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        <h1 id="doctitle" class="pagetitle">Software Tutorial</h1>
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<h2>Contents</h2>
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<ul id="toc-ul">
<li class="toclevel-1"><a href="#r1"><span class="tocnumber"></span> <span class="toctext">Section I: Genome Browser</span></a></li>
<li class="toclevel-1"><a href="#r2"><span class="tocnumber"></span> <span class="toctext">Riboswitch</span></a></li>
<li class="toclevel-1"><a href="#r3"><span class="tocnumber"></span> <span class="toctext">SiRNA</span></a></li>
<li class="toclevel-1"><a href="#r4"><span class="tocnumber"></span> <span class="toctext">KEGG Network</span></a></li>
<li class="toclevel-1"><a href="#r5"><span class="tocnumber"></span> <span class="toctext">Fba</span></a></li>
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<h2 id="r1">Genome Browser</h2>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Procedure: File→Open Fasta→Open xml Component</p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Parts: 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. </p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;On the left, there are two useful tools: you can search the fragment that you want by position or name (Position represents the position of its head and Name stands for its tag or key word of its gene annotation); the slider of Zoom is designed for regulating the display frame rate of the sequence.
</p></div>
<h2 id="r0">Biobrick</h2>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Procedure: Open your biobrick file(in xml format)</p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Component Parts: In the main display window, you can view information of existing biobricks. On the left is the list of the files that you have opened.
</p>
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<h2 id="r2">Riboswitch</h2>
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<p>Procedure: choose a target type→choose a target name→choose an aptamer→choose a regulation direction (up regulation or down regulation) →GO
</p><p>Component Parts: On the right is the main operating area and you can choose your target type (your experimental object) and corresponding target name, aptamer and regulation direction. Attention should be paid to the input box named Input your Target. You can search your target name by key words or even several letters of it. It should be useful to you. Click GO and you will see a picture. The designed riboswitch is in the dotted box on the top left corner. Below it is a diagram to show how the riboswitch works. Besides, there is a list on the left box. It records your choices that you have made in created riboswich project, and you need only click Go next time.
</p></div>
<h2 id="r3">SiRNA</h2>
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<p>Procedure: Input your DNA sequence</p>
<p>Component Parts: The left textbox is for you to input DNA sequence. There are two ways to input that: you can either input the sequence directly or open a file in FASTA format. If you choose the former, click Direct Input, then input your sequence, and click Go. If you choose the latter, you need only click Open Fasta and choose your FASTA file to open. Two solutions are provided on the right——one is solved by Tom Tuschl’s method and the other is by rational design. 
</p></div>
<h2 id="r4">KEGG Network</h2>
<div>
<p>Procedure: open a file (in xml format)</p>
<p>Component Parts: In the main display window, you will see a network from KEGG website. On the left box displays a list of the files you have opened. Pay attention that you can right click the main display window to open another KEGG xml file or to search any element in the network (choose find element).
</p></div>
<h2 id="r5">Fba</h2>
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<p>Procedure: Open a file (in xml format)→select your options→Go</p>
<p>Component Parts: There are 5 options for you to select: exhaustive single deletion, reaction deletion, fva solve, preturbation analysis and PHPP analysis. You can select all of them or part of them, or even nothing, then click Go. If you select none of them, you will see a table showed basic information of each reaction. If you select several of them, the corresponding windows will tiled in the resulting window. If you select reaction deletion option, a selection of the reaction you want to wipe off is required, and if there is any change, it will be highlighted in red font.
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