Team:Rutgers/MYS!S
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- | <td height="58" colspan="2" td background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png"><p class="style3">RUTGERS iGEM TEAM WIKI</ | + | <td height="58" colspan="2" td background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png"><p class="style3">RUTGERS iGEM TEAM WIKI<br /> |
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<tr> | <tr> | ||
- | <td width="9%" valign="top" class="stuff">Menu >> The Bacterial Etch-a-Sketch >> Goals</td> | + | <td width="9%" valign="top" class="stuff"><span class="style3"><img src="https://static.igem.org/mediawiki/2011/9/97/Mysis_title.png" width="978" height="288"></span>Menu >> The Bacterial Etch-a-Sketch >> Goals</td> |
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- | </tr> | + | <td width="69%" class="imgshadow2"><blockquote> |
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+ | <table width="100%" border="0" cellspacing="0" cellpadding="0"><tr> | ||
+ | <td colspan="6" td background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png"><h1><span class="shadow"><img src="https://static.igem.org/mediawiki/2011/5/5c/58-bookmark.png" width="10" height="26" /> the MYS!S Project</span></h1></td> | ||
+ | </tr> | ||
+ | <tr> | ||
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+ | <td colspan="6" class="stuff"></h4> | ||
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+ | <h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/5/5c/58-bookmark.png" width="10" height="26" /> Abstract</h4> | ||
+ | <p class="stuff">MYS!S is a stand alone software tool designed to assist an “iGEMer” when designing a new BioBrick part or modifying an existing one.</p> | ||
+ | <p class="stuff">MYS!S handles several problems that a synthetic biologist might encounter in the lab that can be solved with site directed mutagenesis. The utilities that MYS!S supports to modify DNA sequences on paper, can be “actualized” in the lab using site directed mutagenesis to change physical DNA “stored” in a backbone. </p> | ||
+ | <p class="stuff">MYS!S will determine the most efficient modified sequence by optimizing for the least number of rounds of site directed mutagenesis. Once the changes are finalized primers are designed. In addition to primer design, MYS!S provides lab protocols for both site directed mutagenesis and transformation into competent cells. Currently the lab protocols are supplied as a BioCoder compliant C++ file, that can then be compiled with the BioCoder library.</p> | ||
+ | <p class="stuff"> </p> </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </blockquote> </tr> | ||
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<td width="69%" class="imgshadow2"><blockquote> | <td width="69%" class="imgshadow2"><blockquote> | ||
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+ | <td colspan="7" td background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png"><h1><span class="shadow"><img src="https://static.igem.org/mediawiki/2011/5/5c/58-bookmark.png" width="10" height="26" /> Operations </span></h1></td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
- | <td colspan="6 | + | |
- | + | <td colspan="6" class="stuff"><h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/6/68/16-line-chart.png" width="30" height="24"> I. DNA Optimization</h4> | |
- | + | <p class="stuff">First, it performs DNA codon optimization based on the target organism by removing rare codons and replacing them with more prevalent codons. </p> | |
- | + | <p class="stuff">(We noticed that many teams decided to utilize sequences from a variety of organisms such as firefly luciferase to ultimately be transformed into an experimentally “stable” organism.)</p> | |
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<p class="stuff"> </p> | <p class="stuff"> </p> | ||
+ | <h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/a/a4/40-inbox.png" width="24" height="24"> II. Processing</h4> | ||
+ | <p class="stuff">Secondly, the program checks the coding sequence for any restriction sites that are not allowed by the format specified by the user. After checking the sequence, MYS!S removes the restriction sites while ensuring that the modified sequence is still codon optimized.</p> | ||
+ | <p class="stuff">In addition, it was pointed out that frequently a synthetic biologist would like to change specific amino acids in the DNA coding sequence. MYS!S decides what difference in nucleotide sequence are required to best make the amino acid change. </p> | ||
+ | <p> </p> | ||
+ | <h4 class="shadow"> <img src="https://static.igem.org/mediawiki/2011/7/76/161-calculator.png" width="22" height="28"> III. Restriction site analysis </h4> | ||
+ | <p class="stuff">Alternatively, an iGEMer might also want to add restriction sites to a DNA sequence in order to remove a particularly useful sequence. The program can handle this by either allowing the user to specify where the restriction site should be or by choosing what restriction site is desired and how sites need to be added to the sequence. </p> | ||
<p class="stuff"> </p> </td> | <p class="stuff"> </p> </td> | ||
+ | <td width="25%" align="center" valign="baseline" background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png" td><p> </p></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </blockquote> </tr> | ||
+ | <tr> | ||
+ | <td width="69%" class="imgshadow2"><blockquote> | ||
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+ | <table width="100%" border="0" cellspacing="0" cellpadding="0"> | ||
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+ | <td colspan="7" td="td" background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png"><h1><span class="shadow"><img src="https://static.igem.org/mediawiki/2011/5/5c/58-bookmark.png" width="10" height="26" /> How Mys!S Does it </span></h1></td> | ||
+ | </tr> | ||
+ | <tr > | ||
+ | <td colspan="6" class="stuff"><h4 class="shadow">The MYS!S Environment </h4> | ||
+ | <p class="stuff"> One of the main ideas behind MYS!S was to make synthetic biology more accessible to a wider “spectrum” of people. We want the program to provide an environment that enables the user to understand and explore the changes being made to the DNA in a more intuitive manner. </p> | ||
+ | <h4 class="shadow">Custimization</h4> | ||
+ | <p class="stuff">In addition, MYS!S is designed to be highly customizable by providing the user with the ability to add and modify components such as an organism’s codon usage table and new assembly standards. </p> | ||
+ | <p class="stuff">The ultimate goal is to create a program that can be customized by the user for their specific work and the lab protocols they are comfortable with.</p> | ||
+ | <p class="stuff"> </p></td> | ||
+ | <td width="25%" valign="top" background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png" class="stuff" td="td"></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </blockquote> </tr> | ||
+ | <tr> | ||
+ | <td width="69%" class="imgshadow2"><blockquote> | ||
+ | <table width="100%" border="0" cellspacing="0" cellpadding="0"><tr> | ||
+ | <td colspan="6" td="td" background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png"><h1><span class="shadow"><img src="https://static.igem.org/mediawiki/2011/5/5c/58-bookmark.png" width="10" height="26" /> MYS!S: An Introduction </span></h1></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td colspan="6" class="stuff"><h4 class="shadow">Walkthrough</h4> | ||
+ | <p class="stuff">The MYS!S walkthrough is located here!</p> | ||
+ | <p class="stuff"><a href="https://2011.igem.org/Team:Rutgers/MYS!S_WT">https://2011.igem.org/Team:Rutgers/MYS!S_WT</a></p> | ||
+ | <p class="stuff"> </p></td> | ||
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- | <td colspan="6 | + | <td colspan="6" class="stuff"><h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/6/68/16-line-chart.png" width="30" height="24"> I. Protocols </h4> |
<p class="stuff">In the protocol tab is a BioCoder compatible C++ file that contains the lab procedures for mutating the original Lovtap DNA into a standard safe form. The C++ file can be compiled with the BioCoder software available here. | <p class="stuff">In the protocol tab is a BioCoder compatible C++ file that contains the lab procedures for mutating the original Lovtap DNA into a standard safe form. The C++ file can be compiled with the BioCoder software available here. | ||
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- | <td colspan="6 | + | <td colspan="6" class="stuff"><h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/e/e5/59-flag.png" > beta</h4> |
<p class="stuff">Unfortunately, we’re talking about the capabilities of the future MYS!S v.10, for now all we have is the beta edition. So for the time being, these are the imminent improvements we would like to make for the second version of MYS!S. | <p class="stuff">Unfortunately, we’re talking about the capabilities of the future MYS!S v.10, for now all we have is the beta edition. So for the time being, these are the imminent improvements we would like to make for the second version of MYS!S. | ||
</p> | </p> | ||
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- | <td colspan="6 | + | <td colspan="6" class="stuff"><h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/8/85/56-cloud.png" width="24" height="16"> Github</h4> |
<p class="stuff">MYS!S is currently available as an Eclipse download. It will very soon be available as a java application. </p> | <p class="stuff">MYS!S is currently available as an Eclipse download. It will very soon be available as a java application. </p> | ||
- | <p class="stuff">The downloads can be obtained from our | + | <p class="stuff">The downloads can be obtained from our GitHub site. </p> |
- | <p class="stuff"><img src="https://static.igem.org/mediawiki/2011/8/81/Github_white_black_cat_32.png" width="32" height="32"> https://github.com/RutgersGEARS/iGEM-Rutgers-Software | + | <p class="stuff"><img src="https://static.igem.org/mediawiki/2011/8/81/Github_white_black_cat_32.png" width="32" height="32"> <a href="https://github.com/RutgersGEARS/iGEM-Rutgers-Software">https://github.com/RutgersGEARS/iGEM-Rutgers-Software </a></p> |
<p class="stuff">MYS!S is still a work in progress. Please feel free to report any bugs or crashes that occur as issues on our github page. </p> | <p class="stuff">MYS!S is still a work in progress. Please feel free to report any bugs or crashes that occur as issues on our github page. </p> | ||
- | <p class="stuff"><img src="https://static.igem.org/mediawiki/2011/8/81/Github_white_black_cat_32.png" width="32" height="32"> https://github.com/RutgersGEARS/iGEM-Rutgers-Software/issues</p> | + | <p class="stuff"><img src="https://static.igem.org/mediawiki/2011/8/81/Github_white_black_cat_32.png" width="32" height="32"> <a href="https://github.com/RutgersGEARS/iGEM-Rutgers-Software/issues">https://github.com/RutgersGEARS/iGEM-Rutgers-Software/issues</a></p> |
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<p class="stuff"> </p> </td> | <p class="stuff"> </p> </td> | ||
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Latest revision as of 04:59, 28 September 2011
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