Difference between revisions of "Team:Peking/Modeling"

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{{Peking}}
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    <meta charset="utf-8">
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    <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
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    <meta name="Peking-iGEM-2015" content="iGEM - Peking iGEM 2015">
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    <link rel="stylesheet" type="text/css" href="https://2015.igem.org/Template:Peking/Blue?action=raw&amp;ctype=text/css " title="blue" media="screen" />
  
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<h2> Modeling</h2>
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        .carousel-control.left, .carousel-control.right {background-image:none;}
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        /*universal style*/
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        @media (min-width:1024px){
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        #sidebar1{position:relative;top:120px;}
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        #sidebar2{display:none;}
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        #nav-top{height:88px;}
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        }
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        @media (max-width: 1023px){
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        #sidebar1{display:none;}
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        #sidebar2{display:block;}
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        }
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        .back-to-top{z-index:9999;}
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        /* to style the team page*/
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        .individual-picture{max-width:200px;margin-top:15px; margin-bottom:10px; }
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</head>
  
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<body>
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<div id="container">
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<!-- Start Header -->
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<header class="clearfix" id="fixedNav">
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    <!-- Start  Logo & Naviagtion  -->
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    <div class="navbar navbar-default navbar-top">
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        <div class="container">
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            <div class="navbar-header" >
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                <!-- Stat Toggle Nav Link For Mobiles -->
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                <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse" style="margin-top:40px">
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                    <i class="fa"><img style="margin-left:0;height:30px;"src="https://static.igem.org/mediawiki/2015/4/45/Peking-Hambergur-1.png" ></i>
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                </button>
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                <!-- End Toggle Nav Link For Mobiles -->
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                <a class="navbar-brand" href="https://2015.igem.org/Team:Peking">
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                    <img alt="Peking iGEM 2015" src="https://static.igem.org/mediawiki/2015/8/8b/Peking-header-logo-1.png" style="height:55px;margin-top:7px">
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                </a>
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            </div>
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            <div class="navbar-collapse collapse" style="padding-top:5px;padding-bottom:0">
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                <!-- Start Navigation List -->
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                <ul class="nav navbar-nav navbar-right "id="nav-top" style="padding-bottom:15px;padding-top:10px">
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                    <li>
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                        <a href="https://2015.igem.org/Team:Peking/JudgingCriteria">Achievements</a>
 +
                        <ul class="dropdown">
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                            <li><a href="https://2015.igem.org/Team:Peking/JudgingCriteria">Judging Criteria</a></li>
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                            <li><a href="https://2015.igem.org/Team:Peking/Parts">Parts</a></li>
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                            <li><a href="https://2015.igem.org/Team:Peking/Collaborations">Collaborations</a></li>
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                        </ul>
 +
                    </li>
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                    <li>
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                        <a href="https://2015.igem.org/Team:Peking/Design">Project</a>
 +
                        <ul class="dropdown">
 +
                            <li><a href="https://2015.igem.org/Team:Peking/Design">Overview</a></li>
 +
                            <li><a href="#">CRIPSR</a></li>
 +
                            <li><a href="#">Isothermal PCR</a></li>
 +
                            <li><a href="#">B. subtillis</a></li>
 +
                            <li><a href="#">Device</a></li>
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                        </ul>
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                    </li>
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                    <li>
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                        <a href="https://2015.igem.org/Team:Peking/Modeling" class="active">
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                            Modelling</a>
 +
                        <ul class="dropdown">
 +
                            <li><a href="https://2015.igem.org/Team:Peking/Modeling" class="active">Marker Finder</a></li>
 +
                            <li><a href="#">Signal Processing</a></li>
 +
                        </ul>
 +
                    </li>
 +
                    <li>
 +
                        <a href="https://2015.igem.org/Team:Peking/Practices">Practice</a>
 +
                        <ul class="dropdown">
 +
                            <li><a href="https://2015.igem.org/Team:Peking/Practices">Overview</a></li>
 +
                            <li><a href="#">Link 1</a></li>
 +
                            <li><a href="#">Link 2</a></li>
 +
                            <li><a href="#">Link 3</a></li>
 +
                            <li><a href="#">Link 4</a></li>
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                        </ul>
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                    </li>
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                    <li>
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                        <a href="#">Lab</a>
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                        <ul>
 +
                            <li><a href="https://2015.igem.org/Team:Peking/Team">Team</a></li>
 +
                            <li><a href="https://2015.igem.org/Team:Peking/Notebook">Notebook</a></li>
 +
                            <li><a href="https://2015.igem.org/Team:Peking/Attributions">Attributions</a></li>
 +
                            <li><a href="https://2015.igem.org/Team:Peking/Safety">Safety</a></li>
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                        </ul>
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                    </li>
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                </ul>
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                <!-- End Navigation List -->
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            </div>
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        </div>
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    </div>
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    <!-- End Header Logo & Naviagtion -->
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</header>
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<div class="highlightBox">
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<h4>Note</h4>
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<!-- Start Page Banner -->
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
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<div class="page-banner" style="background-color:#e0e0e0;margin-top:1%;margin-bottom:20px;">
 +
    <div class="container">
 +
        <div class="row">
 +
            <div class="col-md-6">
 +
                <h2><b>Modeling</b></h2>
 +
                <p>Specificity!!!!</p>
 +
            </div>
 +
            <div class="col-md-6">
 +
                <ul class="breadcrumbs">
 +
                    <li><a href="https://2015.igem.org/Team:Peking">Home</a></li>
 +
                    <li>Modeling</li>
 +
                </ul>
 +
            </div>
 +
        </div>
 +
    </div>
 
</div>
 
</div>
 +
<!-- End Page Banner -->
  
  
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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<!-- Start Content -->
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<div id="content">
 +
    <div class="container">
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        <div class="row blog-page">
 +
            <!--Sidebar-->
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            <div class="col-md-3 sidebar left-sidebar">
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                <!-- Sidebar for windows > 1024px -->
 +
                <div id="sidebar1"class="widget widget-categories">
 +
                    <h4 style="font-size:18px">Marker Finder<span class="head-line"></span></h4>
 +
                    <ul>
 +
                        <li><a href="#Modeling-Overview">Overview</a></li>
 +
                        <li><a href="#Modeling-SSPD">SSPD Method</a></li>
 +
                        <li><a href="#Modeling-OligoGenerator">Oligo Generator</a></li>
 +
                    </ul>
 +
                </div>
 +
                <!-- Sidebar for windows < 1024px -->
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                <div id="sidebar2"class="widget widget-categories">
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                    <h4 style="font-size:18px">Team <span class="head-line"></span></h4>
 +
                    <ul>
 +
                        <li><a href="#Modeling-Overview">Overview</a></li>
 +
                        <li><a href="#Modeling-SSPD">SSPD Method</a></li>
 +
                        <li><a href="#Modeling-OligoGenerator">Oligo Generator</a></li>
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                    </ul>
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                </div>
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            </div>
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            <!--End sidebar-->
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            <!-- Page Content -->
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            <div class="col-md-9 page-content">
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                <div id="team-introduction">
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                    <!--annother type of touch slider-->
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                    <div id="myCarousel" class="carousel slide" data-ride="carousel">
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                        <!-- Indicators -->
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                        <ol class="carousel-indicators">
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                            <li data-target="#myCarousel" data-slide-to="0" class="active"></li>
 +
                            <li data-target="#myCarousel" data-slide-to="1"></li>
  
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<p>
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                        </ol>
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Here are a few examples from previous teams:
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                        <!-- Wrapper for slides -->
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</p>
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                        <div class="carousel-inner" role="listbox">
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<ul>
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                            <div class="item active">
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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                                <img src="https://static.igem.org/mediawiki/2015/0/08/Peking-team-about-01.jpg" style="width:100%;" alt="">
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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                            </div>
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</ul>
+
  
 +
                            <div class="item">
 +
                                <img src="https://static.igem.org/mediawiki/2015/0/09/Peking-team-about-02.jpg" style="width:100%;" alt="">
 +
                            </div>
  
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</div>
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                        </div>
 +
                        <!-- Left and right controls -->
 +
                        <a class="left carousel-control" href="#myCarousel" role="button" data-slide="prev">
 +
                            <span class="glyphicon" aria-hidden="true"><img src="https://static.igem.org/mediawiki/2015/d/d1/Peking-left.png" style="margin-top:700%"></span>
 +
                            <span class="sr-only">Previous</span>
 +
                        </a>
 +
                        <a class="right carousel-control" href="#myCarousel" role="button" data-slide="next">
 +
                            <span class="glyphicon" aria-hidden="true"><img src="https://static.igem.org/mediawiki/2015/f/fc/Peking-right.png" style="margin-top:700%"></span>
 +
                            <span class="sr-only">Next</span>
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                        </a>
 +
                    </div>
 +
                    <!--end of touch slider-->
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                    <!-- Classic Heading -->
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                    <h3 class="classic-title"><span>Overview</span></h3>
 +
                    <!-- Some Text -->
 +
                    <p>To increase the accuracy and specificity of the detection, we develop an assay over our Paired dCas9 Reporter System to get more sequence information from the target genome. The core as well as the first step of the design of the array is to screen over the entire genome and get specific sequences (CRISPR target sites) with high specificity as markers. <br>
 +
                        We develop a method named SSPD to achieve our aim, which is composed of 4 steps: <br>
 +
                        Search for guide candidates <br>
 +
                        Specificity test for each candidate <br>
 +
                        Pair left and right guides with optimal spacer length <br>
 +
                        Design PCR fragments <br>
 +
                        We will introduce each step in detail separately with analysis about Mycobacterium tuberculosis (TB) genome as an example. After the target sites are chosen, we developed an Oligo Generator to turn the target sites into oligonucleotides sequences for following sgRNA construction combined with our gRNA generator.
 +
                    </p>
 +
                    <!--Members-introduction-->
 +
                    <!-- Classic Heading -->
 +
                    <div id="Team-SSPD">
 +
                        <h3 class="classic-title"><span>SSPD Methods</span></h3>
 +
                        <!--Modeling-SSPD-S1-->
 +
                        <div id="SSPD-S1" class='col-md-12'>
 +
                            <h4><em>Search for guide candidates</em></h4>
 +
                            <p>Recall the structure of Paired dCas9 Reporter (PC Reporter) System, a protospacer adjacent motif (PAM) sequence in the form of 5’-NGG-3’ at 3’ end of guide sequence, usually 20bp, on the non-complementary strand. (Figure 1) As it is showed in our experimental results that PAM-out orientation (5’-CCNN20-…-N20NGG-3’) was highly efficient for PC Reporter system to work, thus our model would focus on this orientation. (However, it can be more convenient to adjust our program for guide sequence design also with other orientations. See more in supplementary)
 +
                            </p>
 +
                            <div id="Modeling_Fig1">
 +
                                <img alt="Modeling_Fig1" src="https://static.igem.org/mediawiki/2015/0/07/Peking_individual_WEI_Weijia.jpg">
 +
                                <p>Figure 1. Schematic illustration of guide design in PAM-out orientation. Note the 20nt guide sequence is identical to target non-complementary strand.</p>
 +
                            </div>
 +
                            <p>We took advantage of Python 3.4.3 build-in regular expression to search for left guide sequences of gRNA and right guide sequences of gRNA separately, which would be paired later for PC reporter system to function.
 +
                            </p>
 +
                        </div>
 +
                    </div>
 +
                </div>
 +
                <!--End of Team-introduction-->
 +
                <!--Start Instructor-->
 +
                <div id="Team-Instructors">
 +
                    <h3 class="classic-title" style="margin-top:25px"><span>Instructors</span></h3>
 +
                    <div class="row">
 +
                        <div class="col-md-4">
 +
                            <img alt="OUYangqi-Peking"  src="https://static.igem.org/mediawiki/2015/a/a8/Peking_individual_OUYANG_Qi.jpg" style="max-width:150px" >
 +
                            <h4><em>&nbsp;&nbsp;OUYANG Qi</em></h4>
 +
                        </div>
 +
                        <div class="col-md-4">
 +
                            <img alt="LOUChunbo-Peking"  src="https://static.igem.org/mediawiki/2015/8/84/Peking_individual_LOU_Chunbo.jpg"style="max-width:150px" >
 +
                            <h4><em>&nbsp;&nbsp;LOU Chunbo</em></h4>
 +
                        </div>
 +
                        <div class="col-md-4">
 +
                            <img alt="ZHANGHaoqian-Peking"  src="https://static.igem.org/mediawiki/2015/0/0a/Peking_individual_ZHANG_Haoqian.jpg"style="max-width:150px" >
 +
                            <h4><em>&nbsp;&nbsp;ZHANG Haoqian</em></h4>
 +
                        </div>
 +
                    </div>
 +
                </div>
 +
            </div>
  
 +
            <!--End Instructor-->
 +
            <!--Start Acknowledgement-->
 +
            <div id="Team-Acknowledgement">
 +
                <h3 class="classic-title" style="margin-top:25px"><span>Acknowledgement</span></h3>
 +
            </div>
 +
            <!--End Acknowledgement-->
 +
        </div><!-- End Page Content-->
 +
    </div>
 +
</div><!-- End Content -->
 +
<!-- Start Footer -->
 +
<footer style="margin-top:30px;padding-top:25px">
 +
    <div class="container">
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        <div class="row footer-widgets">
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            <!-- Start Subscribe & Social Links Widget -->
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            <div class="col-md-3" style="margin-bottom:0;padding-bottom:0">
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                <div class="col-md-12 footer-widget social-widget row">
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                    <h4>Share This<span class="head-line"></span></h4>
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                    <ul class="social-icons">
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                        <li><a class="twitter" target="_blank" href="https://twitter.com/home/?status=2015.igem.org/Team:Peking/Team"><i class="fa"><img src="https://static.igem.org/mediawiki/2015/d/d0/Peking-twitter.png" style="height:20px;width:auto; margin-top:7px;"></i></a></li>
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                        <li><a class="facebook"target="_blank" href="https://www.facebook.com/sharer/sharer.php?u=2015.igem.org/Team:Peking/Team"><i class="fa"><img src="https://static.igem.org/mediawiki/2015/0/0e/Peking-facebook.png" style="height:20px; margin-top:7px;"></i></a></li>
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                        <li><a class="google"target="_blank" href="https://plus.google.com/share?url=2015.igem.org/Team:Peking/Team"><i class="fa"><img src="https://static.igem.org/mediawiki/2015/7/7a/Peking-google_plus.png" style="height:20px; margin-top:7px;"></i></a></li>
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                    <h4>Follow Us<span class="head-line"></span></h4>
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Revision as of 20:33, 15 September 2015

Peking iGEM 2015

Modeling

Specificity!!!!

Overview

To increase the accuracy and specificity of the detection, we develop an assay over our Paired dCas9 Reporter System to get more sequence information from the target genome. The core as well as the first step of the design of the array is to screen over the entire genome and get specific sequences (CRISPR target sites) with high specificity as markers.
We develop a method named SSPD to achieve our aim, which is composed of 4 steps:
Search for guide candidates
Specificity test for each candidate
Pair left and right guides with optimal spacer length
Design PCR fragments
We will introduce each step in detail separately with analysis about Mycobacterium tuberculosis (TB) genome as an example. After the target sites are chosen, we developed an Oligo Generator to turn the target sites into oligonucleotides sequences for following sgRNA construction combined with our gRNA generator.

SSPD Methods

Search for guide candidates

Recall the structure of Paired dCas9 Reporter (PC Reporter) System, a protospacer adjacent motif (PAM) sequence in the form of 5’-NGG-3’ at 3’ end of guide sequence, usually 20bp, on the non-complementary strand. (Figure 1) As it is showed in our experimental results that PAM-out orientation (5’-CCNN20-…-N20NGG-3’) was highly efficient for PC Reporter system to work, thus our model would focus on this orientation. (However, it can be more convenient to adjust our program for guide sequence design also with other orientations. See more in supplementary)

Modeling_Fig1

Figure 1. Schematic illustration of guide design in PAM-out orientation. Note the 20nt guide sequence is identical to target non-complementary strand.

We took advantage of Python 3.4.3 build-in regular expression to search for left guide sequences of gRNA and right guide sequences of gRNA separately, which would be paired later for PC reporter system to function.

Instructors

OUYangqi-Peking

  OUYANG Qi

LOUChunbo-Peking

  LOU Chunbo

ZHANGHaoqian-Peking

  ZHANG Haoqian

Acknowledgement

Sponsors

Contact us

Peking iGEM 2015 Logo
  • Email: pekingigem@gmail.com
  • Website: 2015.igem.org/Team:Peking
  • Address: Peking University,
    No.5 Yiheyuan Road Haidian District,
    Beijing, P.R.China 100871

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