Team:XMU-China

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<div class="schoolname">Xiamen University</div>
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            <td> <h1 style="line-height: 19px; text-align: center;"> Project Description </h1></td>
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    <strong><span style="font-size: 14px;font-family: Arial, sans-serif">Chemtaxis</span></strong>
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<li><a href="https://2013.igem.org/Team:XMU_Software">Home</a></li>
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<span style="font-size: 14px;font-family: Arial, sans-serif">, which can make strains move, interest us this time. By reprogramming the strain (CL-1), which lacks the <em>CheZ</em> gene, we can create mathematical patterns. <em>CheZ</em> gene belongs to chemotaxis family of <em>E.coli</em>. Protein CheZ can dephosphorylate CheY-P, one that allows <em>E.coli</em> swimming smoothly. The </span><span style="font-size: 13px;font-family: 宋体">Δ</span><span style="font-size: 14px;font-family: Arial, sans-serif">CheZ bacteria can’t dephosphorylate CheY-P, so the strain won’t motile until <em>CheZ</em> is involved in. That means the motility of <em>E.coli</em> can be precisely control by stimulus (e.g. IPTG). We try to construct logic gene circuits to make <em>E.coli</em> recognize environmental stimulation, thus by utilizing the controlled chemotaxis which named pseudotaxis we could command bacteria to form patterns such as ellipse, hyperbola and so on.</span>
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<li><a href="https://2013.igem.org/Team:XMU_Software/Team">Team</a></li>
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<li><a href="https://2013.igem.org/Team:XMU_Software/Project/promoter">Project</a></li>
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    <span style="font-size: 14px;font-family: Arial, sans-serif">The intrinsic motivation that drive us striving for the above project is that we want to simulate the process of stem cell differentiation. In the organs development, stem cells differentiate while aggregate together to form heart, liver and kidney what have precise shapes. <strong>Perhaps some mathematical principles that govern the differentiation process.</strong> By simulating differentiation, we want to get a closer understanding of the differentiation process. However, <em>E.coli</em> can’t sense as much stimulus as stem cell, we intend to utilize RNA aptamers what has the potential to response to almost all stimulus to cover that shortage. Thus, we can get a more precise stimulation.</span>
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    <span style="font-size: 14px;font-family: Arial, sans-serif">Besides, we try to utilize pseudotaxis to accomplish some experimental meaning. As far as we know, the motile ability is proportional to the amount of protein CheZ in certain range. By measuring the average chemotaxis distance, we will get a <strong>precise evaluation on the RBS efficiency</strong> that is evaluated by fluorescence strength previously.</span>
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<div class="home_s4t1">We have designed <span class="home_s4t2">2</span> software tools</div></br></br>
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<div class="home_s4t3">Brick Worker</div>
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<div class="home_s4t4">Brick Worker is designed to analyze and  predict the strength of various biobricks, i.e. promoters, RBS, protein coding sequence and terminators. It uses Position Weight Matrix method to recognize the key determinants of promoter and RBS sequences, predict their strengths and optimizes the protein coding sequences by  codon usage bias. Brick Worker is the first software to give an all-round and reliable evaluation of all biobricks, especially, promoters, and represents a major step towards computational prediction and regulation of gene expression.</div></br></br>
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<div class="home_s4t3">E' NOTE</div>
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<div class="home_s4t4">
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E’ NOTE is a web application for experiments recording.
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<p>It provides a series of intelligent templates for the users which are linked to the plasmid library constructed by the users and can do some simple calculation.Human-orientated data export port facilitates the users to transfer the experiment notes from E’NOTE to their wiki.Integration of web applications designed by the past iGEM software teams and tools provided online helps the users get access to their desirable software easily.</p>
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Revision as of 02:28, 16 August 2014

<!DOCTYPE HTML>

XMU-SOFTWARE
Xiamen University
We have designed 2 software tools


Brick Worker
Brick Worker is designed to analyze and predict the strength of various biobricks, i.e. promoters, RBS, protein coding sequence and terminators. It uses Position Weight Matrix method to recognize the key determinants of promoter and RBS sequences, predict their strengths and optimizes the protein coding sequences by codon usage bias. Brick Worker is the first software to give an all-round and reliable evaluation of all biobricks, especially, promoters, and represents a major step towards computational prediction and regulation of gene expression.


E' NOTE
E’ NOTE is a web application for experiments recording.

It provides a series of intelligent templates for the users which are linked to the plasmid library constructed by the users and can do some simple calculation.Human-orientated data export port facilitates the users to transfer the experiment notes from E’NOTE to their wiki.Integration of web applications designed by the past iGEM software teams and tools provided online helps the users get access to their desirable software easily.

Retrieved from "http://2014.igem.org/Team:XMU-China"