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| − | {{Team:UC Davis }} | + | {{CSS/Main}} |
| − | | + | |
| − | | + | |
| | <html> | | <html> |
| − | <head>
| |
| − |
| |
| − | <meta charset="UTF-8">
| |
| − | <meta name="viewport" content="width=device-width, initial-scale=1.0">
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| − | <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
| |
| − | <script src="http://ajax.googleapis.com/ajax/libs/jquery/1.6.1/jquery.min.js"></script>
| |
| − | <script src="https://code.jquery.com/jquery-2.1.1.min.js"></script>
| |
| − | <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
| |
| − |
| |
| − | <Style>
| |
| − | #avant{
| |
| − | font-family: "Avant Garde", Avantgarde, "Century Gothic", CenturyGothic, "AppleGothic", sans-serif;
| |
| − | }
| |
| − | body{
| |
| − | background-color: #0174DF;
| |
| − |
| |
| − | }
| |
| − | * {
| |
| − | .border-radius(0) !important;
| |
| − | }
| |
| − | h2, h1 {
| |
| − | border-bottom: 0px solid #57c4d0;
| |
| − | }
| |
| | | | |
| − | #nav .btn{
| + | <!-- CHANGE DEFAULT WIKI SETTINGS TO WHITE FULL WIDTH BACKGROUND --> |
| − | //border-right: 2px solid grey;
| + | <style> |
| − |
| + | #contentSub, #footer-box, #catlinks, #search-controls, #p-logo, .printfooter, .firstHeading,.visualClear {display: none;} /*-- hides default wiki settings --*/ |
| − |
| + | </style> |
| − | }
| + | |
| − | p{ | + | |
| − | color: black;
| + | |
| − | } | + | |
| | | | |
| | + | <!-- HEADER --> |
| | | | |
| | + | <table id="menu" width="100%" cellspacing="0" height="135px"> |
| | + | <tr> |
| | + | <td bgColor="#FFFFFF"></td> |
| | + | <td valign="bottom" width="975px" align="center" bgColor="#FFFFFF"> |
| | | | |
| | + | <table align="center"><tr height="50px"> |
| | | | |
| − | #thumbnail-preview-indicators { | + | <td width="162px" align="center" onMouseOver="this.bgColor='#BDBDBD'" onMouseOut="this.bgColor='#6A181B'" bgColor=#6A181B> |
| − | position: relative;
| + | <a href="https://2015.igem.org/Team:UC_Davis/Practices" style="text-decoration:none;color:#FFFFFF">POLICY & PRACTICES </a> </td> |
| − | margin-top: -20px;
| + | |
| − | overflow: hidden;
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .slides .slide-1,
| + | |
| − | #thumbnail-preview-indicators .slides .slide-2, | + | |
| − | #thumbnail-preview-indicators .slides .slide-3 {
| + | |
| − | background-size: cover;
| + | |
| − | background-position: center center;
| + | |
| − | background-repeat: no-repeat;
| + | |
| − |
| + | |
| − |
| + | |
| | | | |
| − | }
| + | <td width="162px" align="center" onMouseOver="this.bgColor='#BDBDBD'" onMouseOut="this.bgColor='#6A181B'" bgColor=#6A181B> |
| − | #thumbnail-preview-indicators,
| + | <a href="https://2015.igem.org/Team:UC_Davis/Design" style="text-decoration:none;color:#FFFFFF">PROJECT</a> </td> |
| − | #thumbnail-preview-indicators .slides,
| + | |
| − | #thumbnail-preview-indicators .slides .slide-1,
| + | |
| − | #thumbnail-preview-indicators .slides .slide-2,
| + | |
| − | #thumbnail-preview-indicators .slides .slide-3 {
| + | |
| − | height: 480px;
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .slides .slide-1 {
| + | |
| − | background-image: url(http://www.desktopaper.com/wp-content/uploads/creative-lajolla-web.jpg);
| + | |
| − |
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .slides .slide-2 {
| + | |
| − | background-image: url(http://i.imgur.com/N40l0eb.png?1);
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .slides .slide-3 {
| + | |
| − | background-image: url(http://i.imgur.com/EfXmCOj.jpg?1);//(http://i.imgur.com/iokYtgR.jpg);
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .carousel-inner .item .carousel-caption {
| + | |
| − | top: 20%;
| + | |
| − | bottom: inherit;
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li,
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li.active {
| + | |
| − | position: relative;
| + | |
| − | width: 100px;
| + | |
| − | height: 8px;
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li > .thumbnail {
| + | |
| − | position: absolute;
| + | |
| − | top: 0;
| + | |
| − | width: 100px;
| + | |
| − | display: none;
| + | |
| − | opacity: 0;
| + | |
| − | left: 50%;
| + | |
| − | margin-top: -80px;
| + | |
| − | margin-left: -50px;
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li:hover > .thumbnail,
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li.active > .thumbnail {
| + | |
| − | display: block;
| + | |
| − | opacity: .8;
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li.active > .thumbnail:hover{
| + | |
| − | opacity: 1;
| + | |
| − | }
| + | |
| − | @media screen and (max-width : 480px) {
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li,
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li.active {
| + | |
| − | width: 50px;
| + | |
| − | height: 8px;
| + | |
| − | position: relative;
| + | |
| − | }
| + | |
| − | #thumbnail-preview-indicators .carousel-indicators li > .thumbnail {
| + | |
| − | width: 50px;
| + | |
| − | left: 50%;
| + | |
| − | margin-top: -50px;
| + | |
| − | margin-left: -25px;
| + | |
| − | }
| + | |
| − | }
| + | |
| − | | + | |
| − | /******************************DEFAULT WIKI SETTINGS CSS: CHANGING IT TO REFLECT OUR OWN PAGE********************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | ******************************* THIS IS TO MAKE THE DISTINCTION CLEAR *******************************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************
| + | |
| − | *******************************/
| + | |
| − | .firstHeading {
| + | |
| − | width: 975px;
| + | |
| − | margin: 0px auto;
| + | |
| − | padding-top: 100px;
| + | |
| − | margin-bottom: 0px;
| + | |
| − | font-family: Georgia, Times, "Times New Roman", serif;
| + | |
| − | }
| + | |
| − | | + | |
| − | h1, h2, h3, h4, h5 { font-family: Georgia, Times, "Times New Roman", serif;}
| + | |
| − | | + | |
| − | | + | |
| − | #top-section { /*-- styling for default menu bar (edit, page, history, etc.) --*/ | + | |
| − | background-color: #003D99;//#383838;
| + | |
| − | border: 0 none;
| + | |
| − | height: 1px; // 46 px
| + | |
| − | z-index: 100;
| + | |
| − | top: 0;
| + | |
| − | color: #fff;
| + | |
| − | //display: none;
| + | |
| − | position: static;
| + | |
| − | width: 100%;//1000px;//2975px;
| + | |
| − | left: 50%;
| + | |
| − | margin-left: -480px;//-687px;
| + | |
| − | }
| + | |
| − | | + | |
| − | #top-section-bar { /*-- styling full width bar which hides behind default menu bar (edit, page, history, etc.) --*/
| + | |
| − | background-color: #333;
| + | |
| − | height: 1px; //DEFAULT 14 PX
| + | |
| − | //display: none;//block;
| + | |
| − | color: #fff;
| + | |
| − | z-index: 10;
| + | |
| − | position: fixed;
| + | |
| − | width: 100%;
| + | |
| − | top: 0;
| + | |
| − | }
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | /*#top-section {
| + | |
| − | background-color: #333;//#383838;
| + | |
| − | border: 0 none;
| + | |
| − | height: 46px; // DEFAULT 14 px
| + | |
| − | z-index: 100;
| + | |
| − | top: 0;
| + | |
| − | //display: none;
| + | |
| − | position: fixed;
| + | |
| − | width: 2975px;
| + | |
| − | left: 50%;
| + | |
| − | margin-left: -687px;
| + | |
| − | }
| + | |
| − | | + | |
| − | #top-section-bar {
| + | |
| − | background-color: #333;
| + | |
| − | height: 1px; //DEFAULT 14 PX
| + | |
| − | display: none;//block;
| + | |
| − |
| + | |
| − | z-index: 10;
| + | |
| − | position: fixed;
| + | |
| − | width: 100%;
| + | |
| − | top: 0;
| + | |
| − | }*/
| + | |
| − | | + | |
| − | #menubar a:link, #menubar a:active, #menubar a:visited, #menubar a:hover, #menubar:hover { /*-- styling for default menu bar links (edit, page, history, etc.) --*/
| + | |
| − | color: #727272;
| + | |
| − | text-decoration: none;
| + | |
| − | background-color: transparent;
| + | |
| − | }
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | #globalWrapper, #content { /*-- changes default wiki settings --*/ | + | |
| − | width: 100%;
| + | |
| − | height: 100%;
| + | |
| − | border: 0px;
| + | |
| − | background-color: transparent;
| + | |
| − | margin: 0px;
| + | |
| − | padding: 0px;
| + | |
| − | }
| + | |
| − | | + | |
| − | html, body, .wrapper { /*-- changes default wiki settings --*/
| + | |
| − | width: 100%;
| + | |
| − | height: 100%;
| + | |
| − | background-color: #003D99;//#5C8AE6;//#003D99;//transparent;
| + | |
| − | }
| + | |
| − | | + | |
| − | #contentcontainer { /*-- creates container for all content on page --*/
| + | |
| − | font-family: Arial, Helvetica, sans-serif;
| + | |
| − | font-weight: normal;
| + | |
| − | font-size: 14px;
| + | |
| − | color: #414141;
| + | |
| − | width: 960px;
| + | |
| − | margin-left: auto;
| + | |
| − | margin-right: auto;
| + | |
| − | background-color: #transparent;
| + | |
| − | margin-top: 0px;
| + | |
| − | }
| + | |
| − | | + | |
| − | | + | |
| − | </style> | + | |
| | | | |
| − |
| + | <td width="162px" align="center" onMouseOver="this.bgColor='#BDBDBD'" onMouseOut="this.bgColor='#6A181B'" bgColor=#6A181B> |
| − |
| + | <a href="https://2015.igem.org/Team:UC_Davis/Parts" style="text-decoration:none;color:#FFFFFF">ACHIEVEMENTS</a> </td> |
| − | </head>
| + | |
| | | | |
| | + | <td width="162px" align="center" onMouseOver="this.bgColor='#BDBDBD'" onMouseOut="this.bgColor='#6A181B'" bgColor=#6A181B> |
| | + | <a href="https://2015.igem.org/Team:UC_Davis/Attributions" style="text-decoration:none;color:#FFFFFF">THE TEAM</a> </td> |
| | | | |
| − | <body> | + | <td width="162px" align="center" onMouseOver="this.bgColor='#BDBDBD'" onMouseOut="this.bgColor='#6A181B'" bgColor=#6A181B> |
| − | <div style="background-color:#fff">
| + | <a href="https://2015.igem.org/Team:UC_Davis/Safety" style="text-decoration:none;color:#FFFFFF">SAFETY & PROTOCOLS</a></td> |
| − | <!--<div class="container-fluid" id="allHome">-->
| + | |
| − | <!--<div class = "nav nav-justified " role = "navigation">-->
| + | |
| − | <!-- UNCOMMENT TO REMOVE FULL WIDTH NAV BAR <div class="container-fluid"> -->
| + | |
| − |
| + | |
| − | <!--navbar -->
| + | |
| − |
| + | |
| − | <!--<nav class="navbar nav-justified" role="navigation" id='nav'>
| + | |
| − | <div class="btn-group btn-group btn-group-justified">
| + | |
| − | <ul class="nav navbar-nav" role="navigation" id='nav'>
| + | |
| − | <li class = "active"><div class="btn btn-lg" id="home">Home</div></li>
| + | |
| − | <li><div class="btn btn-lg" id="team">Team</div></li>
| + | |
| | | | |
| − | <li class="dropdown">
| + | <td width="162px" align="center" onMouseOver="this.bgColor='#BDBDBD'" onMouseOut="this.bgColor='#6A181B'" bgColor=#6A181B > |
| − | <div class="btn btn-lg dropdown-toggle" data-toggle="dropdown" id="project">Project <span class="caret"></span></div>
| + | <a href="https://2015.igem.org/Main_Page"style="text-decoration:none;color:#FFFFFF"><img src="https://static.igem.org/mediawiki/2015/6/68/PPLogo2_igem_UCD.gif" width = "100" > </a> </td> |
| − | <ul class="dropdown-menu" role="menu">
| + | |
| − | <li id = "database"><a href = "#">Database</a></li>
| + | |
| − | <li id = "traversal"><a href = "#">Traversal algorithms</a></li>
| + | |
| − | <li id = "app"><a href = "#">Web application</a></li>
| + | |
| − | <li id = "parts"><a href = " #">Parts</ a></ li> | + | |
| − | <li id = "modeling"><a href = "#">Modeling</a></li>
| + | |
| − | </ul>
| + | |
| − | </li>
| + | |
| − |
| + | |
| − |
| + | |
| − | <li><div class="btn btn-lg" id="notebook">Notebook</div></li>
| + | |
| − | <li><div class="btn btn-lg" id="safety">Safety</div></li>
| + | |
| − | <li><div class="btn btn-lg" id="achieve">Software Achievements</div></li>
| + | |
| − | <li><div class="btn btn-lg" id="attributions">Attributions</div></li>
| + | |
| − | <li><div class="btn btn-lg" id="test">Tester</div></li>
| + | |
| − | </ul>
| + | |
| − |
| + | |
| − | </div>
| + | |
| − |
| + | |
| − |
| + | |
| − |
| + | |
| − | </nav>-->
| + | |
| − | <!-- FOR IMAGE! LOGOS IGEM & UCSD --><!--<nav class="navbar nav-justified" role="navigation" id='nav'>
| + | |
| − | <div class="btn-group btn-group btn-group-justified" >
| + | |
| − | <div class="btn btn-lg " id="avant">UC Davis</div>-->
| + | |
| − | <!--<font size = 4px>UC Davis</font>-->
| + | |
| | | | |
| − | <!--<div class="btn-group btn-group btn-group-justified">
| + | </tr> |
| − | <img src = "http://i.imgur.com/mGHw11P.png?1">
| + | </td> |
| − | </div>
| + | <td bgColor="#FFFFFF"></td> |
| − | </div>
| + | </tr> |
| − | </nav>-->
| + | </table> |
| − | <nav class="navbar nav-justified" role="navigation" id='nav'>
| + | |
| − | <div class="btn-group btn-group btn-group-justified">
| + | |
| − | <div class="btn btn-lg " id="home">Home</div>
| + | |
| − | <div class="btn btn-lg " id="team">Team</div>
| + | |
| − | <div class="btn btn-lg " id="project">Project</div>
| + | |
| − | <div class="btn btn-lg " id="doc">Documentation</div>
| + | |
| − | <div class="btn btn-lg" id="notebook">Notebook</div>
| + | |
| − | <div class="btn btn-lg" id="safety">Safety</div>
| + | |
| − | <div class="btn btn-lg" id="attributions">Sponsors</div>
| + | |
| − | <div class="btn btn-lg" id="achieve">Medals</div>
| + | |
| − | <div class="btn btn-lg" id="logo"><a href = "https://igem.org/Main_Page"><img src = "http://i.imgur.com/mGHw11P.png?1"></a></div>
| + | |
| − |
| + | |
| − | </div>
| + | |
| − |
| + | |
| − | </nav>
| + | |
| − |
| + | |
| − | <!-- container fluid END </div> -->
| + | |
| − |
| + | |
| − | <!--slider-->
| + | |
| | | | |
| − | <div id="thumbnail-preview-indicators" class="carousel slide" data-ride="carousel">
| + | <!-- END OF HEADER --> |
| − |
| + | |
| − | <!--<ol class="carousel-indicators">
| + | |
| − | <li data-target="#thumbnail-preview-indicators" data-slide-to="0" class="active">
| + | |
| − | <div class="thumbnail">
| + | |
| − | <img class="img-responsive" src="http://www.desktopaper.com/wp-content/uploads/creative-lajolla-web.jpg">
| + | |
| − | </div>
| + | |
| − | </li>
| + | |
| − | <li data-target="#thumbnail-preview-indicators" data-slide-to="1">
| + | |
| − | <div class="thumbnail">
| + | |
| − | <img class="img-responsive" src="http://i.imgur.com/iokYtgR.jpg">
| + | |
| − | </div>
| + | |
| − | </li>
| + | |
| − | <li data-target="#thumbnail-preview-indicators" data-slide-to="2">
| + | |
| − | <div class="thumbnail">
| + | |
| − | <img class="img-responsive" src="http://i.imgur.com/N40l0eb.png?1">
| + | |
| − | </div>
| + | |
| − | </li>
| + | |
| − | </ol>-->
| + | |
| − | <div class="carousel-inner">
| + | |
| − | <div class="item slides active">
| + | |
| − | <div class="slide-1"></div>
| + | |
| − | <div class="container">
| + | |
| − | <div class="carousel-caption">
| + | |
| − | <h1><font color = "gold">UC Davis Aggies</font></h1>
| + | |
| − | <p><a class="btn btn-lg btn-primary" href="https://2014.igem.org/Team:UCSD_Software/Teaml" role="button">The Team</a></p>
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| | | | |
| − | <div class="item slides">
| |
| − | <div class="slide-2"></div>
| |
| − | <div class="container">
| |
| − | <div class="carousel-caption">
| |
| − | <h1><font color = "#000000">SBiDer</font></h1>
| |
| − | <p><a class="btn btn-lg btn-primary" href="#" role="button">Take me to the app!</a></p>
| |
| − | </div>
| |
| − | </div>
| |
| − | </div>
| |
| − | <div class="item slides">
| |
| − | <div class="slide-3"></div>
| |
| − | <div class="container">
| |
| − | <div class="carousel-caption">
| |
| − | <br><br><h1><font color = "gold">The Notebook</font></h1>
| |
| − | <p><a class="btn btn-lg btn-primary" href="https://2014.igem.org/Team:UCSD_Software/Notebook" role="button">View the Notebook</a></p>
| |
| − | </div>
| |
| − | </div>
| |
| − | </div>
| |
| − | </div>
| |
| − | <a class="left carousel-control" href="#thumbnail-preview-indicators" role="button" data-slide="prev"><span class="glyphicon glyphicon-chevron-left"></span></a>
| |
| − | <a class="right carousel-control" href="#thumbnail-preview-indicators" role="button" data-slide="next"><span class="glyphicon glyphicon-chevron-right"></span></a>
| |
| − | </div>
| |
| | | | |
| | + | <!-- BANNER --> |
| | + | <table width="100%" height = "100%" cellspacing="0"> |
| | + | <br><br><td align="center"><a href="https://2015.igem.org/Team:UC_Davis"><img src="https://static.igem.org/mediawiki/2015/5/5c/Banner_Final.png" width="907px" height="420" align = "top"></a></td> |
| | | | |
| | | | |
| | | | |
| − | <!--slider end--> | + | <!-------------- OVERVIEW ---------------> |
| − | <!-- TUTORIAL & LAUNCH START -->
| + | <table id="overview" width="100%" cellspacing="0" height="70px"> |
| | + | <tr><td bgColor="#FFFFFF"></td> |
| | + | <td width="100%" align="left" bgColor="#FFFFFF" > |
| | + | <br> |
| | + | <font size="3" face = "Avenir"> |
| | + | A report released by the United States Government Accountability Office revealed that of the 80,000 chemicals in commercial use today, only a few are tested and even fewer are restricted. Triclosan, an antimicrobial agent added to a range of consumer product, is one of these 80,000 chemicals that has undergone scrutiny in recent years due to its environmental and human health consequences. This summer we investigated how we might leverage biotechnology to raise awareness and accountability around triclosan use specifically, and around responsible chemical use at large. After exploring our problem space we realized that any device we built for the detection of triclosan would be but one node in a complex web of social, political and industrial interactions. We thought carefully about where this tool would be most effective and what additional resources would be needed to complement it. After identifying public awareness as an effective catalyst for change, we chose high school students as a potential audience and a lesson plan as a viable medium of delivery. Our project consists of three components: a triclosan biosensor, a hands-on lesson plan, and an antimicrobial footprint app that together are an integrated solution to help promote more responsible chemical use. <br> |
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| − | <h1>Tutorial</h1>
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| + | <font size="2" face = "Avenir"> |
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| + | <b>Sources:</b> Stephenson, John B. "Options Exist to Improve EPA’s Ability to Assess Health Risks and Manage Its Chemical Review Program." GAO, June 2005. Web.</font> |
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| − | <h1>Explore our Code</h1>
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| − | <H1>Launch!</h1>
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| − | <h1>SBiDer: Synthetic Biocircuit Developer <p class = "pull-right"><a href = "https://igem.org/About"><img src = "http://i.imgur.com/Ch9fpo8.png?1" height = 100px width = 100px></a></p></h1>
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| − | <h3>Abstract</h3>
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| − | Genetic circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. SBiDer, a web tool developed by the UCSD Software iGEM team, will leverage existing devices to construct a database with consideration for the function of each device interpreted as boolean logic. The data can be queried by the user through SBiDer's visual interface to explore circuit designs. Users can search for existing circuits that can be used to assemble a complex circuit. The displayed circuit's literature reference, characterization data, and images of included devices can be viewed through the built-in table. We also provide a standalone modelling Python package that can be used to model circuits given by our online webtool. SBiDer's web of information can be expanded through user-generated additions to the database to improve the efficiency of the application and the accuracy of the models. <br>
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| − | <h1>Project Description</h1> | + | <!-- end of first block --> |
| − | <h3>Problem Statement</h3>
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| − | Synthetic genetic circuits created by synthetic biologists have yielded exciting applications such as biofuels production and cancer killing bacteria. These circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. Although there are many genetic devices that have been built, re-using these devices often requires a time-consuming review of the literature. The UCSD Software iGEM team will address this challenge by creating a web-tool that leverages existing genetic devices to create complex genetic circuits. We will accomplish this by:
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| − | <li>building a comprehensive database that captures the behavior, composition, and interactions of existing genetic devices in the literature</li>
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| − | <li>constructing and visualizing the network of all synthetic genetic circuits that can interact with one another</li>
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| − | <li>devising algorithms to search this network for the set of genetic devices that can be used to construct a complex genetic circuit.</li>
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| − | <li>Perform some basic validation via kinetic modelling.</li>
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| − | </ol>
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| − | <h3>Aim 1 - Building a Database</h3>
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| − | <p> | + | |
| − | We will mine the scientific literature for existing genetic devices and then construct a database that captures device characteristics such as:
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| − | <li>composition of devices</li>
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| − | <li>function</li>
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| − | <li>characterization data</li>
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| − | <li>literature reference</li>
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| − | </ol>
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| − | We will design our database by rigorously constructing an entity relationship diagram and then normalizing these relationships to construct tables for a relational database.
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| − | <h3>Aim 2 - Constructing Network of Interacting Devices</h3>
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| − | We will connect known genetic devices together via device input and outputs to create a network of devices that can interact. We define a genetic device as a DNA construct transformed into cells that can cause expression of some protein in response to stimuli (or input). We will develop a web interface to facilitate access to the complex network that we have constructed. Our Web interface makes extensive use of Cytoscape, an open source bioinformatics software package for metabolic network visualization and simulation. In addition, the interface will generate SBOL Visual Images, a standard language that is easily understood by synthetic biologists all over the world. Users can also update our database with additional devices through this interface. Using the Cynetshare framework, users can share their circuit designs</p>
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| − | <h3>Aim 3 - Searching the Network</h3> | + | |
| − | <p>
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| − | This interface will allow researchers to query our database network for a circuit design expressed as logical operators such as “AND”, “OR”, and “NOR”, and retrieve the subnetwork of genetic devices that satisfies the circuit design. To Perform our search we modified several traditional graph search algorithms to traverse this graph, including but not limited to Prim’s algorithm (minimum spanning tree), Dijkstra’s algorithm and a breadth-first search. Results are visualized graphically in our web interface.
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