|
|
| Line 2: |
Line 2: |
| | {{Rice/Backdrop}} | | {{Rice/Backdrop}} |
| | <html> | | <html> |
| | + | <style> |
| | | | |
| − | <head>
| + | #top_title { |
| − | <meta name="viewport" content="width=device-width, initial-scale=1">
| + | display: none; |
| − | <style>
| + | } |
| − | * {
| + | |
| − | box-sizing: border-box;
| + | |
| − | }
| + | |
| | | | |
| − | #top_title {
| + | #content { |
| − | display: none;
| + | left: 0px; |
| − | }
| + | height: 100%; |
| − | | + | padding: 0px; |
| − | #home_logo,
| + | width: 100%; |
| − | #sideMenu {
| + | margin-top: -20px; |
| − | display: none;
| + | margin-left: 0px; |
| − | }
| + | margin-bottom: -20px; |
| − | | + | background-color: #26849c!important; |
| − | #sideMenu,
| + | } |
| − | #top_title,
| + | |
| − | .patrollink {
| + | |
| − | display: none;
| + | |
| − | }
| + | |
| − | | + | |
| − | #content {
| + | |
| − | margin-left: -7px;
| + | |
| − | margin-top: -7px;
| + | |
| − | padding: 0px;
| + | |
| − | width: 100%;
| + | |
| − | }
| + | |
| − | | + | |
| − | #topbox {
| + | |
| − | height: 30vh;
| + | |
| − | background-image: url(https://static.igem.org/mediawiki/2019/a/a9/T--Rice--Modeling.svg));
| + | |
| − | background-size: cover;
| + | |
| − | background-position: 50% 50%;
| + | |
| − | background-attachment: absolute;
| + | |
| − | display: table;
| + | |
| − | background-color: #1f9ec1;
| + | |
| − | }
| + | |
| − | | + | |
| − | #topbox h1 {
| + | |
| − | font-size: 80px;
| + | |
| − | color: white !important;
| + | |
| − | text-align: center;
| + | |
| − | margin: 0px;
| + | |
| − | display: table-cell;
| + | |
| − | vertical-align: middle;
| + | |
| − | line-height: 80px;
| + | |
| − | font-family: comfortaa;
| + | |
| − | }
| + | |
| − | | + | |
| − | #content {
| + | |
| − | left: 0px;
| + | |
| − | height: 80%;
| + | |
| − | padding: 0px;
| + | |
| − | width: 100%;
| + | |
| − | margin-left: 0px;
| + | |
| − | margin-top: 0px;
| + | |
| − | margin-bottom: 0px;
| + | |
| − | background-color: #1f9ec1 !important;
| + | |
| − | }
| + | |
| − | | + | |
| − | .container {
| + | |
| − | background-color: white !important;
| + | |
| − | }
| + | |
| − | | + | |
| − | .column {
| + | |
| − | float: left;
| + | |
| − | width: 50%;
| + | |
| − | padding: 10px;
| + | |
| − | }
| + | |
| − | | + | |
| − | .row:after {
| + | |
| − | content: "";
| + | |
| − | display: table;
| + | |
| − | clear: both;
| + | |
| − | }
| + | |
| − | | + | |
| − | p {
| + | |
| − | color: #000000 !important;
| + | |
| − | font-family: raleway !important;
| + | |
| − | font-size: 20px !important;
| + | |
| − | padding: 40px !important;
| + | |
| − | margin-top: -10px !important;
| + | |
| − | | + | |
| − | }
| + | |
| − | | + | |
| − | h1 {
| + | |
| − | color: #000000 !important;
| + | |
| − | font-family: comfortaa !important;
| + | |
| − | font-size: 60px !important;
| + | |
| − | text-align: center;
| + | |
| − | color: #fff !important;
| + | |
| − | padding: 40px !important;
| + | |
| − | | + | |
| − | }
| + | |
| − | | + | |
| − | h2 {
| + | |
| − | color: #000000 !important;
| + | |
| − | font-family: comfortaa !important;
| + | |
| − | font-size: 30px !important;
| + | |
| − | text-align: center;
| + | |
| − | padding: 10px !important;
| + | |
| − | }
| + | |
| − | | + | |
| − | body {
| + | |
| − | margin: 0;
| + | |
| − | background-color: #fff !important;
| + | |
| − | }
| + | |
| − | | + | |
| − | ol {
| + | |
| − | font-size: 20px !important;
| + | |
| − | font-family: raleway !important;
| + | |
| − | }
| + | |
| − | | + | |
| − | li {
| + | |
| − | font-size: 20px !important;
| + | |
| − | font-family: raleway !important;
| + | |
| − | }
| + | |
| − | | + | |
| − | @media screen and (max-width: 600px) {
| + | |
| − | .column {
| + | |
| − | width: 100%;
| + | |
| − | }
| + | |
| − | }
| + | |
| − | </style>
| + | |
| − | </head>
| + | |
| | | | |
| | + | body { |
| | + | background-color: #26849c!important; |
| | + | width: 100%; |
| | + | } |
| | + | |
| | + | </style> |
| | <body> | | <body> |
| − | <div id="topbox">
| + | </br> |
| − | <h1></h1>
| + | </br> |
| − | </div>
| + | <img src="https://static.igem.org/mediawiki/2019/c/c6/T--Rice--homepage.svg" width = "100%" > |
| − | <br />
| + | </body> |
| − | | + | </html> |
| − | <div class="container"> | + | {{Rice/footer}} |
| − | | + | <html> |
| − | <div class="column" style="background-color: #d2e8c5!important; height: 65vh;">
| + | <body> |
| − | <h2>Basis for a Genetic Algorithm</h2>
| + | </br> |
| − | <p>
| + | |
| − | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed id porta lacus. Proin vel urna nec ex
| + | |
| − | rhoncus tristique at ut felis. Integer pharetra ipsum sapien, a bibendum nisi facilisis egestas. Nam
| + | |
| − | molestie urna quis porttitor vulputate. Cras nibh leo, fringilla eget luctus et, rutrum ut risus.
| + | |
| − | Aliquam finibus nulla eu nunc luctus vulputate. Duis euismod pellentesque dictum. Curabitur blandit diam
| + | |
| − | et porttitor sollicitudin. In hac habitasse platea dictumst.
| + | |
| − | </p>
| + | |
| − | </div>
| + | |
| − | <div class="column" style="background-color: #ffffff!important; height: 65vh;">
| + | |
| − | <img class="img-responsive" style="width:100%; padding:10px;" | + | |
| − | src="https://static.igem.org/mediawiki/2019/1/18/T--Rice--basic_heat_response.png" />
| + | |
| − | </div>
| + | |
| − | <div class="row" style="background-color:#9bc4cf!important; padding-top: 5vh;">
| + | |
| − | <h2>Percentage base pair optimization algorithm</h2>
| + | |
| − | <ol>
| + | |
| − | <li>
| + | |
| − | <p>
| + | |
| − | For each base of the complement of the context containing the RBS, create three other
| + | |
| − | permutations which have that base mutated. All of these permutations combined form the initial
| + | |
| − | population. The baseline is defined as the full sequence containing the context before the
| + | |
| − | variable region, the variable region which is the complement of the RBS-containing context, and
| + | |
| − | the RBS-containing context.
| + | |
| − | </p>
| + | |
| − | </li>
| + | |
| − | <li>
| + | |
| − | <p>
| + | |
| − | Calculate the base pairing probabilities at the two given temperatures for each test sequence
| + | |
| − | using the NuPack command <code>pairs -T TEMP -pseudo -material rna sequencename.</code>
| + | |
| − | </p>
| + | |
| − | </li>
| + | |
| − | <li>
| + | |
| − | <p>
| + | |
| − | The output of the command consists in part of a list of every base and the base(s) which it has
| + | |
| − | a > 0.001 probability of base pairing with by position number. Find the base pairings where one
| + | |
| − | of the bases is in the RBS-containing region and add up the probabilities corresponding to that
| + | |
| − | base pairing. The nature of this NuPack command should prevent duplicates. Then, subtract the
| + | |
| − | probability that these bases are unpaired.
| + | |
| − | </p>
| + | |
| − | </li>
| + | |
| − | <li>
| + | |
| − | <p>
| + | |
| − | Subtract the number of base pairings at 30°C from the number of base pairings at 25°C. We want
| + | |
| − | to maximize the number of RBS-base pairings that disappear as the temperature increases from
| + | |
| − | 25°C to 30°C (for reference, the command I use for the minimum free energy calculation is
| + | |
| − | <code>mfe -T TEMP -pseudo -material rna sequencename</code>)
| + | |
| − | </p>
| + | |
| − | </li>
| + | |
| − | <li>
| + | |
| − | <p>
| + | |
| − | Using the library DEAP, select 50 individuals through the tournament selection method.
| + | |
| − | </p>
| + | |
| − | </li>
| + | |
| − | </ol>
| + | |
| − | </div>
| + | |
| − | | + | |
| − | </div>
| + | |
| | </body> | | </body> |
| − |
| |
| | </html> | | </html> |
