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| - | <p>This page provides instructions on downloading Autogene on a Mac or on a PC.</p> | + | <p> You can download the Autogene as an application <a href="http://ugrad.cs.jhu.edu/~eisinger/iGEM/Download.html"> here</a>. </p> |
| - | <div id="title">
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| - | Mac
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| - | </div> | + | |
| - | <br> | + | |
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| - | <b>Step 1</b>
| + | <p> You can download the source code for Autogene <a href=" https:// github.com/ igemsoftware/ Johns_Hopkins_Software_2012 here</a>. </p> |
| - | <p>Download MySQL as a .dmg file <a href="http://cdn.mysql.com/Downloads/MySQL-5.5/mysql-5.5.28-osx10.6-x86.dmg">here</a>. After it has downloaded, double click it to view the files inside of the .dmg. You'll see a two .pkg files as well as a .prefPane file. | + | |
| - | <li>First, double click MySQLStartupItem.pkg. The Installer will open. Proceed through the steps until it finishes.</li>
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| - | <li>Next, double click MySQL.prefPane to configure MySQL through the System Preferences on your Mac. Be sure to select to turn MySQL on.</li>
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| - | <li>Lastly, run the mysql-5.5.28-osx10.6-x86.pkg file by double clicking it. Follow the steps to complete the installation.</li> </p>
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| - | <b>Step 2</b>
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| - | <p>Download MySQL Workbench as a .dmg file <a href=" http:// cdn.mysql.com/ Downloads/ MySQLGUITools/mysql-workbench-gpl-5.2.44-osx-i686.dmg">here</a> . After it has downloaded, double click it and step through the installation process.</p > | + | |
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| - | <center><img src="https://static.igem.org/mediawiki/2012/9/9c/SoftwareGoals11.png" width=700 height=420/></center>
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| - | <br><br> Each of these goals encompasses an extensive list of sub-goals. Here, we discuss the more detailed goals for our primary milestones listed above.<br>
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| - | <br>
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| - | <a name="futuregoals">
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| - | <div id="title">
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| - | Future Goals
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| - | </div>
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| - | </a>
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| - | <br>
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| - | Autogene is still evolving as we both finish up the design module, and fine tune the plasmid mapper. There are several features we’d like to develope in the future, including 3d protein visualization using MAYA, codon optimization, and primer design.
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| - | <br><br>
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| - | Codon optimization is a common synthetic biology technique used to improve the efficiency of protein translation. DNA is translated into amino acids in groups of three bases called codons, but only the first two bases determine into which amino acid the codon in translated. This allows researchers to change this third letter without affecting the resulting proteins. When a codon is ‘optimized’, this means that the codon is replaced with a version producing the same protein as the original, but which is more common in the organism’s DNA. If the codon is more common, then the thought is that it can be produced more efficiently.
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| - | <br><br>
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| - | Primer design is one of the most common computational tasks in synthetic biology. In order to synthesize a DNA sequence, it is necessary to break the total sequence into small, overlapping parts, which are then combined using PCR. Once we finish this feature, Autogene will truly encompass all portions of plasmid design, using the simple philosophy of Scan/Edit/Print. From the annotation of the starting sequence, to the gathering and arranging of desired features, to the development of building blocks to actually synthesize the given sequence, everything will be done through Autogene.
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| - | <br><br>
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| - | Autogene is the first tool of its kind in many ways, and we hope that its development will demonstrate the potential of many new techniques and technologies when applied to synthetic biology. By exporting our alignments to the cloud, we’ve shown that complex computation, the kind that before could only be performed on very high-powered computers, can be accessed by anyone with an internet connection. An increase in computational power for every researcher across the board could revolutionize synthetic biology, and scientific research in general.
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| | {{:Team:Johns_Hopkins-Software/header}} | | {{:Team:Johns_Hopkins-Software/header}} |
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