> | | <div id="content"> <div class="entry page clear"> |
| - | <h1 id="doctitle" class="pagetitle">Our Project</h1> | + | <h1 id="doctitle" class="pagetitle">Tutorial</h1> |
| | <table class="doc-toc"> | | <table class="doc-toc"> |
| | <tbody> | | <tbody> |
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| | </div> | | </div> |
| | <ul id="toc-ul"> | | <ul id="toc-ul"> |
| - | <li class="toclevel-1"><a href="#r0"><span class="tocnumber"></span> <span class="toctext"> Introduction</span></a></li> | + | <li class="toclevel-1"><a href="#r1">Genome Browser</a></li> |
| - | <li class="toclevel-1"><a href="#r2">Genome Browser</a></li> | + | <li class="toclevel-1"><a href="#r2">Biobrick</a></li> |
| - | <li class="toclevel-1"><a href="#r3">Biobrick</a></li> | + | <li class="toclevel-1"><a href="#r3">Riboswitch</a></li> |
| - | <li class="toclevel-1"><a href="#r4">Riboswitch</a></li> | + | <li class="toclevel-1"><a href="#r4">SiRNA</a></li> |
| - | <li class="toclevel-1"><a href="#r5">SiRNA</a></li> | + | <li class="toclevel-1"><a href="#r5">Meta Network</a></li> |
| - | <li class="toclevel-1"><a href="#r6">Meta Network</a></li> | + | <li class="toclevel-1"><a href="#r6">Simulator</a></li> |
| - | <li class="toclevel-1"><a href="#r7">Simulator</a></li> | + | <li class="toclevel-1"><a href="#r7">G-Circle</a></li> |
| - | <li class="toclevel-1"><a href="#r8">G-Circle</a></li> | + | <li class="toclevel-1"><a href="#r8">Clotho</a></li> |
| | </ul> | | </ul> |
| | </td> | | </td> |
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| | </tbody> | | </tbody> |
| | </table> | | </table> |
| - | <div id="doc-contents"> | + | </div> |
| - | <h1><a name="_Toc336260397">Genome </a>Browser</h1> | + | <span></span> |
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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> |
| - | <p> | + | <o:p></o:p> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/1/1e/Image0003.jpg" style="width: 650px;"><br clear="ALL"> | + | </p> |
| - | <span lang="EN-US"> | + | |
| - | <v:shape id="图片_x0020_8" o:spid="_x0000_i1046" | + | <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> |
| - | type="#_x0000_t75">
| + | </p> |
| - | <v:imagedata src="image003.jpg" o:title=""/>
| + | <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><a name="_Toc336260391"><span lang="EN-US">Biobrick</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="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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| | "> | | "> |
| - | <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image004.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><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> | + | |
| - | < 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> </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> </o:p></span></p> | + | Procedure</span></i><span lang="EN-US">: <o:p></o:p> |
| - | <h1><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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| - | "> | + | |
| - | <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image006.png" o:title=""
| + | |
| - | croptop="-7957f" cropbottom="-1952f"/>
| + | |
| - | <o:lock v:ext="edit" aspectratio="f"/>
| + | |
| - | </v:shape><v:shape id="图片_x0020_17" o:spid="_x0000_i1043" type="#_x0000_t75"> | + | |
| - | <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image007.jpg" o:title=""/>
| + | |
| - | </v:shape></span><o:p></o:p>
| + | |
| | </span></p> | | </span></p> |
| - | <p> | + | |
| - | < 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 |
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| + | 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> </o:p></span></p> | + | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> |
| - | <h1><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> |
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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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| + | |
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| + | |
| - | 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> | + | |
| - | < 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> </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> </o:p></span></p> | + | |
| - | <h1><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> </o:p></span></p> |
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| + | <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"> |
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| + | Procedure</span></i><span lang="EN-US">: |
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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_image011.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:<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=""/> </p> |
| - | <v:shape id="图片_x0020_13" | + | <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> </o:p></span></p> | + | mso-wrap-distance-right:9pt;mso-wrap-distance-bottom:0; |
| - | <h1><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
| + | <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/></v:shape></o:wrapblock><br style="mso-ignore:vglayout" clear="ALL"> |
| - | 90j8Q+QtStx2gRBq0kVTVggQlA+4sm9Sq34E20mbv8dJU1U8Ctl06cfMHF2PPF/slYwatE4YnZJp
| + | <span lang="EN-US">There are 5 options for you to select: exhaustive single |
| - | MiERama40GVK3tcP8R2JnAfNQRqNKWnRkUV2fTVftxW6KKi1S8nG++qeUsc2qMAlpkIdTgpjFfiw
| + | 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 |
| - | 5gJKC8pRDh6mIzK+jnvI44bVKgw54RZ24TWVTAbjPNiOZpDQmtpfgOKxNx7N8VELtn3zrcQLsPS+
| + | 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 |
| - | AwQUAAYACAAAACEAOP0h/9YAAACUAQAACwAAAF9yZWxzLy5yZWxzpJDBasMwDIbvg72D0X1xmsMY
| + | information of each reaction. If you select several of them, the corresponding |
| - | o04vo9Br6R7A2IpjGltGMtn69jODwTJ621G/0PeJf3/4TItakSVSNrDrelCYHfmYg4H3y/HpBZRU
| + | 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 |
| - | GDdMdfIG+OQHUJdbaeY/7BQdk9BUO0dJ0zRFd4+qPX3kM66NYjlgNeBZvkPGtWvPgb7v3f3TG9iW
| + | there is any change, it will be highlighted in red font.<o:p></o:p></span></p> |
| - | Oboj24Rv5LZ+HKhlP3q96XL8AgAA//8DAFBLAwQUAAYACAAAACEAdqJnwlALAABOQAAAFgAAAGRy
| + | <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]> |
| - | tmbGqGw5kmZ3JkGue9HLAr3qIxR9g75Nm+foR1n22POT1czu7M4mEyAem7YYnsPDc77zncN88unp
| + | <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"> |
| - | 06IMMMui2cPY/ui4bZd743EzOS7mefOoWhYLfHtY1fO8xcf6aDyt89eYf16OGaXxeDrLj+p8Puon
| + | <span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman""> |
| - | yW8xxTyfLUaPuzUt26dNu34bzP3qnkz3R987xp2kMiVRpiMiDBVEhlFEQscko5nQKqQ/jIL2bAkp
| + | </span></span></span><![endif]><span lang="EN-US">FBA_solve<o:p></o:p></span></p> |
| - | p9VkPV39omiDsnqJcT/PSb3Ym88mddVUh+2jSTUfV4eHs0nR/8nr1gsVjeW4zM+qk3YMNbyqq0U4
| + | <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 |
| - | 3x2T9MtRkJft0+5zsSBfv/BTj7snxt7EMG33d3nVnmprEpPSkISZ00REiSFGCkfSULg440Jb7X7Y
| + | 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> </o:p></span></p> |
| - | Is65Uv261xMs66b9rKjmgX+zP+qtAGvJ9/JXsNBeyv5XfhhnYOpmZRnUVfv7WXv84jj3pki7Z46a
| + | <p class="MsoNormal"><span lang="EN-US">2. exanstive single deletion<o:p></o:p></span></p> |
| - | zqrxqyZYVs16uKmPDtKyDl7l5f5IOBka2/38+KR4Bgm64X7pTd5eHCpP5heH8nJ5nF8cbI7zabGa
| + | <p class="MsoNormal"><span lang="EN-US">Calculate the flux amount of the |
| - | LAopPZ8QZ381HHIMd+PYun5R3TYeNZ1o/aJl9ys/8t4XrvwKV5sITdx04V5qPP5hVi6uWXnUj1+h
| + | objective reaction when each other reaction is deleted one by one.<o:p></o:p></span></p> |
| - | cgxtLKacLYLueIUxPJN/JmgmeVnAEa13bG16Xr5y4V8XlTfFlZGuRorDw2Ky8q04HidtUb84nr4O
| + | <p class="MsoNormal"> |
| - | DsqT+qscc/lVYurpzJs767SND3AWUfcNvrrKrnfswM/Qa7mzw5Vt8Wvk3KyhM7St5XX+wnumlY96
| + | <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 |
| - | IeYwn+Bsp3k5O6hnvW/Jt7753XxBinz1xaS58MWk6SfHmv1q2scvq6psvNv07hKy+NGB7vbDyvm/
| + | reactions <o:p></o:p></span></p> |
| - | f//tv//5+5vkPBelEw/R5M2xIU5lKNMwIY5GIWKDzoih1BEWCZuoNHRhxjfxfpnXL+t8gZA8OV10
| + | <p class="MsoNormal"><span lang="EN-US">The right one displays the flux amount |
| - | cMHYjDntYsKkFkRIoYi2SUSscM5mXKtEZzuhBWfFx6sPHBGtSQFtTEJ0yDgRVifEMGUJlwnXNkxZ
| + | of objective reaction the user has chosen, when each other reaction is deleted |
| - | lEYbqZvZwc9D6lhhZ2kak0hbSgRNEgJ/r0jMuaSRTdPY2J3NWgGZl4NxQMiiKKKI91dAgSjkcQiU
| + | one by one.<o:p> </o:p></span></p> |
| - | 8AAFOrjxAAX27gx9qQcoAHywQiXbKPOOocC9D//PkGMHeXA4K4tgBwUAC3SpV/dyJcy597L9BojJ
| + | <span lang="EN-US" style="mso-no-proof:yes"> |
| - | cxQrAuG3O+INBjnvX8q7AzbG2jRKlSBKxJbgX0VMZhzRqWVamsgoGW9C/GVgY3lsjPEUiEoUERmy
| + | <v:shape id="图片_x0020_24" |
| - | Z5kC3WSRM05lMWUCuKgnUDz5cT+AjXGJTrNQE600Uv3YCaT6yuAjVzpBnp8mbiP1ZWDzkUqdKapU
| + | o:spid="_x0000_i1045" type="#_x0000_t75" alt="说明: super optimal dels.bmp" |
| - | xEIAGwYUGkJ+k8oMWy9jowBkgXx2NuumwIbFTMFergQ2DxzH3i2oggeO4xa00gOw8cTHA7C5yGs0
| + | style='width:117.6pt;height:40.2pt;visibility:visible;mso-wrap-style:square'><p><span lang="EN-US" style="mso-no-proof:yes"> |
| - | RQnSKQCRXgfVskWN4pYsx88JAMQ0ilG00MRmUUpEEhoiY1QyDIJimmoXCS42ofAyAIi4MmnGEVMY
| + | <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" |
| - | wongNiWa2xCMQUJDxlKm3H0EAKlNktDSmFhqYoAXhhw/lTGhKnKWChOnFqGwr99cBgAfqdTSujCR
| + | croptop="3449f" cropbottom="34000f"/></span></p></v:shape> |
| - | YUZsbMDn0MwjHitJyDQVTnNn2bWb5W1+XY6o+nqGlIzR5CHcP5Q0Hkoae1s1g4eSRnPPShqfVbdL
| + | </span><p class="MsoNormal"><span lang="EN-US">when rolling down the screen, you can |
| - | 9T9UxebuEn6BRE/TBBm+iZAEcpUSRTliAFWxS1wqXGQ2ke9yvDcRZyxDaVwjiUQOKS3RcSqIdSLM
| + | see the reaction-names related to lethal deletions, sub optimal deletions and |
| - | hMpkopOdHPJ+JPyRdXFiQUx0pRthue/XSDnhLlMZVZpLe05zXI73H6nUiVKh4iIkMU1Qtco4wFma
| + | super optimaldeletions<span style="mso-no-proof:yes">.<o:p></o:p></span></span></p> |
| - | UeJiJrmKaMZSfb7XNZpxtpga9BoUjW6aavLEDu948Q99mc9RjvSvqNP6ga51I120q0YDX9jyo0+7
| + | <p class="MsoNormal"> |
| - | lpZv8hpVfT+G+m5vLPliNn/6Cp1EvhGhfFV6IO9/gYdm3xWfo3+oLJrVt8VpPmk7oH/VtKtmD887
| + | <o:p><img src="https://static.igem.org/mediawiki/igem.org/b/b7/Tutorial_%2823%29.png" o:title=""/></o:p></p> |
| - | rSb4wPU0JZXisU5J7CgqSwIGqEPgL3BlwmgZs5QP3o9h3Sqd+lf74c/y6bNFeba1J08PoOAFuppQ
| + | <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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| + | |
| - | "> | + | |
| - | <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> | + | |
| - | <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> </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"
| + | |
| - | 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> </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> <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> </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> </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> </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> </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> </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> </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>
| + | </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> </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> </o:p></span></p> | + | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><o:p> </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> </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>
| + | </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> </o:p></span></p>
| + | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> |
| - | <p><span lang="EN-US"><o:p> </o:p></span></p> | + | <h1><a name="_Toc338881885"> |
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| | "> | | "> |
| - | <v:imagedata src="file:///I:\msohtmlclip1\01\clip_image027.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 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"/>
| + | |
| - | <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/>
| + | <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> | + | |
| - | </span></p> | + | <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"> <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 | + | </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> </o:p></span></p> | + | <p class="MsoNormal"><span lang="EN-US"><o:p> </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 "Times New Roman""> |
| | + | </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 "Times New Roman""> |
| | + | </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'> |
| | + | </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 "Times New Roman""> |
| | + | </span></span></span><![endif]><span lang="EN-US" class="style3"><strong>Biobrick</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_642" |
| | + | o:spid="_x0000_i1035" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\biobrick2.png" |
| | + | style='width:414.6pt;height:319.2pt;visibility:visible;mso-wrap-style:square'> |
| | + | <img src="https://static.igem.org/mediawiki/igem.org/1/1d/Biobrick2.png" style="width: 650px;" o:title="biobrick2"/> |
| | + | </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_643" |
| | + | o:spid="_x0000_i1034" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\biobrick.png" |
| | + | style='width:418.2pt;height:263.4pt;visibility:visible;mso-wrap-style:square'> |
| | + | </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="mso-fareast-font-family:Wingdings; |
| | + | mso-bidi-font-family:Wingdings"><span style="mso-list:Ignore"> |
| | + | <span style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;" class="style3"> |
| | + | <strong> |
| | + | </strong> |
| | + | </span></span></span><![endif]><span lang="EN-US" class="style3"><strong>RiboSwitch</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_647" |
| | + | o:spid="_x0000_i1032" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\riboswitch down.png" |
| | + | style='width:418.2pt;height:352.2pt;visibility:visible;mso-wrap-style:square'> |
| | + | <img src="https://static.igem.org/mediawiki/igem.org/0/03/Riboswitch1.png" style="width: 650px;" o:title="riboswitch down"/> |
| | + | </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"> |
| | + | <span lang="EN-US" style="mso-no-proof:yes"> |
| | + | <v:shape id="图片_x0020_657" |
| | + | o:spid="_x0000_i1032" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\riboswitch down.png" |
| | + | style='width:418.2pt;height:352.2pt;visibility:visible;mso-wrap-style:square'> |
| | + | <img src="https://static.igem.org/mediawiki/igem.org/5/51/Riboswitch_down.png" style="width: 650px;" o:title="riboswitch down"/></v:shape></span><![if !supportLists]><![endif]></p> |
| | + | <p style="mso-char-indent-count: 0; mso-list: l1 level1 lfo1; text-justify: inter-ideograph;" class="style1"> |
| | + | <![if !supportLists]> |
| | + | <![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"> |
| | + | <![if !supportLists]> |
| | + | <![endif]><span lang="EN-US" class="style3"><strong>SiRNA</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_648" |
| | + | o:spid="_x0000_i1031" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\sirna.png" |
| | + | style='width:415.2pt;height:258.6pt;visibility:visible;mso-wrap-style:square'> |
| | + | <img src="https://static.igem.org/mediawiki/igem.org/f/ff/Sirna2.png" style="width: 650px;" o:title="sirna"/> |
| | + | </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 "Times New Roman""> |
| | + | </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>Network Illustrator</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_649" |
| | + | o:spid="_x0000_i1030" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\metanetwork2.png" |
| | + | style='width:414.6pt;height:319.2pt;visibility:visible;mso-wrap-style:square'> |
| | + | <img src="https://static.igem.org/mediawiki/igem.org/d/d7/Network.png" style="width: 650px;" o:title="metanetwork2"/> |
| | + | </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_650" |
| | + | o:spid="_x0000_i1029" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\network.png" |
| | + | style='width:414.6pt;height:281.4pt;visibility:visible;mso-wrap-style:square'> |
| | + | </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="mso-fareast-font-family:Wingdings; |
| | + | mso-bidi-font-family:Wingdings"><span style="mso-list:Ignore"> |
| | + | <span style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;" class="style3"> |
| | + | <strong> |
| | + | </strong> |
| | + | </span></span></span><![endif]><span lang="EN-US" class="style3"><strong>Simulator</strong></span><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_651" |
| | + | o:spid="_x0000_i1028" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\fba.png" |
| | + | style='width:414.6pt;height:316.2pt;visibility:visible;mso-wrap-style:square'> </v:shape><v:shape id="图片_x0020_652" |
| | + | o:spid="_x0000_i1027" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\fba1.png" |
| | + | style='width:414.6pt;height:298.8pt;visibility:visible;mso-wrap-style:square'><img src="https://static.igem.org/mediawiki/igem.org/1/1a/Fba_main.png" style="width: 650px;" o:title="fba1"/> |
| | + | </v:shape></span><o:p></o:p> |
| | + | </p> |
| | + | <p class="MsoNormal"> |
| | + | <o:p></o:p> |
| | + | <span lang="EN-US" style="mso-no-proof:yes"> |
| | + | <v:shape id="图片_x0020_656" |
| | + | o:spid="_x0000_i1027" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\fba1.png" |
| | + | style='width:414.6pt;height:298.8pt;visibility:visible;mso-wrap-style:square'> |
| | + | <img src="https://static.igem.org/mediawiki/igem.org/0/04/Fba1.png" style="width: 650px;" o:title="fba1"/></v:shape></span><o:p></o:p></p> |
| | + | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"> |
| | + | <v:shape id="图片_x0020_653" |
| | + | o:spid="_x0000_i1026" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\gcircle3.png" |
| | + | style='width:414.6pt;height:319.2pt;visibility:visible;mso-wrap-style:square'> |
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| | + | <strong> |
| | + | </strong> |
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| | + | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_655" |
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| | + | style='width:414.6pt;height:312.6pt;visibility:visible;mso-wrap-style:square'> |
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| | + | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> |
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| | + | </span></p> |
| | + | </div><!--end content--> |
| | | | |
| | <div id="sidebar"> | | <div id="sidebar"> |
| Line 1,645: |
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| | <ul> | | <ul> |
| | <li> | | <li> |
| - | <a href="https://2012.igem.org/Team:SYSU-Software/Download">Source Code</a> | + | <a href="https://2012.igem.org/Team:SYSU-Software/Download"> |
| | + | Download</a> |
| | </li> | | </li> |
| | <li> | | <li> |
| Line 1,671: |
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| | </li> | | </li> |
| | <li> | | <li> |
| - | <a href="https://2012.igem.org/Team:SYSU-Software/Faq">Troubleshooting</a> | + | <a href="https://2012.igem.org/Team:SYSU-Software/Trouble">Troubleshooting</a> |
| | </li> | | </li> |
| | <li> | | <li> |
| Line 1,677: |
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| | </li> | | </li> |
| | <li> | | <li> |
| - | <a href="">Contact Us</a> | + | <a href="https://2012.igem.org/Team:SYSU-Software/Contact">Contact Us</a> |
| | </li> | | </li> |
| | </ul> | | </ul> |
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