Team:Rutgers/MYS!S

From 2011.igem.org

(Difference between revisions)
m
m
 
(24 intermediate revisions not shown)
Line 1: Line 1:
 +
__NOTOC__
 +
{{:Team:Rutgers/Template/Header}}
 +
<html>
<html>
<head>
<head>
Line 5: Line 8:
-
<!--CSS-->
+
</style>
-
<link rel='stylesheet' type='text/css' href='https://2011.igem.org/Template:Team:Rutgers/menu?action=raw&amp;ctype=text/css' />
+
-
 
+
-
<link rel='stylesheet' type='text/css' href='https://2011.igem.org/Template:Team:Rutgers/style?action=raw&amp;ctype=text/css' />
+
-
 
+
-
<!--REHOST-->
+
-
<link rel="stylesheet" href="http://zacstewart.github.com/Meow/jquery.meow.css" type="text/css" media="screen" title="no title" charset="utf-8">
+
-
 
+
-
 
+
-
<!-- jquery -->
+
-
<script type="text/javascript" src="http://code.jquery.com/jquery-1.4.2.js"></script>
+
-
 
+
-
<!-- JS -->
+
-
<script src="http://zacstewart.github.com/Meow/jquery.meow.js" type="text/javascript" charset="utf-8"></script>
+
-
 
+
-
<script type="text/javascript" src="https://2011.igem.org/Template:Team:Rutgers/css_menu?action=raw&amp;ctype=text/javascript"></script>
+
-
 
+
-
 
+
-
<--!
+
-
<link rel="stylesheet" href="menu.css" type="text/css" media="screen" />
+
-
<link rel="stylesheet" href="style.css" /
+
-
>-->
+
-
 
+
-
<script type="text/javascript">
+
-
 
+
-
$(document).ready(function()
+
-
{
+
-
$("#showcase").awShowcase(
+
-
{
+
-
content_width: 800,
+
-
content_height: 600,
+
-
fit_to_parent: false,
+
-
auto: false,
+
-
interval: 3000,
+
-
continuous: false,
+
-
loading: true,
+
-
tooltip_width: 200,
+
-
tooltip_icon_width: 32,
+
-
tooltip_icon_height: 32,
+
-
tooltip_offsetx: 18,
+
-
tooltip_offsety: 0,
+
-
arrows: true,
+
-
buttons: true,
+
-
btn_numbers: true,
+
-
keybord_keys: true,
+
-
mousetrace: false, /* Trace x and y coordinates for the mouse */
+
-
pauseonover: true,
+
-
stoponclick: false,
+
-
transition: 'fade', /* hslide/vslide/fade */
+
-
transition_delay: 0,
+
-
transition_speed: 500,
+
-
show_caption: 'onload', /* onload/onhover/show */
+
-
thumbnails: false,
+
-
thumbnails_position: 'outside-last', /* outside-last/outside-first/inside-last/inside-first */
+
-
thumbnails_direction: 'vertical', /* vertical/horizontal */
+
-
thumbnails_slidex: 1, /* 0 = auto / 1 = slide one thumbnail / 2 = slide two thumbnails / etc. */
+
-
dynamic_height: false, /* For dynamic height to work in webkit you need to set the width and height of images in the source. Usually works to only set the dimension of the first slide in the showcase. */
+
-
speed_change: true, /* Set to true to prevent users from swithing more then one slide at once. */
+
-
viewline: false, /* If set to true content_width, thumbnails, transition and dynamic_height will be disabled. As for dynamic height you need to set the width and height of images in the source. */
+
-
custom_function: null /* Define a custom function that runs on content change */
+
-
});
+
-
});
+
-
 
+
-
</script>
+
-
+
-
<!-- stick in its own global file -->
+
-
    <script>
+
-
      $(document).ready(function() {
+
-
        $.meow({
+
-
          message: $('#onready'),
+
-
          icon: 'folder_32.png'
+
-
        });
+
-
        $('#button').click(function () {
+
-
          $.meow({
+
-
            message: $('#onclick'),
+
-
            icon: 'folder_32.png'
+
-
          });
+
-
        });
+
-
        $('#onchange').change(function () {
+
-
          $.meow({
+
-
            title: 'I have a defined title!',
+
-
            message: $('#onchange'),
+
-
            /*icon: '/icons/chart_16.png'*/
+
-
          });
+
-
        });
+
-
+
-
$('#Link').click(function () {
+
-
          $.meow({
+
-
            message: 'What goes here?',
+
-
            icon: "83-calendar.png"
+
-
          });
+
-
});
+
-
+
-
        $('#selectonchange').change(function () {
+
-
          $.meow({
+
-
            message: $('#selectonchange'),
+
-
            icon: 'folder_32.png'
+
-
          });
+
-
        });
+
-
        $('#sticky').click(function () {
+
-
          $.meow({
+
-
            message: 'I\'m a sticky meow!',
+
-
            icon: 'folder_32.png',
+
-
            sticky: true
+
-
          });
+
-
        });
+
-
        $('#uncloseable').click(function () {
+
-
          $.meow({
+
-
            message: 'I am uncloseable!',
+
-
            icon: 'folder_32.png',
+
-
            closeable: false
+
-
          });
+
-
        });
+
-
        $('#callbacks').click(function () {
+
-
          $.meow({
+
-
            message: 'I have callbacks!',
+
-
            icon: 'folder_32.png',
+
-
            beforeCreateFirst: function () {
+
-
              alert(this + ' is the first meow!');
+
-
            },
+
-
            beforeCreate: function () {
+
-
              alert('About to create ' + this);
+
-
            },
+
-
            afterCreate: function () {
+
-
              alert('Just created ' + this);
+
-
            },
+
-
            onTimeout: function () {
+
-
              alert(this + ' just timed out.');
+
-
            },
+
-
            beforeDestroy: function () {
+
-
              alert('About to destroy ' + this);
+
-
            },
+
-
            afterDestroy: function () {
+
-
              alert('And it\'s gone');
+
-
            },
+
-
            afterDestroyLast: function () {
+
-
              alert('There are no meows left :3');
+
-
            }
+
-
          });
+
-
        });
+
-
      });
+
-
    </script>
+
-
 
+
-
 
+
<style type="text/css">
<style type="text/css">
-
 
<!--
<!--
-
table.mesa {
+
.style3 {
-
color: #f1f1f1;
+
-
}
+
-
table.mesa th {
+
-
padding: 0px;
+
-
background-color: #f1f1f1;
+
-
}
+
-
table.mesa td {
+
-
padding: 0px;
+
-
background-color: #f1f1f1;
+
-
}
+
-
body,td,th {
+
-
font-family: Arial, Helvetica, sans-serif;
+
-
font-size: 36px;
+
text-align: center;
text-align: center;
-
color: #CCC;
 
-
}
 
-
body {
 
-
margin-left: 0px;
 
-
margin-top: 0px;
 
-
margin-right: 0px;
 
-
margin-bottom: 0px;
 
-
}
 
-
.Test {
 
-
color: #252525;
 
-
text-align: right; font-size: px;
 
-
}
 
-
.Test strong {
 
-
color: #666;
 
-
font-size: 48px;
 
-
font-weight: bold;
 
-
}
 
-
 
-
 
-
<style type="text/css">
 
-
html, body { height:100% }
 
-
body, h1, h2, p {
 
-
border:0;
 
-
margin:0;
 
-
padding:0;
 
-
text-align: left;
 
-
}
 
-
body {
 
-
font-family: helvetica, arial, sans-serif;
 
-
background-image:-webkit-gradient(radial, 50% 50%, 0, 50% 50%, 300, from(#888), to(#444));
 
-
background-image:url();
 
-
background-size:100% 100%;
 
-
-webkit-perspective:500px;
 
-
-moz-perspective:500px;
 
-
background-repeat: repeat-x;
 
-
 
-
/* IE10 */
 
-
background-image: -ms-linear-gradient(top right, #212121 40%, #D4D4D4 70%, #FFFFFF 100%);
 
-
 
-
/* Mozilla Firefox */
 
-
background-image: -moz-linear-gradient(top right, #212121 40%, #D4D4D4 70%, #FFFFFF 100%);
 
-
 
-
/* Opera */
 
-
background-image: -o-linear-gradient(top right, #212121 40%, #D4D4D4 70%, #FFFFFF 100%);
 
-
 
-
/* Webkit (Safari/Chrome 10) */
 
-
background-image: -webkit-gradient(linear, right top, left bottom, color-stop(.4, #212121), color-stop(0.7, #D4D4D4), color-stop(1, #FFFFFF));
 
-
 
-
/* Webkit (Chrome 11+) */
 
-
background-image: -webkit-linear-gradient(top right, #212121 40%, #D4D4D4 70%, #FFFFFF 100%);
 
-
 
-
/* Proposed W3C Markup */
 
-
background-image: linear-gradient(top right, #212121 40%, #D4D4D4 70%, #FFFFFF 100%);
 
-
 
-
background-color: transparent;
 
-
 
-
 
-
 
-
 
-
 
-
}
 
-
a { color:#bbb; }
 
-
#text {
 
-
position:absolute;
 
-
width:998px;
 
-
height:53px;
 
-
left:601px;
 
-
top:398px;
 
-
margin-left:-300px;
 
-
margin-top:-60px;
 
-
text-align:center;
 
-
text-transform:uppercase;
 
-
-webkit-tranform:translateZ(0);
 
-
-webkit-transition-duration:0.05s;
 
-
-moz-tranform:translateZ(0);
 
-
color:#f3f3f3;
 
-
text-shadow:0 0 1px rgba(0,0,0,.2);
 
-
}
 
-
 
-
 
-
 
-
p {
 
-
top:0;
 
-
width:90%;
 
-
font-size:16px;
 
-
color:#333;
 
-
text-shadow:0 -1px 0 rgba(0,0,0,0.1);
 
-
font-family: Arial, Helvetica, sans-serif;
 
-
padding-top: 10px;
 
-
padding-right: 10;
 
-
padding-bottom: 10px;
 
-
padding-left: 10;
 
-
right: 2px;
 
-
text-align: left;
 
-
}
 
-
a:link {
 
-
color: #333;
 
-
}
 
-
a:visited {
 
-
color: #333;
 
-
}
 
-
a:hover {
 
-
color: #666;
 
-
}
 
-
a:active {
 
-
color: #FFF;
 
-
}
 
-
.floatingHeader {
 
-
  position: fixed;
 
-
  top: 0;
 
-
  visibility: hidden;
 
-
}
 
-
.imgshadow2 table {
 
-
text-align: left;
 
-
}
 
-
.imgshadow2 table tr td div p {
 
-
text-align: left;
 
-
}
 
-
.imgshadow2 table {
 
-
font-size: 24px;
 
-
text-align: justify;
 
-
}
 
-
.imgshadow2 table tr td div p {
 
-
text-align: justify;
 
-
}
 
-
.imgshadow2 {
 
-
text-align: left;
 
-
}
 
-
 
-
.style2 {font-family: Verdana, Geneva, sans-serif; text-align: center; color: #333333; }
 
-
.style3 {
 
-
color: #666666;
 
-
font-size: 24px;
 
-
}
 
-
.imgshadow2 blockquote table {
 
-
text-align: left;
 
-
}
 
-
.imgshadow2 blockquote table {
 
-
text-align: left;
 
-
}
 
-
.imgshadow2 blockquote table {
 
-
text-align: left;
 
}
}
 +
-->
</style>
</style>
 +
</head>
-
 
-
 
-
 
-
</head>
 
<body leftmargin="0" topmargin="0" marginwidth="0" marginheight="0">
<body leftmargin="0" topmargin="0" marginwidth="0" marginheight="0">
-
<p>&nbsp;</p>
+
<table width="900px" border="0" align="center" cellpadding="0" cellspacing="20" bordercolor="#F1F1F1" background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png" >
-
<p>&nbsp;</p>
+
-
<table width="60%" border="0" align="center" cellpadding="0" cellspacing="20" bordercolor="#F1F1F1" background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png" bgcolor="#F1F1F1" >
+
   <tr>
   <tr>
-
     <td height="58" colspan="2" td background="https://static.igem.org/mediawiki/2011/9/96/Stripe.png"><p class="style3">RUTGERS iGEM TEAM WIKI</p>
+
     <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 />
-
       <p class="style3">MYS!S<br />
+
       </p></td>
-
        </p></td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td width="9%" valign="top" class="stuff">Menu &gt;&gt; The Bacterial Etch-a-Sketch &gt;&gt; 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 &gt;&gt; The Bacterial Etch-a-Sketch &gt;&gt; Goals</td>
   </tr>
   </tr>
   <tr>
   <tr>
Line 340: Line 39:
         <tr>
         <tr>
          
          
-
           <td colspan="6" bgcolor="#F1F1F1" class="stuff"></h4>
+
           <td colspan="6" class="stuff"></h4>
            
            
-
 
-
 
-
 
-
<div style="width: 800px; margin: auto;">
 
-
 
-
<!-- This is the button used to switch between One Page and Slideshow. -->
 
-
<p><a id="awOnePageButton" href="#showcase"><span class="view-page">View As One Page</span><span class="view-slide">View As Slideshow</span></a></p>
 
-
 
-
<div id="showcase" class="showcase">
 
-
<!-- Each child div in #showcase represents a slide -->
 
-
<div class="showcase-slide">
 
-
<!-- Put the slide content in a div with the class .showcase-content -->
 
-
 
-
<div class="showcase-content">
 
-
<!-- If the slide contains multiple elements you should wrap them in a div with the class .showcase-content-wrapper.
 
-
We usually wrap even if there is only one element, because it looks better. :-) -->
 
-
<div class="showcase-content-wrapper">
 
-
<h1>&nbsp;</h1>
 
-
<h1>&nbsp;</h1>
 
-
<h1>The MYS!S Project: BioBrick Optimizer </div>
 
-
</div>
 
-
</div>
 
-
<!-- Each child div in #showcase represents a slide -->
 
-
<div class="showcase-slide">
 
-
<!-- Put the slide content in a div with the class .showcase-content. -->
 
-
 
-
<div class="showcase-content">
 
-
<img src="https://static.igem.org/mediawiki/2011/f/ff/Screen_Shot_2011-09-25_at_9.57.01_AM.jpg" alt="01" width="766" height="546" /> </div>
 
-
</div>
 
-
<!-- Each child div in #showcase represents a slide -->
 
-
<div class="showcase-slide">
 
-
<!-- Put the slide content in a div with the class .showcase-content. -->
 
-
</div>
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
-
 
<h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/5/5c/58-bookmark.png" width="10" height="26" /> Abstract</h4>
<h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/5/5c/58-bookmark.png" width="10" height="26" /> Abstract</h4>
Line 404: Line 59:
         <tr>
         <tr>
          
          
-
           <td colspan="6" bgcolor="#f1f1f1" 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>
+
           <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 tRNAs and replacing them with more prevalent tRNAs.  </p>
+
             <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>
             <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>
             <p class="stuff">&nbsp;</p>
             <p class="stuff">&nbsp;</p>
Line 428: Line 83:
           <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>
           <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>
-
         <tr bgcolor="#F1F1F1">
+
         <tr >
           <td colspan="6" class="stuff"><h4 class="shadow">The MYS!S Environment </h4>
           <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>
             <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>
Line 445: Line 100:
           </tr>
           </tr>
         <tr>
         <tr>
-
           <td colspan="6" bgcolor="#F1F1F1" class="stuff"><h4 class="shadow">Walkthrough</h4>
+
           <td colspan="6" class="stuff"><h4 class="shadow">Walkthrough</h4>
             <p class="stuff">The MYS!S walkthrough is located here!</p>
             <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"><a href="https://2011.igem.org/Team:Rutgers/MYS!S_WT">https://2011.igem.org/Team:Rutgers/MYS!S_WT</a></p>
Line 465: Line 120:
         <tr>
         <tr>
          
          
-
           <td colspan="6" bgcolor="#f1f1f1" 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>
+
           <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.
Line 495: Line 150:
         <tr>
         <tr>
          
          
-
           <td colspan="6" bgcolor="#f1f1f1" class="stuff"><h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/e/e5/59-flag.png" > beta</h4>
+
           <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>
Line 533: Line 188:
         <tr>
         <tr>
          
          
-
           <td colspan="6" bgcolor="#f1f1f1" class="stuff"><h4 class="shadow"><img src="https://static.igem.org/mediawiki/2011/8/85/56-cloud.png" width="24" height="16"> Github</h4>
+
           <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 github site.              </p>
+
             <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"> <a href="https://github.com/RutgersGEARS/iGEM-Rutgers-Software">https://github.com/RutgersGEARS/iGEM-Rutgers-Software </a></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">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>
Line 560: Line 215:
</table>
</table>
-
  <p>&nbsp;</p>
+
<p>&nbsp;</p>
   <p>&nbsp;</p>
   <p>&nbsp;</p>
   <p>&nbsp;</p>
   <p>&nbsp;</p>

Latest revision as of 04:59, 28 September 2011

Rutgers 2011 iGEM Team: Complex Circuits in Synthetic Biology

Rutgers 2011 iGEM Team: Complex Circuits in Synthetic Biology

RUTGERS iGEM TEAM WIKI
Menu >> The Bacterial Etch-a-Sketch >> Goals

the MYS!S Project

Abstract

MYS!S is a stand alone software tool designed to assist an “iGEMer” when designing a new BioBrick part or modifying an existing one.

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.

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.

 

Operations

I. DNA Optimization

First, it performs DNA codon optimization based on the target organism by removing rare codons and replacing them with more prevalent codons.

(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.)

 

II. Processing

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.

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.

 

III. Restriction site analysis

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.

 

 

How Mys!S Does it

The MYS!S Environment

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.

Custimization

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.

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.

 

MYS!S: An Introduction

Walkthrough

The MYS!S walkthrough is located here!

https://2011.igem.org/Team:Rutgers/MYS!S_WT

 

Features

I. Protocols

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. http://research.microsoft.com/en-us/um/india/projects/biocoder/

 

II. Rna Structure Analysis

In the RNA structure tab there are images of the unmodified and modified RNA structure. We hope that this will help the user decide whether the changes are structurally advantageous. Hopefully in the future more advanced RNA structure modeling algorithms can be implemented to help the user make an informed decision.

 

 

Future of MYS!S

beta

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.

Better algorithms for modifying DNA

Currently, when determining how to modify DNA MYS!S does not take into account the eventual RNA structure and whether the changes will inhibit protein production. We would like to incorporate algorithms that make changes to DNA in a way that will increase the amount of protein formed by translation. On the same note, it might also be helpful for a synthetic biologist not just to increase protein production but maybe to limit it.

 

Not just support site directed mutagenesis

Right now MYS!S for a codon optimization creates a large number of primers for a sequence of say 700bp. We’re talking about upwards of 50 primers making site directed mutagenesis realistically impossible. We would like MYS!S to support other methods of manipulating physical DNA.

 

Better visualization methods for RNA structure

We want the user to be able to visually check whether the RNA structure is acceptable. If it is not acceptable the user should be able to manually modify the DNA sequence to improve the RNA structure. Preference for lab protocols : Not all labs do things the same, MYS!S should be able to customize lab protocols to how the user’s lab gets things done.

 

 

Where can I get MYS!S?

Github

MYS!S is currently available as an Eclipse download. It will very soon be available as a java application.

The downloads can be obtained from our GitHub site.

https://github.com/RutgersGEARS/iGEM-Rutgers-Software

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.

https://github.com/RutgersGEARS/iGEM-Rutgers-Software/issues

 

 

 

 

 

 

 

 

 

 

 

 

 

Retrieved from "http://2011.igem.org/Team:Rutgers/MYS!S"