Team:SYSU-Software/Tutorial
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style=" | style=" | ||
text-align:center; | text-align:center; | ||
- | width: | + | width:970px; |
margin:0 auto;> | margin:0 auto;> | ||
- | <div class="skip-content" | + | <div class="skip-content"></div> |
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<div class="wrapper"> | <div class="wrapper"> | ||
- | <a href="/" class="sysu-title"></a> | + | <a href="https://2012.igem.org/Team:SYSU-Software" class="sysu-title"></a> |
<!--end navigation--> | <!--end navigation--> | ||
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<div id="menu"> | <div id="menu"> | ||
<ul id="nav"> | <ul id="nav"> | ||
- | <li class="mainlevel" id="mainlevel_01"><a href=" | + | <li class="mainlevel" id="mainlevel_01"><a href="https://2012.igem.org/Team:SYSU-Software"> Home</a> |
</li> | </li> | ||
- | <li class="mainlevel" id="mainlevel_02"><a href=" | + | <li class="mainlevel" id="mainlevel_02"><a href="https://2012.igem.org/Team:SYSU-Software/Project">Project</a> |
</li> | </li> | ||
- | + | ||
- | <li class="mainlevel"><a href=" | + | <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Models">Models</a> |
+ | </li> | ||
+ | <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Tutorial">Tutorial</a> | ||
+ | |||
+ | </li> | ||
+ | <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Team">Team</a> | ||
</li> | </li> | ||
- | + | ||
- | |||
- | |||
- | |||
- | |||
- | <li class="mainlevel"><a href=" | + | <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Notebook">Notebook</a></li> |
+ | <li class="mainlevel"><a href="https://2012.igem.org/Team:SYSU-Software/Practice"> | ||
+ | Tips</a><!--input an em tag as a space,IE is gread need--> | ||
+ | </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> | ||
</div> | </div> | ||
- | <img src=" | + | <img src=" https://static.igem.org/mediawiki/2012/6/6d/Little-boy.png" id="little-boy"></img> |
<div id="content"> <div class="entry page clear"> | <div id="content"> <div class="entry page clear"> | ||
- | <h1 id="doctitle" class="pagetitle"> | + | <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="#r1"> | + | <li class="toclevel-1"><a href="#r1">Genome Browser</a></li> |
- | <li class="toclevel-1"><a href="#r2">< | + | <li class="toclevel-1"><a href="#r2">Biobrick</a></li> |
- | <li class="toclevel-1"><a href="# | + | <li class="toclevel-1"><a href="#r3">Riboswitch</a></li> |
- | <li class="toclevel-1"><a href="# | + | <li class="toclevel-1"><a href="#r4">SiRNA</a></li> |
- | <li class="toclevel-1"><a href="# | + | <li class="toclevel-1"><a href="#r5">Meta Network</a></li> |
+ | <li class="toclevel-1"><a href="#r6">Simulator</a></li> | ||
+ | <li class="toclevel-1"><a href="#r7">G-Circle</a></li> | ||
+ | <li class="toclevel-1"><a href="#r8">Clotho</a></li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
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</tbody> | </tbody> | ||
</table> | </table> | ||
- | <div | + | </div> |
- | < | + | <span></span> |
- | < | + | <h1><a name="_Toc338881878"> |
- | <p> | + | <span lang="EN-US" style="font-size:14.0pt;line-height:240%">Home<o:p></o:p></span></a></h1> |
- | <p> | + | <p><span style="mso-bookmark:_Toc338881878"> |
- | + | <span lang="EN-US" style="font-size:14.0pt;line-height:240%;mso-no-proof:yes"><v:shape id="图片_x0020_29" o:spid="_x0000_i1060" type="#_x0000_t75" | |
- | + | style='width:400.2pt;height:314.4pt;visibility:visible;mso-wrap-style:square'> | |
- | + | <img src="https://static.igem.org/mediawiki/igem.org/e/ef/Tutorial_%281%29.png" style="width: 650px;" o:title=""/ ></span></span></v:shape><o:p></o:p></p> | |
- | + | <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 | |
- | + | SYSU-software igem team.<o:p></o:p></span></p> | |
- | + | <p class="MsoNormal"><span lang="EN-US">In the main display window, there are | |
- | + | six buttons, G-Circle, Network Illustrator, RiboSwitch, Genome Browser, SiRNA, | |
- | <p> | + | Biobrick, and Simulator, which will take you to corresponding parts once |
- | </ | + | clicking.<o:p></o:p></span></p> |
- | < | + | <h1><a name="_Toc338881879"> |
- | < | + | <span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r1">Genome Browser</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"> <o:p></o:p> |
- | <p> | + | </span></h1> |
- | <p> | + | <p> |
+ | <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> | ||
+ | <o:p></o:p> | ||
</p> | </p> | ||
- | </ | + | <p> |
- | < | + | <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> |
- | < | + | </p> |
- | <p>Procedure: | + | <p class="MsoNormal"><span lang="EN-US">In the main display window, the first |
- | </p><p> | + | ribbon is the sequence that the user has inputted, and the third ribbon shows |
- | </p></ | + | the corresponding gene annotation. You can click any annotation that you want, |
- | < | + | and then the sequence site will automatically jump to the fragment related to |
- | < | + | it. Between those ribbons is an adjustable slider, which can adjust your view |
- | <p>Procedure: | + | location by sliding to the left or to the right. Above the sequence are the head |
- | <p> | + | and tail of the location that you are viewing while the head and tail of the |
- | </p></ | + | whole sequence are displayed in the bottom textbox. What’s more, the textbox |
- | < | + | contains the length, product, tag of the sequence, and links of related papers |
- | < | + | are also included sometimes. <o:p></o:p></span></p> |
- | <p>Procedure: | + | <p class="MsoNormal"><span lang="EN-US">On the left, there are two useful tools: |
- | <p> | + | you can search the fragment that you want by position, product or name (Position |
- | </p></ | + | represents the position of its head, Product and Name stand for products and |
- | < | + | names of related genes, both of them support fuzzy search), besides, whether you |
- | < | + | choose product or name, a dialog box that contains names of related genes will |
- | <p>Procedure: | + | appear; the slider of Zoom is designed for regulating the display frame rate of |
- | <p> | + | the sequence. <o:p></o:p></span></p> |
- | </p></ | + | <h1><a name="_Toc338881880"> |
- | + | <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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+ | "> | ||
+ | <o:lock v:ext="edit" aspectratio="f"/><w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/></v:shape></o:wrapblock><i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> | ||
+ | </span></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/4/46/Tutorial_%284%29.png" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/0/08/Tutorial_%286%29.png" style="width: 650px;" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/5/58/Tutorial_%285%29.png" style="width: 650px;" o:title="Biobrick"/></o:p> | ||
+ | </p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">Notice that there is a finder on the | ||
+ | left; you can search biobricks by key words and then a window showing the search | ||
+ | result will pop up. Bellow it is a list of biobrick. Turning to the right, a | ||
+ | schematic diagram that shows components of the biobrick is on the top. And | ||
+ | related information about the biobrick is below it.<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <h1><a name="_Toc338881881"> | ||
+ | <span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r3">RiboSwitch</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> | ||
+ | <p class="MsoNormal"><i style="mso-bidi-font-style:normal"><span lang="EN-US"> | ||
+ | Procedure</span></i><span lang="EN-US">: <o:p></o:p> | ||
+ | </span></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/7/71/Tutorial_%287%29.png" style="width: 650px;" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/9/92/Tutorial_%288%29.png" style="width: 650px;" o:title="Biobrick"/></o:p> | ||
+ | </p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">On the right is the main operating area | ||
+ | and you can choose your target type (your experimental object) and corresponding | ||
+ | target name, aptamer and regulation direction. Attention should be paid to the | ||
+ | input box named Input your Target. You can search your target name by key words | ||
+ | or even several letters of it. It should be useful to you. Click | ||
+ | <b style="mso-bidi-font-weight:normal">GO</b> and you will see a picture. The | ||
+ | designed riboswitch is in the dotted box on the top left corner. Below it is a | ||
+ | diagram to show how the riboswitch works. Besides, there is a list on the left | ||
+ | box. It records your choices that you have made in created riboswich project, | ||
+ | and you need only click <b style="mso-bidi-font-weight:normal">GO</b> next time.<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <h1><a name="_Toc338881882"> | ||
+ | <span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r4">SiRNA</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> | ||
+ | <p class="MsoNormal"> | ||
+ | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> | ||
+ | </span></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/1/18/Tutorial_%289%29.png" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/1/10/Tutorial_%2810%29.png" style="width: 650px;" o:title=""/></o:p> | ||
+ | </p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <h1><a name="_Toc338881883"> | ||
+ | <span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r5">Network Illustrator</span></a><o:p></o:p></h1> | ||
+ | <p class="MsoNormal"> | ||
+ | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">: <o:p></o:p> | ||
+ | </span></p> | ||
+ | <p> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/7/72/Tutorial_%2811%29.png" o:title=""/><img src="https://static.igem.org/mediawiki/igem.org/c/ce/Tutorial_%2812%29.png" style="width: 650px;" o:title=""/></o:p></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">In the main display window, you will see | ||
+ | a network from KEGG website. On the left, there is a finder; you can search | ||
+ | elements in the network and a window that shows the search result will pop up. | ||
+ | Bellow it is a box containing a list of files that you have opened. Pay | ||
+ | attention that you can right click the main display window to open another KEGG | ||
+ | xml file or to search any element in the network (choose | ||
+ | <b style="mso-bidi-font-weight:normal">find element</b>).<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <h1><a name="_Toc338881884"> | ||
+ | <span lang="EN-US" style="font-size:14.0pt;line-height:240%" id="r5">Simulator</span></a><span lang="EN-US" style="font-size:14.0pt;line-height:240%"><o:p></o:p></span></h1> | ||
+ | <p class="MsoNormal"><i style="mso-bidi-font-style:normal"><span lang="EN-US"> | ||
+ | Procedure</span></i><span lang="EN-US">: | ||
+ | </span></p> | ||
+ | <p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/f/f7/Tutorial_%2813%29.png" style="width: 650px;" o:title=""/></p> | ||
+ | <p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/a/ae/Tutorial_%2814%29.png" o:title="main"/></p> | ||
+ | <p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/b/be/Tutorial_%2815%29.png" style="width: 650px;" o:title=""/></p> | ||
+ | <p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/e/e9/Tutorial_%2816%29.png" style="width: 650px;" o:title=""/></p> | ||
+ | <p class="MsoNormal"><img src="https://static.igem.org/mediawiki/igem.org/d/da/Tutorial_%2817%29.png" style="width: 650px;" o:title=""/> </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; | ||
+ | margin-left:0;margin-top:3.9pt;width:414.7pt;height:319.2pt;z-index:251666432; | ||
+ | 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'> | ||
+ | <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 | ||
+ | deletion, reaction deletion, Fva analysis, <span style="mso-no-proof:yes"> | ||
+ | Perturbation analysis</span> and <span style="mso-no-proof:yes">PhPP analysis</span>. | ||
+ | They with FBA solve will be introduced in detail. You can select all of them or | ||
+ | part of them, or even nothing, then click <b style="mso-bidi-font-weight:normal"> | ||
+ | Go</b>. If you select none of them, you will see a table showed basic | ||
+ | information of each reaction. If you select several of them, the corresponding | ||
+ | windows will tiled in the resulting window. If you select reaction deletion | ||
+ | option, a selection of the reaction you want to wipe off is required, and if | ||
+ | there is any change, it will be highlighted in red font.<o:p></o:p></span></p> | ||
+ | <p style="mso-para-margin-top: .5gd; mso-para-margin-right: 0cm; mso-para-margin-bottom: 0cm; mso-para-margin-left: 18.0pt; mso-para-margin-bottom: .0001pt; mso-char-indent-count: 0; mso-list: l0 level1 lfo2; text-justify: inter-ideograph;" class="style1"> | ||
+ | <![if !supportLists]> | ||
+ | <span lang="EN-US" style="mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin; | ||
+ | mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"> | ||
+ | <span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman""> | ||
+ | </span></span></span><![endif]><span lang="EN-US">FBA_solve<o:p></o:p></span></p> | ||
+ | <p style="mso-para-margin-top: .5gd; mso-para-margin-right: 0cm; mso-para-margin-bottom: 0cm; mso-para-margin-left: 18.0pt; mso-para-margin-bottom: .0001pt; mso-char-indent-count: 0; mso-list: l0 level1 lfo2; text-justify: inter-ideograph;" class="style1"> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/b/b6/Tutorial_%2818%29.png" style="width: 650px;" o:title=""/></o:p></p> | ||
+ | <p class="MsoNormal">Above<span lang="EN-US"> column displays names of the | ||
+ | reactions while the right one displays the flux amount of each reaction<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">2. exanstive single deletion<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">Calculate the flux amount of the | ||
+ | objective reaction when each other reaction is deleted one by one.<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/4/47/Tutorial_%2819%29.png" style="width: 650px;" o:title=""/></o:p></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">Left column display names of the | ||
+ | reactions <o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">The right one displays the flux amount | ||
+ | of objective reaction the user has chosen, when each other reaction is deleted | ||
+ | one by one.<o:p> </o:p></span></p> | ||
+ | <span lang="EN-US" style="mso-no-proof:yes"> | ||
+ | <v:shape id="图片_x0020_24" | ||
+ | o:spid="_x0000_i1045" type="#_x0000_t75" alt="说明: super optimal dels.bmp" | ||
+ | style='width:117.6pt;height:40.2pt;visibility:visible;mso-wrap-style:square'><p><span lang="EN-US" style="mso-no-proof:yes"> | ||
+ | <img src="https://static.igem.org/mediawiki/igem.org/5/5b/Tutorial_%2820%29.png" o:title="lethal deletions" height="284"/><img src="https://static.igem.org/mediawiki/igem.org/d/d3/Tutorial_%2821%29.png" o:title="sub optimal dels"/><img src="https://static.igem.org/mediawiki/igem.org/3/3b/Tutorial_%2822%29.png" o:title="super optimal dels" | ||
+ | croptop="3449f" cropbottom="34000f"/></span></p></v:shape> | ||
+ | </span><p class="MsoNormal"><span lang="EN-US">when rolling down the screen, you can | ||
+ | see the reaction-names related to lethal deletions, sub optimal deletions and | ||
+ | super optimaldeletions<span style="mso-no-proof:yes">.<o:p></o:p></span></span></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/b/b7/Tutorial_%2823%29.png" o:title=""/></o:p></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">This graph shows how many lethal | ||
+ | knockouts in each reaction subsystem. The information of the reaction subsystem | ||
+ | can be attained in SBML <o:p></o:p> | ||
+ | </span></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/1/19/Tutorial_%2824%29.png" o:title=""/></o:p></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">This hist graph shows the frequency of | ||
+ | reaction which has different quantified effect showed in the X-axis opon | ||
+ | objective reaction.<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">3. reaction deletion<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <o:p><img src="https://static.igem.org/mediawiki/igem.org/4/48/Tutorial_%2825%29.png" style="width: 650px;" o:title=""/></o:p></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">Middle column displays the flux amount | ||
+ | of the wild type while the right column displays the mutant type, which is | ||
+ | calculated based on the deletion of one chosen reaction.<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US">4. FVA analysis<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><o:p> <img src="https://static.igem.org/mediawiki/igem.org/a/a9/Tutorial_%2826%29.png" style="width: 650px;" o:title=""/></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">5.Perturbation | ||
+ | analysis:<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"> | ||
+ | <v:shape id="图片_x0020_11" | ||
+ | o:spid="_x0000_i1041" type="#_x0000_t75" style='width:414pt;height:411pt; | ||
+ | visibility:visible;mso-wrap-style:square'> | ||
+ | </v:shape><o:p><img src="https://static.igem.org/mediawiki/igem.org/c/ce/Tutorial_%2827%29.png" o:title=""/></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">X-axis refers | ||
+ | to the continuously increasing flux value of the chosen reaction.<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">Y-axis refers | ||
+ | to the flux value of the objective reaction according to the variation of the | ||
+ | flux value of chosen reaction in the X-axis<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"><o:p> </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">6.PhPP analysis <o:p></o:p> | ||
+ | </span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"> | ||
+ | <v:shape id="图片_x0020_10" | ||
+ | o:spid="_x0000_i1040" type="#_x0000_t75" style='width:409.2pt;height:433.8pt; | ||
+ | visibility:visible;mso-wrap-style:square'> | ||
+ | </v:shape><o:p><img src="https://static.igem.org/mediawiki/igem.org/7/78/Tutorial_%2828%29.png" o:title=""/></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes">The value | ||
+ | marked on the contour represents the flux value of the objective reaction based | ||
+ | on the variation of two chosen reactions The color of the graph changes | ||
+ | according to the altitude, namely, the objective flux value.<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <h1><a name="_Toc338881885"> | ||
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+ | "> | ||
+ | <o:lock v:ext="edit" aspectratio="f"/><w:wrap type="topAndBottom" xmlns:w="urn:schemas-microsoft-com:office:word"/></v:shape></o:wrapblock><br style="mso-ignore:vglayout" clear="ALL"> | ||
+ | <i style="mso-bidi-font-style:normal"><span lang="EN-US">Procedure</span></i><span lang="EN-US">:</span></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <img src="https://static.igem.org/mediawiki/igem.org/a/ab/Tutorial_%2829%29.png" o:title="" | ||
+ | croptop="-3052f"/></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <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"> <o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US" style="mso-no-proof:yes"> | ||
+ | <v:shape id="图片_x0020_18" | ||
+ | o:spid="_x0000_i1039" type="#_x0000_t75" style='width:442.2pt;height:249pt; | ||
+ | visibility:visible;mso-wrap-style:square'> | ||
+ | </v:shape></span><span lang="EN-US">You can open several file so that you can | ||
+ | compare the difference of these genomes. Each genome have 2 circles in the | ||
+ | picture: the outer one is the genes of the genome, the inner is the expression | ||
+ | level of corresponding genes. By the way, right click different sites in the | ||
+ | small panoramic window or left click and drag the picture in the zoom window, | ||
+ | you can move to anywhere you want to enlarge and see more details in the | ||
+ | amplifier window.<o:p></o:p></span></p> | ||
+ | <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p> | ||
+ | <h1><a name="_Toc338881886"><span lang="EN-US" id="r8">Clotho</span></a><span lang="EN-US"><o:p></o:p></span></h1> | ||
+ | <p class="MsoNormal"><span lang="EN-US">All above seven parts have been | ||
+ | developed into <b style="mso-bidi-font-weight:normal"> | ||
+ | <i style="mso-bidi-font-style:normal">Clotho</i></b> apps and have been updated | ||
+ | into <b style="mso-bidi-font-weight:normal"> | ||
+ | <i style="mso-bidi-font-style:normal">Clotho, </i></b>which has met the | ||
+ | requirements for gold medal of IGEM.<o:p></o:p></span></p> | ||
+ | <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'> | ||
+ | </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>G-Circle</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_655" | ||
+ | o:spid="_x0000_i1025" type="#_x0000_t75" alt="说明: E:\Biology\iGEM\软件组\biarkit截图(1)\biarkit截图\clotho\gcircle2.png" | ||
+ | style='width:414.6pt;height:312.6pt;visibility:visible;mso-wrap-style:square'> | ||
+ | <img src="https://static.igem.org/mediawiki/igem.org/c/cd/Gcircle3.png" style="width: 650px;" o:title="gcircle2"/> | ||
+ | </v:shape></span><span lang="EN-US"><o:p></o:p></span></p> | ||
+ | <p></p> | ||
+ | <p class="MsoNormal"> | ||
+ | <span lang="EN-US" style="mso-bidi-font-size:10.5pt"> | ||
+ | </span></p> | ||
+ | </div><!--end content--> | ||
<div id="sidebar"> | <div id="sidebar"> | ||
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- | <a href="/ | + | <a href="https://2012.igem.org/Team:SYSU-Software/Team">Album</a> |
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- | <a href="/ | + | <a href="https://2012.igem.org/Team:SYSU-Software/SecondEdition">Second Edition</a> |
+ | </li> | ||
+ | <li> | ||
+ | <a href="https://2012.igem.org/Team:SYSU-Software/Accomplishment">Accomplishment</a> | ||
</li> | </li> | ||
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- | <a href="/ | + | <a href="https://2012.igem.org/Team:SYSU-Software/Video">Video</a> |
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- | <a href="">Troubleshooting</a> | + | <a href="https://2012.igem.org/Team:SYSU-Software/Trouble">Troubleshooting</a> |
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- | <a href=" | + | <a href="https://2012.igem.org/Team:SYSU-Software/Uninstalling">Uninstalling</a> |
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- | <h2>About</h2> | + | <h2> About</h2> |
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- | <a href="/ | + | <a href="https://2012.igem.org/Team:SYSU-Software/Team">Developers</a> |
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- | <li><a href="http://lifescience.sysu.edu.cn/main/default/index.aspx"> | + | <li><a href="http://lifescience.sysu.edu.cn/main/default/index.aspx">SYSU LifeScience</a></li> |
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Latest revision as of 23:56, 26 October 2012
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![](http://preview.zcool.com.cn/upimg/allimg/070622/0304268.gif)
![]( https://static.igem.org/mediawiki/2012/6/6d/Little-boy.png)
Tutorial
Contents |
Home
On the left is the logo of
BiArkit which is created by 2012
SYSU-software igem team.
In the main display window, there are
six buttons, G-Circle, Network Illustrator, RiboSwitch, Genome Browser, SiRNA,
Biobrick, and Simulator, which will take you to corresponding parts once
clicking.
Genome Browser
In the main display window, the first
ribbon is the sequence that the user has inputted, and the third ribbon shows
the corresponding gene annotation. You can click any annotation that you want,
and then the sequence site will automatically jump to the fragment related to
it. Between those ribbons is an adjustable slider, which can adjust your view
location by sliding to the left or to the right. Above the sequence are the head
and tail of the location that you are viewing while the head and tail of the
whole sequence are displayed in the bottom textbox. What’s more, the textbox
contains the length, product, tag of the sequence, and links of related papers
are also included sometimes.
On the left, there are two useful tools:
you can search the fragment that you want by position, product or name (Position
represents the position of its head, Product and Name stand for products and
names of related genes, both of them support fuzzy search), besides, whether you
choose product or name, a dialog box that contains names of related genes will
appear; the slider of Zoom is designed for regulating the display frame rate of
the sequence.
Biobrick
Notice that there is a finder on the
left; you can search biobricks by key words and then a window showing the search
result will pop up. Bellow it is a list of biobrick. Turning to the right, a
schematic diagram that shows components of the biobrick is on the top. And
related information about the biobrick is below it.
RiboSwitch
Procedure:
On the right is the main operating area
and you can choose your target type (your experimental object) and corresponding
target name, aptamer and regulation direction. Attention should be paid to the
input box named Input your Target. You can search your target name by key words
or even several letters of it. It should be useful to you. Click
GO and you will see a picture. The
designed riboswitch is in the dotted box on the top left corner. Below it is a
diagram to show how the riboswitch works. Besides, there is a list on the left
box. It records your choices that you have made in created riboswich project,
and you need only click GO next time.
SiRNA
Procedure:
Network Illustrator
Procedure:
In the main display window, you will see
a network from KEGG website. On the left, there is a finder; you can search
elements in the network and a window that shows the search result will pop up.
Bellow it is a box containing a list of files that you have opened. Pay
attention that you can right click the main display window to open another KEGG
xml file or to search any element in the network (choose
find element).
Simulator
Procedure:
There are 5 options for you to select: exhaustive single
deletion, reaction deletion, Fva analysis,
Perturbation analysis and PhPP analysis.
They with FBA solve will be introduced in detail. You can select all of them or
part of them, or even nothing, then click
Go. If you select none of them, you will see a table showed basic
information of each reaction. If you select several of them, the corresponding
windows will tiled in the resulting window. If you select reaction deletion
option, a selection of the reaction you want to wipe off is required, and if
there is any change, it will be highlighted in red font.
1.
FBA_solve
Above column displays names of the
reactions while the right one displays the flux amount of each reaction
2. exanstive single deletion
Calculate the flux amount of the
objective reaction when each other reaction is deleted one by one.
Left column display names of the
reactions
The right one displays the flux amount
of objective reaction the user has chosen, when each other reaction is deleted
one by one.
when rolling down the screen, you can
see the reaction-names related to lethal deletions, sub optimal deletions and
super optimaldeletions.
This graph shows how many lethal
knockouts in each reaction subsystem. The information of the reaction subsystem
can be attained in SBML
This hist graph shows the frequency of
reaction which has different quantified effect showed in the X-axis opon
objective reaction.
3. reaction deletion
Middle column displays the flux amount
of the wild type while the right column displays the mutant type, which is
calculated based on the deletion of one chosen reaction.
4. FVA analysis
5.Perturbation
analysis:
X-axis refers
to the continuously increasing flux value of the chosen reaction.
Y-axis refers
to the flux value of the objective reaction according to the variation of the
flux value of chosen reaction in the X-axis
6.PhPP analysis
The value
marked on the contour represents the flux value of the objective reaction based
on the variation of two chosen reactions The color of the graph changes
according to the altitude, namely, the objective flux value.
G-Circle
Procedure:
Clotho
All above seven parts have been
developed into
Clotho apps and have been updated
into
Clotho, which has met the
requirements for gold medal of IGEM.
Home
Genome Browser
Biobrick
RiboSwitch
SiRNA
Network Illustrator
Simulator
G-Circle