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| | </tbody> | | </tbody> |
| | </table> | | </table> |
| - | <div id="doc-contents"> | + | </div> |
| | + | <span></span> |
| | <h1><a name="_Toc338881878"> | | <h1><a name="_Toc338881878"> |
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| | <p class="MsoNormal"><span lang="EN-US">On the left is the logo of | | <p class="MsoNormal"><span lang="EN-US">On the left is the logo of |
| | <b style="mso-bidi-font-weight:normal">BiArkit</b> which is created by 2012 | | <b style="mso-bidi-font-weight:normal">BiArkit</b> which is created by 2012 |
| Line 144: |
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| - | ">
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/c/cd/Tutorial_%282%29.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">
| + | |
| | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> | | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> |
| - | </span></p> | + | </span> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_8" | + | <o:p></o:p> |
| - | o:spid="_x0000_i1059" type="#_x0000_t75" style='width:418.8pt;height:250.2pt; | + | </p> |
| - | visibility:visible;mso-wrap-style:square'>
| + | <p> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/2/20/Tutorial_%283%29.png" style="width: 650px; " o:title=""/> | + | < 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> |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | + | </p> |
| | <p class="MsoNormal"><span lang="EN-US">In the main display window, the first | | <p class="MsoNormal"><span lang="EN-US">In the main display window, the first |
| | ribbon is the sequence that the user has inputted, and the third ribbon shows | | ribbon is the sequence that the user has inputted, and the third ribbon shows |
| Line 358: |
Line 150: |
| | <h1><a name="_Toc338881880"> | | <h1><a name="_Toc338881880"> |
| | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">Biobrick</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> | | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">Biobrick</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> |
| - | <p class="MsoNormal"><o:wrapblock><v:shape id="图示_x0020_4" o:spid="_x0000_s2056" | + | <p class="MsoNormal"> |
| | + | <o:wrapblock> |
| | + | <v:shape id="图示_x0020_4" o:spid="_x0000_s2056" |
| | type="#_x0000_t75" style='position:absolute;left:0;text-align:left; | | type="#_x0000_t75" style='position:absolute;left:0;text-align:left; |
| | margin-left:1.15pt;margin-top:21.05pt;width:230.9pt;height:45.6pt;z-index:251659264; | | margin-left:1.15pt;margin-top:21.05pt;width:230.9pt;height:45.6pt;z-index:251659264; |
| Line 526: |
Line 320: |
| | LnhtbFBLBQYAAAAACgAKAOYCAABMIAAAAAA= | | LnhtbFBLBQYAAAAACgAKAOYCAABMIAAAAAA= |
| | "> | | "> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/4/46/Tutorial_%284%29.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 style="mso-ignore:vglayout" clear="ALL">
| + | |
| - | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> | + | |
| | </span></p> | | </span></p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_644" | + | |
| - | o:spid="_x0000_i1058" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\截图with注释\Biobrick.png"
| + | < 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/5/58/Tutorial_%285%29.png" style="width: 650px;" o:title="Biobrick"/><img src="https://static.igem.org/mediawiki/igem.org/0/08/Tutorial_%286%29.png" style="width: 650px;" o:title=""/></o:p> |
| - | style='width:419.4pt;height:248.4pt;visibility:visible;mso-wrap-style:square'>
| + | </p> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/5/58/Tutorial_%285%29.png" style="width: 650px;" o:title="Biobrick"/> | + | |
| - | </v:shape><v:shape id="图片_x0020_19" o:spid="_x0000_i1057" type="#_x0000_t75"
| + | |
| - | style='width:419.4pt;height:330pt;visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/0/08/Tutorial_%286%29.png" style="width: 650px;" o:title=""/> | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | + | |
| | <p class="MsoNormal"><span lang="EN-US">Notice that there is a finder on the | | <p class="MsoNormal"><span lang="EN-US">Notice that there is a finder on the |
| | left; you can search biobricks by key words and then a window showing the search | | left; you can search biobricks by key words and then a window showing the search |
| Line 549: |
Line 334: |
| | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">RiboSwitch</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> | | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">RiboSwitch</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> |
| | <p class="MsoNormal"><i style="mso-bidi-font-style:normal"><span lang="EN-US"> | | <p class="MsoNormal"><i style="mso-bidi-font-style:normal"><span lang="EN-US"> |
| - | Procedure</span></i><span lang="EN-US">: <o:p></o:p></span></p> | + | Procedure</span></i><span lang="EN-US">: <o:p></o:p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图示_x0020_2" | + | </span></p> |
| - | o:spid="_x0000_i1056" type="#_x0000_t75" style='width:474.6pt;height:50.4pt;
| + | |
| - | visibility:visible' o:gfxdata="UEsDBBQABgAIAAAAIQC2MIQfXAEAANEEAAATAAAAW0NvbnRlbnRfVHlwZXNdLnhtbLSUy07DMBBF
| + | <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/ 5/ 58/Tutorial_% 285%29.png" style="width: 650px;" o:title=" Biobrick"/></o:p> |
| - | 90j8Q+QtStyyQAg17aKFFQIkygcM9iS16he2U5q/x80DQVWgkegmSmLPPUfWeCazrZLJBp0XRudk
| + | </p> |
| - | nI1IgpoZLnSZk5flXXpNEh9Ac5BGY05q9GQ2PT+bLGuLPonV2udkFYK9odSzFSrwmbGo40phnIIQ
| + | |
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| | <p class="MsoNormal"><span lang="EN-US">On the right is the main operating area | | <p class="MsoNormal"><span lang="EN-US">On the right is the main operating area |
| | and you can choose your target type (your experimental object) and corresponding | | and you can choose your target type (your experimental object) and corresponding |
| Line 769: |
Line 352: |
| | <h1><a name="_Toc338881882"> | | <h1><a name="_Toc338881882"> |
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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> | | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> |
| | </span></p> | | </span></p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_5" | + | |
| - | o:spid="_x0000_i1054" type="#_x0000_t75" style='width:413.4pt;height:244.2pt;
| + | < 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> |
| - | visibility:visible;mso-wrap-style:square'>
| + | </p> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/1/10/Tutorial_%2810%29.png" style="width: 650px;" o:title=""/ > | + | |
| - | </v:shape></span><span lang="EN-US">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
| + | |
| - | <b style="mso-bidi-font-weight:normal">Direct Input</b>, then input your
| + | |
| - | sequence, and click <b style="mso-bidi-font-weight:normal">Go</b>. If you choose
| + | |
| - | the latter, you need only click <b style="mso-bidi-font-weight:normal">Open
| + | |
| - | Fasta</b> and choose your FASTA file to open. Two solutions are provided on the
| + | |
| - | right</span><span style="font-family:宋体;mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;
| + | |
| - | mso-fareast-font-family:宋体;mso-fareast-theme-font:minor-fareast;mso-hansi-font-family:
| + | |
| - | Calibri;mso-hansi-theme-font:minor-latin">——</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>
| + | |
| | <p class="MsoNormal"><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="_Toc338881883"> | | <h1><a name="_Toc338881883"> |
| - | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">Network Illustrator</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> | + | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">Network Illustrator</span></a><o:p></o:p></h1> |
| - | <p class="MsoNormal"><o:wrapblock><v:shape id="图示_x0020_7" o:spid="_x0000_s2053" | + | <p class="MsoNormal"> |
| - | type="#_x0000_t75" style='position:absolute;left:0;text-align:left;
| + | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> |
| - | margin-left:-3.35pt;margin-top:23pt;width:169.45pt;height:46.55pt;z-index:251661312;
| + | </span></p> |
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| - | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">:<span style="mso-no-proof:yes">
| + | |
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| | <p class="MsoNormal"><span lang="EN-US">In the main display window, you will see | | <p class="MsoNormal"><span lang="EN-US">In the main display window, you will see |
| | a network from KEGG website. On the left, there is a finder; you can search | | a network from KEGG website. On the left, there is a finder; you can search |
| Line 1,158: |
Line 377: |
| | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">Simulator</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> | | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">Simulator</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> |
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| - | AB8AAAAAAAAAAAAAAAAA0iUAAGNsaXBib2FyZC9kaWFncmFtcy9kcmF3aW5nMS54bWxQSwUGAAAA
| + | |
| - | AAoACgDmAgAA7yYAAAAA
| + | |
| - | ">
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/f/f7/Tutorial_%2813%29.png" style="width: 650px;" o:title=""/ > | + | |
| - | <o:lock v:ext="edit" aspectratio="f"/>
| + | |
| - | </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_641" | + | |
| - | o:spid="_x0000_i1052" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图3\biarkit截图\fba\main.png"
| + | |
| - | style='width:414pt;height:310.2pt;visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/a/ae/Tutorial_%2814%29.png" o:title="main"/ > | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p>
| + | |
| - | <p class="MsoNormal"><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_16"
| + | |
| - | o:spid="_x0000_i1051" type="#_x0000_t75" style='width:415.2pt;height:159pt;
| + | |
| - | visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/b/be/Tutorial_%2815%29.png" style="width: 650px;" o:title=""/ > | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p>
| + | |
| - | <p class="MsoNormal"><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_640" | + | |
| - | o:spid="_x0000_i1050" type="#_x0000_t75" style='width:414pt;height:156pt;
| + | |
| - | visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/ e/ e9/Tutorial_% 2816%29.png" style="width: 650px;" o:title=""/ > | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p>
| + | |
| - | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
| + | |
| - | <p class="MsoNormal"><o:wrapblock><v:shape id="图片_x0020_15" o:spid="_x0000_s2052" | + | |
| | type="#_x0000_t75" style='position:absolute;left:0;text-align:left; | | type="#_x0000_t75" style='position:absolute;left:0;text-align:left; |
| | margin-left:0;margin-top:3.9pt;width:414.7pt;height:319.2pt;z-index:251666432; | | margin-left:0;margin-top:3.9pt;width:414.7pt;height:319.2pt;z-index:251666432; |
| Line 1,382: |
Line 396: |
| | mso-width-percent:0;mso-height-percent:0;mso-width-relative:margin; | | mso-width-percent:0;mso-height-percent:0;mso-width-relative:margin; |
| | mso-height-relative:margin'> | | mso-height-relative:margin'> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/d/da/Tutorial_%2817%29.png" style="width: 650px;" o:title=""/> | + | <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/></v:shape></o:wrapblock><br style="mso-ignore:vglayout" clear="ALL"> |
| - | <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/>
| + | |
| - | </v:shape></o:wrapblock><br style="mso-ignore:vglayout" clear="ALL">
| + | |
| | <span lang="EN-US">There are 5 options for you to select: exhaustive single | | <span lang="EN-US">There are 5 options for you to select: exhaustive single |
| | deletion, reaction deletion, Fva analysis, <span style="mso-no-proof:yes"> | | deletion, reaction deletion, Fva analysis, <span style="mso-no-proof:yes"> |
| Line 1,401: |
Line 413: |
| | <span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman""> | | <span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman""> |
| | </span></span></span><![endif]><span lang="EN-US">FBA_solve<o:p></o:p></span></p> | | </span></span></span><![endif]><span lang="EN-US">FBA_solve<o:p></o:p></span></p> |
| - | <p style="mso-para-margin-top: .5gd; mso-para-margin-right: 0cm; mso-para-margin-bottom: 0cm; mso-para-margin-left: 18.0pt; mso-para-margin-bottom: .0001pt; mso-char-indent-count: 0; mso-list: l0 level1 lfo2; text-justify: inter-ideograph;" class="style1"> | + | <p style="mso-para-margin-top: .5gd; mso-para-margin-right: 0cm; mso-para-margin-bottom: 0cm; mso-para-margin-left: 18.0pt; mso-para-margin-bottom: .0001pt; mso-char-indent-count: 0; mso-list: l0 level1 lfo2; text-justify: inter-ideograph;" class="style1"> |
| - | <![if !supportLists]> | + | <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> |
| - | <span lang="EN-US" style="mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
| + | <p class="MsoNormal">Above<span lang="EN-US"> column displays names of the |
| - | mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin">
| + | |
| - | <span style="mso-list:Ignore">2.<span style="font:7.0pt "Times New Roman"">
| + | |
| - | </span></span></span><![endif]><span lang="EN-US" style="mso-no-proof:yes"><v:shape
| + | |
| - | id="图片_x0020_28" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:426.6pt;
| + | |
| - | height:307.8pt;visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/b/b6/Tutorial_%2818%29.png" style="width: 650px;" o:title=""/> | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | + | |
| - | <p class="MsoNormal"><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> | | reactions while the right one displays the flux amount of each reaction<o:p></o:p></span></p> |
| | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> |
| Line 1,417: |
Line 421: |
| | <p class="MsoNormal"><span lang="EN-US">Calculate the flux amount of the | | <p class="MsoNormal"><span lang="EN-US">Calculate the flux amount of the |
| | objective reaction when each other reaction is deleted one by one.<o:p></o:p></span></p> | | objective reaction when each other reaction is deleted one by one.<o:p></o:p></span></p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_27" | + | |
| - | o:spid="_x0000_i1048" type="#_x0000_t75" style='width:412.2pt;height:297.6pt;
| + | <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> |
| - | visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/4/47/Tutorial_%2819%29.png" style="width: 650px;" o:title=""/> | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | + | |
| | <p class="MsoNormal"><span lang="EN-US">Left column display names of the | | <p class="MsoNormal"><span lang="EN-US">Left column display names of the |
| | reactions <o:p></o:p></span></p> | | reactions <o:p></o:p></span></p> |
| | <p class="MsoNormal"><span lang="EN-US">The right one displays the flux amount | | <p class="MsoNormal"><span lang="EN-US">The right one displays the flux amount |
| | of objective reaction the user has chosen, when each other reaction is deleted | | of objective reaction the user has chosen, when each other reaction is deleted |
| - | one by one.<o:p></o:p></span></p> | + | one by one.<o:p> </o:p></span></p> |
| - | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
| + | <span lang="EN-US" style="mso-no-proof:yes"> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_26"
| + | <v:shape id="图片_x0020_24" |
| - | o:spid="_x0000_i1047" type="#_x0000_t75" alt="说明: lethal deletions.bmp"
| + | |
| - | style='width:225pt;height:209.4pt;visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/5/5b/Tutorial_%2820%29.png" o:title="lethal deletions"/>
| + | |
| - | </v:shape></span><span lang="EN-US">.<span style="mso-no-proof:yes"><v:shape
| + | |
| - | id="图片_x0020_25" o:spid="_x0000_i1046" type="#_x0000_t75" alt="说明: sub optimal dels.bmp"
| + | |
| - | style='width:222.6pt;height:270.6pt;visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/d/d3/Tutorial_%2821%29.png" o:title="sub optimal dels"/>
| + | |
| - | </v:shape></span><o:p></o:p></span></p>
| + | |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_24"
| + | |
| | o:spid="_x0000_i1045" type="#_x0000_t75" alt="说明: super optimal dels.bmp" | | o:spid="_x0000_i1045" type="#_x0000_t75" alt="说明: super optimal dels.bmp" |
| - | style='width:117.6pt;height:40.2pt;visibility:visible;mso-wrap-style:square'> | + | style='width:117.6pt;height:40.2pt;visibility:visible;mso-wrap-style:square'><p><span lang="EN-US" style="mso-no-proof:yes"> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/3/3b/Tutorial_%2822%29.png" o:title="super optimal dels" | + | <img src="https://static.igem.org/mediawiki/igem.org/5/5b/Tutorial_%2820%29.png" o:title="lethal deletions" height="284"/><img src="https://static.igem.org/mediawiki/igem.org/d/d3/Tutorial_%2821%29.png" o:title="sub optimal dels"/><img src="https://static.igem.org/mediawiki/igem.org/3/3b/Tutorial_%2822%29.png" o:title="super optimal dels" |
| - | croptop="3449f" cropbottom="34000f"/> | + | croptop="3449f" cropbottom="34000f"/></span></p></v:shape> |
| - | </v:shape><o:p></o:p></span></p> | + | </span><p class="MsoNormal"><span lang="EN-US">when rolling down the screen, you can |
| - | <p class="MsoNormal"><span lang="EN-US">when rolling down the screen, you can | + | |
| | see the reaction-names related to lethal deletions, sub optimal deletions and | | see the reaction-names related to lethal deletions, sub optimal deletions and |
| | super optimaldeletions<span style="mso-no-proof:yes">.<o:p></o:p></span></span></p> | | super optimaldeletions<span style="mso-no-proof:yes">.<o:p></o:p></span></span></p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_23" | + | |
| - | o:spid="_x0000_i1044" type="#_x0000_t75" style='width:409.2pt;height:315pt;
| + | <o: p><img src="https://static.igem.org/mediawiki/igem.org/b/b7/Tutorial_%2823%29.png" o:title=""/></o:p></p> |
| - | visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/b/b7/Tutorial_%2823%29.png" o:title=""/> | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | + | |
| | <p class="MsoNormal"><span lang="EN-US">This graph shows how many lethal | | <p class="MsoNormal"><span lang="EN-US">This graph shows how many lethal |
| | knockouts in each reaction subsystem. The information of the reaction subsystem | | knockouts in each reaction subsystem. The information of the reaction subsystem |
| - | can be attained in SBML <o:p></o:p></span></p> | + | can be attained in SBML <o:p></o:p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_22" | + | </span></p> |
| - | o:spid="_x0000_i1043" type="#_x0000_t75" style='width:415.8pt;height:433.8pt;
| + | |
| - | visibility:visible;mso-wrap-style:square'>
| + | <o: p><img src="https://static.igem.org/mediawiki/igem.org/1/19/Tutorial_%2824%29.png" o:title=""/></o:p></p> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/1/19/Tutorial_%2824%29.png" o:title=""/> | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | + | |
| | <p class="MsoNormal"><span lang="EN-US">This hist graph shows the frequency of | | <p class="MsoNormal"><span lang="EN-US">This hist graph shows the frequency of |
| | reaction which has different quantified effect showed in the X-axis opon | | reaction which has different quantified effect showed in the X-axis opon |
| Line 1,464: |
Line 450: |
| | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> |
| | <p class="MsoNormal"><span lang="EN-US">3. reaction deletion<o:p></o:p></span></p> | | <p class="MsoNormal"><span lang="EN-US">3. reaction deletion<o:p></o:p></span></p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_21" | + | |
| - | o:spid="_x0000_i1042" type="#_x0000_t75" style='width:415.8pt;height:300pt;
| + | <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> |
| - | visibility:visible;mso-wrap-style:square'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/4/48/Tutorial_%2825%29.png" style="width: 650px;" o:title=""/> | + | |
| - | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | + | |
| | <p class="MsoNormal"><span lang="EN-US">Middle column displays the flux amount | | <p class="MsoNormal"><span lang="EN-US">Middle column displays the flux amount |
| | of the wild type while the right column displays the mutant type, which is | | of the wild type while the right column displays the mutant type, which is |
| Line 1,474: |
Line 457: |
| | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> |
| | <p class="MsoNormal"><span lang="EN-US">4. FVA analysis<o:p></o:p></span></p> | | <p class="MsoNormal"><span lang="EN-US">4. FVA analysis<o:p></o:p></span></p> |
| - | <p class="MsoNormal"><o:wrapblock><v:shape id="图片_x0020_20" o:spid="_x0000_s2051" | + | <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> |
| - | type="#_x0000_t75" style='position:absolute;left:0;text-align:left;
| + | |
| - | margin-left:0;margin-top:3.9pt;width:415.55pt;height:319.75pt;z-index:251667456;
| + | |
| - | visibility:visible;mso-wrap-style:square;mso-width-percent:0;
| + | |
| - | mso-height-percent:0;mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;
| + | |
| - | mso-wrap-distance-right:9pt;mso-wrap-distance-bottom:0;
| + | |
| - | mso-position-horizontal:absolute;mso-position-horizontal-relative:text;
| + | |
| - | mso-position-vertical:absolute;mso-position-vertical-relative:text;
| + | |
| - | mso-width-percent:0;mso-height-percent:0;mso-width-relative:margin;
| + | |
| - | mso-height-relative:margin'>
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/a/a9/Tutorial_%2826%29.png" style="width: 650px;" o:title=""/> | + | |
| - | <w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/>
| + | |
| - | </v:shape></o:wrapblock><br style="mso-ignore:vglayout" clear="ALL">
| + | |
| - | <span lang="EN-US" style="mso-no-proof:yes">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 style="font-family:宋体;mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;
| + | |
| - | mso-fareast-font-family:宋体;mso-fareast-theme-font:minor-fareast;mso-hansi-font-family:
| + | |
| - | Calibri;mso-hansi-theme-font:minor-latin;mso-no-proof:yes">‘</span><span lang="EN-US" style="mso-no-proof:yes">lower
| + | |
| - | flux limit </span>
| + | |
| - | <span style="font-family:宋体;mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;
| + | |
| - | mso-fareast-font-family:宋体;mso-fareast-theme-font:minor-fareast;mso-hansi-font-family:
| + | |
| - | Calibri;mso-hansi-theme-font:minor-latin;mso-no-proof:yes">’</span><span lang="EN-US" style="mso-no-proof:yes">and
| + | |
| - | </span>
| + | |
| - | <span style="font-family:宋体;
| + | |
| - | mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
| + | |
| - | 宋体;mso-fareast-theme-font:minor-fareast;mso-hansi-font-family:Calibri;
| + | |
| - | mso-hansi-theme-font:minor-latin;mso-no-proof:yes">‘</span><span lang="EN-US" style="mso-no-proof:yes">upper
| + | |
| - | flux limit</span><span style="font-family:宋体;
| + | |
| - | mso-ascii-font-family:Calibri;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
| + | |
| - | 宋体;mso-fareast-theme-font:minor-fareast;mso-hansi-font-family:Calibri;
| + | |
| - | mso-hansi-theme-font:minor-latin;mso-no-proof:yes">’</span><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"><o:p> </o:p></span></p>
| + | |
| | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">5.Perturbation | | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">5.Perturbation |
| | analysis:<o:p></o:p></span></p> | | analysis:<o:p></o:p></span></p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_11" | + | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"> |
| | + | <v:shape id="图片_x0020_11" |
| | o:spid="_x0000_i1041" type="#_x0000_t75" style='width:414pt;height:411pt; | | o:spid="_x0000_i1041" type="#_x0000_t75" style='width:414pt;height:411pt; |
| | visibility:visible;mso-wrap-style:square'> | | visibility:visible;mso-wrap-style:square'> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/c/ce/Tutorial_%2827%29.png" o:title=""/> | + | </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> |
| - | </v:shape><o:p></o:p></span></p>
| + | |
| | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">X-axis refers | | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">X-axis refers |
| | to the continuously increasing flux value of the chosen reaction.<o:p></o:p></span></p> | | to the continuously increasing flux value of the chosen reaction.<o:p></o:p></span></p> |
| Line 1,524: |
Line 474: |
| | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">6.PhPP analysis <o:p></o: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 class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_10" | + | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"> |
| | + | <v:shape id="图片_x0020_10" |
| | o:spid="_x0000_i1040" type="#_x0000_t75" style='width:409.2pt;height:433.8pt; | | o:spid="_x0000_i1040" type="#_x0000_t75" style='width:409.2pt;height:433.8pt; |
| | visibility:visible;mso-wrap-style:square'> | | visibility:visible;mso-wrap-style:square'> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/7/78/Tutorial_%2828%29.png" o:title=""/> | + | </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> |
| - | </v:shape><o:p></o:p></span></p>
| + | |
| | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">The value | | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">The value |
| | marked on the contour represents the flux value of the objective reaction based | | marked on the contour represents the flux value of the objective reaction based |
| Line 1,536: |
Line 486: |
| | <h1><a name="_Toc338881885"> | | <h1><a name="_Toc338881885"> |
| | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">G-Circle</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> | | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">G-Circle</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> |
| - | <p class="MsoNormal"><o:wrapblock><v:shape id="图示_x0020_9" o:spid="_x0000_s2050" | + | <p class="MsoNormal"> |
| | + | <o:wrapblock> |
| | + | <v:shape id="图示_x0020_9" o:spid="_x0000_s2050" |
| | type="#_x0000_t75" style='position:absolute;left:0;text-align:left; | | type="#_x0000_t75" style='position:absolute;left:0;text-align:left; |
| | margin-left:-2.4pt;margin-top:18.75pt;width:254.9pt;height:42.7pt;z-index:251662336; | | margin-left:-2.4pt;margin-top:18.75pt;width:254.9pt;height:42.7pt;z-index:251662336; |
| Line 1,727: |
Line 679: |
| | BQYAAAAACgAKAOYCAABlJQAAAAA= | | BQYAAAAACgAKAOYCAABlJQAAAAA= |
| | "> | | "> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/a/ab/Tutorial_%2829%29.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"/>
| + | <p class="MsoNormal"> |
| - | <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 style="mso-ignore:vglayout" clear="ALL">
| + | croptop="-3052f"/></p> |
| - | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> | + | <p class="MsoNormal"> |
| - | </span></p> | + | <img src="https://static.igem.org/mediawiki/igem.org/1/1d/Tutorial_%2830%29.png" style="width: 650px;" o:title=""/></p> |
| - | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><v:shape id="图片_x0020_18" | + | <p class="MsoNormal"><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_18" |
| | o:spid="_x0000_i1039" type="#_x0000_t75" style='width:442.2pt;height:249pt; | | o:spid="_x0000_i1039" type="#_x0000_t75" style='width:442.2pt;height:249pt; |
| | visibility:visible;mso-wrap-style:square'> | | visibility:visible;mso-wrap-style:square'> |
| - | <img src="https://static.igem.org/mediawiki/igem.org/1/1d/Tutorial_%2830%29.png" style="width: 650px;" o:title=""/> | + | </v:shape></span><span lang="EN-US">You can open several file so that you can |
| - | </v:shape></span><span lang="EN-US">You can open several file so that you can | + | |
| | compare the difference of these genomes. Each genome have 2 circles in the | | 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 | | picture: the outer one is the genes of the genome, the inner is the expression |
| Line 1,863: |
Line 816: |
| | <img src="https://static.igem.org/mediawiki/igem.org/2/22/Tutorial_%2844%29.png" style="width: 650px;" o:title="gcircle2"/> | | <img src="https://static.igem.org/mediawiki/igem.org/2/22/Tutorial_%2844%29.png" style="width: 650px;" o:title="gcircle2"/> |
| | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> |
| - | </div> | + | <p></p> </div><!--end content--> |
| - | </div><!--end entry-->
| + | |
| - | </div><!--end content-->
| + | |
| | | | |
| | <div id="sidebar"> | | <div id="sidebar"> |
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