Team:Johns Hopkins-Software

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A cloud-based tool for plasmid annotation and design
 
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<i>AutoGene is an all-encompassing plasmid design suite meant to streamline the process of both annotating and building sequences. Consisting of two modules -- AutoPlasmid and AutoDesign -- it first uses a highly curated database of features to search an imported plasmid, scanning the sequence for both perfect and imperfect alignments, and generates an interactive visualization of the annotated plasmid. Once a plasmid is annotated, a user is then able to alter its contents, using the AutoGene feature database, the biobrick database, as well as custom components. The design module enables structural optimization by maintaining sets of sequence rules and taking an algorithmic approach to minimizing structural violations. Additionally the program reduces the problems caused by restriction sites during application of designs, and proposes the most suitable enzyme selections through an analysis of standard restriction sites libraries.
 
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The process will be run on the cloud as a standard web server gateway interface service to dramatically increasing its speed and accessibility while maintaining the same level of accuracy. As a cloud service, it will run its algorithms in parallel and thus have the ability to perform more computationally intense procedures, such as optimizing codons to increase gene expression, and designing the most efficient oligonucleotide sequences for PCR assembly.
 
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Furthermore, AutoGene has the potential for integrating fabrication or design software in the future. 3D visualization techniques could provide users with views of protein structures created from the sequences or that of a related ortholog. A process for fabrication of synthetic DNA sequences could be automated through a building block design and benefit the user in assembling the oligonucleotides together. A number of additional features such as evaluating overlapping segments of oligonucleotides and melting temperatures for PCR assembly may also be built on top of this project.
 
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Using a clear user interface, a large, highly curated feature database, and a novel approach through cloud computing, we hope to simplify the process of plasmid design. AutoGene aims on making it faster and easier for a user to both identify and modify the contents of any plasmid, and enhancing sequences for greater viability and expression.
 
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<a href="index.html"><img width=74.1%; src="https://static.igem.org/mediawiki/2012/0/09/AutogeneHeader.png"></a><a class="returnLink" title="Return to iGem" href="https://igem.org"></a>
 
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<li><a href="#">the Software</a>
 
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  <li><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/comingsoon">Overview</a></li>
 
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                  <li><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/comingsoon">Screencast</a></li>
 
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  <li><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/comingsoon">Cloud</a></li>
 
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  <li><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/comingsoon">Database</a></li>
 
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                <li><a href="#">the Team</a>
 
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  <li><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/comingsoon">Members</a></li>
 
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                  <li><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/comingsoon">Advisors</a></li>
 
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  <li><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/comingsoon">Attributions</a></li>
 
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<li><a href="#">Human Practices</a>
 
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<div style="position: relative; left: 0px; top: 0px;"><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/AutoPlasmid"><img style="border: 0;" width="130px" src="https://static.igem.org/mediawiki/2012/5/5a/Plasmidicon.png"></a></div>
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<div style="width:150px; position: relative; top: -155px; left: 140px; width: 125px; "><font color="white" size="+1"><br><b>AutoPlasmid</b><br></font><font color="white">AutoPlasmid is a module meant to simplify the process of plasmid annotation and visualization.</font></div>
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<div style="position: absolute; left: 290px; top: 0px;"><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/AutoDesign"><img  width="130px" style="border: 0;" src="https://static.igem.org/mediawiki/2012/4/42/Designicon.png"></a></div>
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<div style="width:130px; position: absolute; top: -25px; left:430px; width: 125px"><font color="white" size="+1"><b><br>AutoDesign</b></font><font color="white"><br>AutoDesign allows a user to create their own sequences from features from the Autogene database, and from custom features.</font></div>
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<div style="position: absolute; left: 580px; top: 0px;"><a href="http://www.ugrad.cs.jhu.edu/~eisinger/iGEM/Screencast.mov"><img  width = "130px" style="border: 0;" src="https://static.igem.org/mediawiki/2012/2/24/Screencasticon.png"></a></div>
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<div style="width:200px; position: absolute; top: -25px; left:720px; width: 125px"><font color="white" size="+1"><font color="white" size="+1"><br><b>Screencast</b><br></font></font><font color="white">Learn how to use Autogene by watching our screencast.</font></div>
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<div style="position: absolute; left: 0px; top: 170px;"><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/Cloud"><img  style="border: 0;" width="130" src="https://static.igem.org/mediawiki/2012/9/92/Cloudicon.png"></a></div>
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<div style="width:200px; position: absolute; top: 167px; left: 140px; width: 120px; "><font color="white" size="+1"><b>Cloud<br></b></font><font color="white">Autogene harnesses the power of cloud computing to greatly increase alignment speed, without sacrificing accuracy.</font></div>
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<div style="position: absolute; left: 290px; top: 170px;"><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/Compatibility"><img  width = "130px" style="border: 0;" src="https://static.igem.org/mediawiki/2012/b/b3/Compatibilityicon.png"></a></div>
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<div style="width:200px; position: absolute; top: 167px; left:430px; width: 120px"><font color="white" size="+1"><b>Compatibility</b><br></font><font color="white">Autogene is compatible with many other synthetic biology software tools, and can handle many file formats.</font></div>
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<div style="position: absolute; left: 580px; top: 170px;"><a href="https://2012.igem.org/Team:Johns_Hopkins-Software/PathogenDetection"><img  style="border: 0;" src="https://static.igem.org/mediawiki/2012/9/9d/Humanpracticesicon.png" width="130px"></a></div>
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<div style="width:200px; position: absolute; top: 167px; left: 720px; width: 120px; "><font color="white" size="+1"><b>Applications</b><br></font><font color="white">Using our software tools, we analyze the BioBrick registry.</font></div>
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Latest revision as of 02:48, 27 October 2012


AutoPlasmid
AutoPlasmid is a module meant to simplify the process of plasmid annotation and visualization.

AutoDesign
AutoDesign allows a user to create their own sequences from features from the Autogene database, and from custom features.

Screencast
Learn how to use Autogene by watching our screencast.
Cloud
Autogene harnesses the power of cloud computing to greatly increase alignment speed, without sacrificing accuracy.
Compatibility
Autogene is compatible with many other synthetic biology software tools, and can handle many file formats.
Applications
Using our software tools, we analyze the BioBrick registry.















































































Autogene

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