Team:METU Turkey SoftLab

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<div id="home" class="item">
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<div class="homepage">
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<div id="homecontainer"><h3>Abstract</h3>
 +
<p>Firedamp explosions is frequently seen cases at all mines over the world. Every year, 50 miners lose their lives in Turkey because of firedamp explosions. Firedamp is a flammable gas found in coal mines and it mainly contains methane. 5%-15% methane level in firedamp is risky amount that makes gas mixture explosive enough to explode by just one spark.  Beside its explosive property, methane is also the main contributor to global warming and recent mine mechanisms release obtained methane into air.  Since, it is important to convert methane gas in mines into other derives to reduce its effect on global warming. 
 +
 +
Our aim to design a device which will work on E.coli that provides solutions for side effects of methane. Device that we are planning to construct involves the genes of bacteria encoding methane monooxygenase (MMo), and the mechanism will help by working through a series of compact systems in mines. First part of this compact system is the sensation of methane, hence the second is the entrapment and the last part will be the conversion of methane to methanol.</p>
 +
<p>...</p>
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</div>
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</div>
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</div>
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<div class="content2">
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<div class="text">
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<h2>Team</h2>
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<div id="slider">
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<img alt="" src="...">
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<img alt="" src="...">
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<img alt="" src="...">
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<img alt="" src="...">
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<img alt="" src="...">
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<img alt="" src="...">
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</div>
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<p></p>
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<div id="smallwrap">
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</div>
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<div class="smallbox">
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<h2 class="black">......</h2>
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<img src="....">
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<div class="smalltext">
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<p>.....</p>
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</div>
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</div>
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<div class="smallbox">
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<h2 class="black">......</h2>
 +
<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
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</div>
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<div class="smallbox">
 +
<h2 class="black">......</h2>
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<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
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</div>
 +
 +
<div class="smallbox">
 +
<h2 class="black">......</h2>
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<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
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</div>
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<div class="clear">
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</div>
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<div class="smallbox">
 +
<h2 class="black">......</h2>
 +
<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
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</div>
 +
<div class="smallbox">
 +
<h2 class="black">......</h2>
 +
<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
 +
</div>
 +
<div class="smallbox">
 +
<h2 class="black">......</h2>
 +
<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
 +
</div>
 +
<div class="smallbox">
 +
<h2 class="black">......</h2>
 +
<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
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</div>
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<div class="smallbox">
 +
<h2 class="black">......</h2>
 +
<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
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</div>
 +
<div class="smallbox">
 +
<h2 class="black">......</h2>
 +
<img src="....">
 +
<div class="smalltext">
 +
<p>.....</p>
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</div>
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</div>
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</div>
 +
</div>
 +
</div>
 +
<div id="motivation" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Motivation</h2>
 +
<p>...</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div id="scope" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Scope and Future Aspects</h2>
 +
<p>.....</p>
 +
<p>.....</p>
 +
<p>....</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div id="project" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Project Introduction</h2>
 +
<p>...</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div id="notebook" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Notebook</h2>
 +
<div id="notebook2">
 +
<div class="month">
 +
January</div>
 +
<div class="general">
 +
<p>...</p>
 +
</div>
 +
<div class="month">
 +
February</div>
 +
<div class="general">
 +
 +
</div>
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<div class="month">
 +
March</div>
 +
<div class="general">
 +
 +
</div>
 +
<div class="month">
 +
April</div>
 +
<div class="general">
 +
At this month we have started regular workshop about Synthetic
 +
Biology, Bioengineering, and Bioinformatics.
 +
 +
</div>
 +
<div class="lower">
 +
<div class="week1" style="height: 150px;">
 +
<div id="week">
 +
Week 1</div>
 +
<p>Workshop -1</p>
 +
<p>[Biology basics, What is Synthetic Biology?, and the
 +
works in this field ]</p>
 +
</div>
 +
<div class="week2" style="height: 150px;">
 +
<div id="week">
 +
Week 2</div>
 +
<p>Workshop -2</p>
 +
<p>[What is Synthetic Biology?, and the works in this field
 +
]</p>
 +
</div>
 +
<div class="week3" style="height: 150px;">
 +
<div id="week">
 +
Week 3</div>
 +
<p>Workshop -3</p>
 +
<p>[iGEM, Parts, Biobricks, and Devices ]</p>
 +
</div>
 +
<div class="week4" style="height: 150px;">
 +
<div id="week">
 +
Week 4</div>
 +
<p>Workshop – 4</p>
 +
<p>[iGEM, Parts, Biobricks, and Devices ]</p>
 +
</div>
 +
</div>
 +
<div class="month">
 +
May</div>
 +
<div class="general">
 +
 +
</div>
 +
<div class="lower">
 +
<div class="week1" style="height: 180px;">
 +
<div id="week">
 +
Week 1</div>
 +
<p>Meeting -1</p>
 +
 +
</div>
 +
<div class="week2" style="height: 180px;">
 +
<div id="week">
 +
Week 2</div>
 +
<p>Meeting -2[with consulters ]</p>
 +
 +
</div>
 +
<div class="week3" style="height: 180px;">
 +
<div id="week">
 +
Week 3</div>
 +
<p>Meeting -3</p>
 +
 +
</div>
 +
<div class="week4" style="height: 180px;">
 +
<div id="week">
 +
Week 4</div>
 +
<p>Meeting -4</p>
 +
 +
</div>
 +
<div class="month">
 +
June</div>
 +
<div class="general">
 +
 +
</div>
 +
<div class="lower">
 +
<div class="week1" style="height: 250px;">
 +
<div id="week">
 +
Week 1</div>
 +
<p>Meeting – 5</p>
 +
</p>
 +
</div>
 +
<div class="week2" style="height: 250px;">
 +
<div id="week">
 +
Week 2</div>
 +
<p>Meeting – 6 </p>
 +
 +
</div>
 +
<div style="height: 250px; background-color: #1e6dd4; padding: 10px;">
 +
<div id="week">
 +
Week 3 and Week 4</div>
 +
<p align="center">HAVE a NICE HOLIDAY</p>
 +
<p align="center">SEE YOU ON JULY 1 as a POWERFUL TEAM;
 +
<em>“METU TURKEY SOFTWARE”</em>.</p>
 +
</div>
 +
</div>
 +
<div class="month">
 +
July</div>
 +
<div class="general">
 +
<P>...</P>
 +
</div>
 +
<div class="lower">
 +
<div class="week1" style="height: 600px;">
 +
<div id="week">
 +
Week 1</div>
 +
<p>Meeting-7</p>
 +
 +
</div>
 +
<div class="week2" style="height: 600px;">
 +
<div id="week">
 +
Week 2</div>
 +
 +
<p>· Design Group</p>
 +
 +
</div>
 +
<div style="height: 600px; background-color: #1e6dd4; padding: 10px">
 +
<div id="week">
 +
Week 3 and Week 4
 +
<p>DOING THE TASKS.</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div class="month">
 +
August</div>
 +
<div class="general">
 +
<p>At this month we have started to apply graph theory on iGEM
 +
parts. We have specified nodes, edges, graph types. Furthermore,
 +
we have started to develop a new “ Part Registery Form ” to
 +
be able to more standardize the part entry to be able to apply
 +
some algorithms on the parts more efficiently.</p>
 +
</div>
 +
<div class="lower">
 +
<div class="week1" style="height: 350px;">
 +
<div id="week">
 +
Week 1</div>
 +
<p>Meeting -8</p>
 +
 +
</div>
 +
<div class="week2" style="height: 350px;">
 +
<div id="week">
 +
Week 2</div>
 +
<p>Meeting -9</p>
 +
 +
</div>
 +
<div class="week3" style="height: 350px;">
 +
<div id="week">
 +
Week 3</div>
 +
<p>Meeting -10</p>
 +
 +
 +
</div>
 +
<div class="week4" style="height: 350px;">
 +
<div id="week">
 +
Week 4</div>
 +
<p>Meeting -11</p>
 +
 +
</div>
 +
</div>
 +
<div class="month">
 +
September</div>
 +
<div class="general">
 +
At this time all bases for application were nearly to finish,
 +
the software group was waiting row data from the gene group.
 +
Meanwhile, they were working on code bases.</div>
 +
<div class="lower">
 +
<div class="week1" style="height: 350px;">
 +
<div id="week">
 +
Week 1 </div>
 +
<p>... </p>
 +
</div>
 +
<div class="week2" style="height: 350px;">
 +
<div id="week">
 +
Week 2</div>
 +
<p>Meeting -12</p>
 +
 +
</div>
 +
<div class="week3" style="height: 350px;">
 +
<div id="week">
 +
Week 3</div>
 +
<p>Meeting -13</p>
 +
 +
</div>
 +
<div class="week4" style="height: 350px;">
 +
<div id="week">
 +
Week 4</div>
 +
 +
</div>
 +
</div>
 +
<div class="month">
 +
October</div>
 +
<div class="general">
 +
<p>Now everything is nearly over, it is time to put everything
 +
together.</p>
 +
 +
</div>
 +
<div class="lower">
 +
<div class="week1" style="height: 170px;">
 +
<div id="week">
 +
Week 1</div>
 +
<p>Meeting -15</p>
 +
 +
</div>
 +
<div style="float: left; width: 540px; height: 170px; font-weight: normal; background-color: #3fff72; padding: 10px;">
 +
<div id="week">
 +
Week 2, Week 3, &amp; Week 4
 +
<p>GOOD NEWS Infinite meetings started :) </p>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="month">
 +
November</div>
 +
<div class="general">
 +
<p align="center">November 1 – 12 is our ticket dates,</p>
 +
 +
<p align="center">METU ANKARA</p>
 +
</div>
 +
</div>
 +
</div><h3>Follow our discussion topic at ...our googlegroups</a></h3>
 +
 +
</div>
 +
</div>
 +
<div id="download" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Download Executable and Code</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div id="miscellaneous" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Collaboration</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="clear">
 +
</div>
 +
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 +
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 +
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 +
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<div class="content2">
 +
<div class="text">
 +
<h2>Design</h2>
 +
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="item">
 +
</div>
 +
<div id="download2" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>User Guide</h2>
 +
<object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Znb1o7cr5dc?hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Znb1o7cr5dc?hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Fk7eJ-Ig_IQ?hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Fk7eJ-Ig_IQ?hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object><p>For new users whom want to interest with synthetic biology and for experienced scientists, in our program you have two options for Input Output properties ;</p>
 +
<p>To find input-output related biobrick parts or larger constructs! If you want to provide specific chemical or physical inputs from external environment, you may choose these inputs from the list. if you want other specific inputs which will be expressed from a coding sequence, the list can provide these specified protein names.</p>
 +
<img src="https://static.igem.org/mediawiki/2010/6/60/Metu-guide1.jpg">
 +
<p>Wanted features of outputs can be selected by either from list or entering individually into text boxes.</p>
 +
<img src="https://static.igem.org/mediawiki/2010/c/c0/Metu-guide2.jpg">
 +
<p>Then click on the “Show Parts ” button.</p>
 +
<img src="https://static.igem.org/mediawiki/2010/9/95/Metu-guide3.jpg">
 +
<p>Then the program will show you the parts have specified I/O properties</p>
 +
<img src="https://static.igem.org/mediawiki/2010/7/7f/Metu-guide4.jpg">
 +
<p>To see the properties of a part just click on it.</p>
 +
<img src="https://static.igem.org/mediawiki/2010/3/33/Metu-guide5.jpg">
 +
<img src="https://static.igem.org/mediawiki/2010/2/27/Metu-guide6.jpg">
 +
<p>After clicking, you will see a highlighted pathway on the 2nd graph. Which are the subparts of the clicked part. Showing the sub graph in network.</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div id="miscellaneous2" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Human Practices</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="clear">
 +
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 +
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 +
</div>
 +
<div id="project3" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Material</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="item">
 +
</div>
 +
<div id="download3" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Supporting Tools</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div id="miscellaneous3" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Safety</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="clear">
 +
</div>
 +
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 +
<div class="content2">
 +
<div class="text">
 +
<h2>Methods</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="item">
 +
</div>
 +
<div id="download4" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Contact</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div id="miscellaneous4" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Future Plan</h2>
 +
</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div class="clear">
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</div>
 +
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 +
<div class="item">
 +
</div>
 +
<div id="project5" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Database Standardization</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="item">
 +
</div>
 +
<div class="item">
 +
</div>
 +
<div id="miscellaneous5" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Sponsors</h2>
 +
<ul id="sponsorlist">
 +
<li>...</li>
 +
<li>...</li>
 +
<li>...</li>
 +
<li>...</li>
 +
</ul>
 +
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 +
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 +
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 +
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 +
</div>
 +
<div id="project6" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2>Algorithm</h2>
 +
 +
</div>
 +
</div>
 +
</div>
 +
<div class="item">
 +
</div>
 +
<div class="item">
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 +
<div id="project7" class="item">
 +
<div class="content2">
 +
<div class="text">
 +
<h2></h2>
 +
<h3></h3>
 +
<h4>Introduction</h4>
 +
 +
<p><span><a href="http://en.wikipedia.org/wiki/Graph_(mathematics)">
 +
[1] http://en.wikipedia.org/wiki/Graph_(mathematics)</a></span></p>
 +
</div>
 +
</div>
 +
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<div class="content2">
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<div class="text">
 +
<h2>Results</h2>
 +
<ul>
 +
<li>... </li>
 +
<li>...</li>
 +
<li>...</li>
 +
<li>...</li>
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 +
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 +
<p>... </p>
 +
<p>...</p>
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<h2>Development Plans and Project Management</h2>
 +
<p>... </p>
 +
<p>...</p>
 +
<p>..</p>
 +
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Revision as of 13:02, 12 September 2011

Abstract

Firedamp explosions is frequently seen cases at all mines over the world. Every year, 50 miners lose their lives in Turkey because of firedamp explosions. Firedamp is a flammable gas found in coal mines and it mainly contains methane. 5%-15% methane level in firedamp is risky amount that makes gas mixture explosive enough to explode by just one spark. Beside its explosive property, methane is also the main contributor to global warming and recent mine mechanisms release obtained methane into air. Since, it is important to convert methane gas in mines into other derives to reduce its effect on global warming. Our aim to design a device which will work on E.coli that provides solutions for side effects of methane. Device that we are planning to construct involves the genes of bacteria encoding methane monooxygenase (MMo), and the mechanism will help by working through a series of compact systems in mines. First part of this compact system is the sensation of methane, hence the second is the entrapment and the last part will be the conversion of methane to methanol.

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Team

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Motivation

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Scope and Future Aspects

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Project Introduction

...

Notebook

January

...

February
March
April
At this month we have started regular workshop about Synthetic Biology, Bioengineering, and Bioinformatics.
Week 1

Workshop -1

[Biology basics, What is Synthetic Biology?, and the works in this field ]

Week 2

Workshop -2

[What is Synthetic Biology?, and the works in this field ]

Week 3

Workshop -3

[iGEM, Parts, Biobricks, and Devices ]

Week 4

Workshop – 4

[iGEM, Parts, Biobricks, and Devices ]

May
Week 1

Meeting -1

Week 2

Meeting -2[with consulters ]

Week 3

Meeting -3

Week 4

Meeting -4

June
Week 1

Meeting – 5

Week 2

Meeting – 6

Week 3 and Week 4

HAVE a NICE HOLIDAY

SEE YOU ON JULY 1 as a POWERFUL TEAM; “METU TURKEY SOFTWARE”.

July

...

Week 1

Meeting-7

Week 2

· Design Group

Week 3 and Week 4

DOING THE TASKS.

August

At this month we have started to apply graph theory on iGEM parts. We have specified nodes, edges, graph types. Furthermore, we have started to develop a new “ Part Registery Form ” to be able to more standardize the part entry to be able to apply some algorithms on the parts more efficiently.

Week 1

Meeting -8

Week 2

Meeting -9

Week 3

Meeting -10

Week 4

Meeting -11

September
At this time all bases for application were nearly to finish, the software group was waiting row data from the gene group. Meanwhile, they were working on code bases.
Week 1

...

Week 2

Meeting -12

Week 3

Meeting -13

Week 4
October

Now everything is nearly over, it is time to put everything together.

Week 1

Meeting -15

Week 2, Week 3, & Week 4

GOOD NEWS Infinite meetings started :)

November

November 1 – 12 is our ticket dates,

METU ANKARA

Follow our discussion topic at ...our googlegroups

Download Executable and Code

Collaboration

Design

User Guide

For new users whom want to interest with synthetic biology and for experienced scientists, in our program you have two options for Input Output properties ;

To find input-output related biobrick parts or larger constructs! If you want to provide specific chemical or physical inputs from external environment, you may choose these inputs from the list. if you want other specific inputs which will be expressed from a coding sequence, the list can provide these specified protein names.

Wanted features of outputs can be selected by either from list or entering individually into text boxes.

Then click on the “Show Parts ” button.

Then the program will show you the parts have specified I/O properties

To see the properties of a part just click on it.

After clicking, you will see a highlighted pathway on the 2nd graph. Which are the subparts of the clicked part. Showing the sub graph in network.

Human Practices

Material

Supporting Tools

Safety

Methods

Contact

Future Plan

Database Standardization

Sponsors

  • ...
  • ...
  • ...
  • ...

Algorithm

Results

  • ...
  • ...
  • ...
  • ...
  • ...
  • ...
  • ...
  • ...

Attribution and Contributions

...

...

...

Development Plans and Project Management

...

...

..

Retrieved from "http://2011.igem.org/Team:METU_Turkey_SoftLab"