Team:UCSD Software/Safety

From 2014.igem.org

(Difference between revisions)
(Prototype team page)
Line 1: Line 1:
-
<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->
 
-
 
-
 
{{CSS/Main}}
{{CSS/Main}}
<html>
<html>
 +
<head>
 +
     
 +
        <meta charset="UTF-8">
 +
        <meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
        <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>
-
<!--main content -->
+
body{
-
<table width="70%" align="center">
+
    background-color: white;
 +
   
 +
}
 +
#nav{
 +
    background-color: rgba(0,0,0,0.5);
 +
    color: white;
 +
    //border: 1px solid white;
 +
    padding: 1px;
 +
  box-sizing: border-box;   
 +
}
 +
#nav .btn{
 +
    //border-right: 2px solid grey;
 +
   
 +
   
 +
}
 +
p{
 +
color: black;
 +
}
 +
#nav .btn:hover{
 +
    color: white;
 +
  background-color: rgba(204,204,204,0.5);
 +
 
 +
}
-
<!--welcome box -->
+
#nav .btn:active{
-
<tr>
+
    color: white;  
-
<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
+
  background-color: rgba(204,204,204,0.5);
-
<h1 >WELCOME TO iGEM 2014! </h1>
+
}
-
<p>Your team has been approved and you are ready to start the iGEM season!
+
-
<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
+
-
<br>
+
-
<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:UCSD_Software/Safety&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
+
-
</td>
+
-
</tr>
+
-
<tr> <td colspan="3"  height="5px"> </td></tr>
 
-
<!-- end welcome box -->
 
-
<tr>
 
-
<!--navigation menu -->
+
#thumbnail-preview-indicators {
-
<td align="center" colspan="3">
+
  position: relative;
 +
  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;
 +
}
 +
    #thumbnail-preview-indicators,
 +
    #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(https://s3.amazonaws.com/ooomf-com-files/wdXqHcTwSTmLuKOGz92L_Landscape.jpg);
 +
}
 +
#thumbnail-preview-indicators .slides .slide-2 {
 +
  background-image: url(https://s3.amazonaws.com/ooomf-com-files/tU3ptNgGSP6U2fE67Gvy_SYDNEY-162.jpg);
 +
}
 +
#thumbnail-preview-indicators .slides .slide-3 {
 +
  background-image: url(https://s3.amazonaws.com/ooomf-com-files/mtNrf7oxS4uSxTzMBWfQ_DSC_0043.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;
 +
    }
 +
}
 +
</style>
 +
    </head>
-
<table  width="100%">
 
-
<tr heigth="15px"></tr>
 
-
<tr heigth="75px">
 
 +
<body>
 +
<div class="container-fluid" id="allHome">
 +
       
 +
 
 +
<div class="container-fluid">
 +
           
 +
            <!--navbar -->
 +
       
 +
            <nav class="navbar navbar-header nav-justified" role="navigation" id='nav'>
 +
                <div class="btn-group  btn-group btn-group-justified">
 +
                <ul class="nav navbar-nav">
 +
                    <li><div class="btn btn-lg" id="home">Home</div></li>
 +
                    <li><div class="btn btn-lg" id="team">Team</div></li>
 +
                   
 +
                    <li><div class="btn btn-lg" id="officialTeam" >Profile</div></li>
 +
                    <li><div class="btn btn-lg" id="poject">Project</div></li>
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
                    <li class="dropdown">
-
<a href="https://2014.igem.org/Team:UCSD_Software"style="color:#000000">Home </a> </td>
+
              <div class="btn btn-lg dropdown-toggle" data-toggle="dropdown" id="project">Project <span class="caret"></span></div>
 +
              <ul class="dropdown-menu" role="menu">
 +
                <li><a href="#">Database</a></li>
 +
                <li><a href="#">Traversal algorithms</a></li>
 +
                <li><a href="#">Web application</a></li>
 +
                <li><a href="#">Parts</a></li>
 +
                <li><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">Achievements</div></li>
 +
                    <li><div class="btn btn-lg" id="attributions">Attributions</div></li>
 +
                    </ul>
 +
              </div>
 +
             
 +
               
 +
               
 +
        </nav>
 +
     
 +
        </div>
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
<!--slider-->
-
<a href="https://2014.igem.org/Team:UCSD_Software/Team"style="color:#000000"> Team </a> </td>
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
<!--<div id="thumbnail-preview-indicators" class="carousel slide" data-ride="carousel">
-
<a href="https://igem.org/Team.cgi?year=2014&team_name=UCSD_Software"style="color:#000000"> Official Team Profile </a></td>
+
         
 +
          <ol class="carousel-indicators">
 +
            <li data-target="#thumbnail-preview-indicators" data-slide-to="0" class="active">
 +
              <div class="thumbnail">
 +
                <img class="img-responsive" src="">
 +
              </div>
 +
            </li>
 +
            <li data-target="#thumbnail-preview-indicators" data-slide-to="1">
 +
            <div class="thumbnail">
 +
                <img class="img-responsive" src="">
 +
              </div>
 +
            </li>
 +
            <li data-target="#thumbnail-preview-indicators" data-slide-to="2">
 +
            <div class="thumbnail">
 +
                <img class="img-responsive" src="">
 +
              </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>SBiDer</h1>
 +
                  <p>Our site</p>
 +
               
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <div class="item slides">
 +
              <div class="slide-2"></div>
 +
              <div class="container">
 +
                <div class="carousel-caption">
 +
                  <h1>Another example headline.</h1>
 +
                  <p>Cras justo odio, dapibus ac facilisis in, egestas eget quam.</p>
 +
                  <p><a class="btn btn-lg btn-primary" href="#" role="button">Learn more</a></p>
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <div class="item slides">
 +
              <div class="slide-3"></div>
 +
              <div class="container">
 +
                <div class="carousel-caption">
 +
                  <h1>One more for good measure.</h1>
 +
                  <p>Nullam id dolor id nibh ultricies vehicula ut id elit.</p>
 +
                  <p><a class="btn btn-lg btn-primary" href="#" role="button">Browse gallery</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>  
-
<td style="border:1px solid black" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
 
-
<a href="https://2014.igem.org/Team:UCSD_Software/Project"style="color:#000000"> Project</a></td>
 
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
-
<a href="https://2014.igem.org/Team:UCSD_Software/Parts"style="color:#000000"> Parts</a></td>
 
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
-
<a href="https://2014.igem.org/Team:UCSD_Software/Modeling"style="color:#000000"> Modeling</a></td>
 
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
<!--slider end-->
-
<a href="https://2014.igem.org/Team:UCSD_Software/Notebook"style="color:#000000"> Notebook</a></td>
+
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
-
<a href="https://2014.igem.org/Team:UCSD_Software/Safety"style=" color:#000000"> Safety </a></td>
 
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
-
<a href="https://2014.igem.org/Team:UCSD_Software/Attributions"style="color:#000000"> Attributions </a></td>
 
-
<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
 
-
</tr>
 
-
</table>
 
-
<!--end navigation menu -->
 
-
</tr>
 
-
</tr>
 
-
</td>
 
-
<tr> <td colspan="3" height="15px"> </td></tr>
+
<h1>SBiDer: Synthetic Biocircuit Developer</h1>
-
<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
+
<h3>Abstract</h3>
-
<tr> <td colspan="3" height="5px"> </td></tr>
+
<p>
 +
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. The displayed circuit's literature reference, characterization data, and images of included devices can be viewed through the built-in table. Basic validation of the circuit performance is also provided within in the interface. 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.  
 +
<p>
 +
<h1>Project Description</h1>
 +
<h3>Problem Statement</h3>
 +
<p>
 +
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:
 +
</p>
 +
<ol>
 +
<li>building a comprehensive database that captures the behavior, composition, and interactions of existing genetic devices in the literature</li>
 +
<li>constructing and visualizing the network of all synthetic genetic circuits that can interact with one another</li>
 +
<li>devising algorithms to search this network for the set of genetic devices that can be used to construct a complex genetic circuit.</li>
 +
<li>Perform some basic validation via kinetic modelling.</li>
 +
</ol>
 +
<h3>Aim 1 - Building a Database</h3>
 +
<p>
 +
We will mine the scientific literature for existing genetic devices and then construct a database that captures device characteristics such as:
 +
</p>
 +
<li>composition of devices</li>
 +
<li>function</li>
 +
<li>characterization data</li>
 +
<li>literature reference</li>
 +
</ol>
 +
We will design our database by rigorously constructing an entity relationship diagram and then normalizing these relationships to construct tables for a relational database.
 +
<h3>Aim 2 - Constructing Network of Interacting Devices</h3>
 +
<p>
 +
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>
 +
<h3>Aim 3 - Searching the Network</h3>
 +
<p>
 +
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
 +
</p>
 +
<!--main content -->
 +
<table width="70%" align="center">
-
<!--safety content-->
+
<tr>  
-
<tr><td > <h3> Welcome! </h3></td>
+
-
<td ></td >
+
-
<td > <h3> Timeline</h3></td>
+
-
</tr>
+
-
<tr>
 
-
<td width="45%"  valign="top">
 
-
<p> Visit the <a href="https://2014.igem.org/Safety" >Safety Hub</a> to see this year's safety requirements. The Safety Hub is the central page for everything related to safety in iGEM. You can also go there to learn about general biosafety topics, and how to think about the future implications of your project.</p>
 
 +
</tr>
-
<br>
+
</tr>
-
<h3> Edit this page!</h3>
+
-
<p>
+
-
Please use this page to write about anything related to safety in your project. <!--Be sure to talk about both
+
-
<ul>
+
-
<li> <a href=" ">Learn about lab Safety for Today</a></li>
+
-
<li> <a href="">Learn about Safety for the future of your project.</a></li>
+
-
</ul>
+
-
-->
+
-
</p>
+
-
<h3> Your Lab </h3>
 
-
<p> Use this section to tell us about your laboratory. Where is it located? What sort of equipment do you use every day? Have you decorated it for the summer? How do you look wearing a lab coat? Take pictures! Show off your space! </p>
 
-
<!--
 
-
<gallery>
 
-
Image:Example2_Lab_1.png|The building our lab is in!
 
-
Image:Example2_Lab_2.png|The inside of our lab!
 
-
Image:Example2_Lab_3.png|Team Member 3 doing an experiment
 
-
Image:Example2_Lab_4.png|Working in biosafety cabinets
 
-
Image:Example2_Lab_5.png|Team all gloved up and ready for work!
 
-
Image:Example2_Lab_6.png|Equipment that we use to do SCIENCE!
 
-
Image:Example2_Lab_7.png|We decorated this part of our lab
 
-
Image:Example2_Lab_8.png|Whatever else you want
 
-
</gallery>-->
 
</td>
</td>
-
<td></td>
 
 +
<tr> <td colspan="3"  height="15px"> </td></tr>
 +
<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
 +
<tr> <td colspan="3"  height="5px"> </td></tr>
 +
 +
<!--requirements section -->
 +
<tr><td colspan="3"> <h3> Requirements </h3></td></tr>
 +
<tr>
<td width="45%"  valign="top">  
<td width="45%"  valign="top">  
 +
<p> Please be sure to keep these links, your audience will want to find your: </p>
 +
<!-- Links to other team pages -->
<ul>
<ul>
-
<li> <b>Now :</b>  Read the <a href="https://2014.igem.org/Safety">Safety Hub </a> and learn about safety in iGEM. Ask questions by emailing safety at <i> igem DOT org </i>. </li>
+
<li><a href="https://2014.igem.org/Team:UCSD_Software">Home</a> </li>
-
<li><b>Now - Jamboree:</b> Complete <b>Check-Ins</b> and receive approval before acquiring and using certain materials in your lab</li>
+
<li><a href="https://2014.igem.org/Team:UCSD_Software/Team">Team</a> </li>
-
<li><b>Now - Wiki Freeze:</b> Edit this Safety page to tell us about what you're doing</li>
+
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=UCSD_Software">Official Team Profile</a> </li>
-
<li><b>June 9: </b>Submit the About Our Lab form.</li>
+
<li><a href="https://2014.igem.org/Team:UCSD_Software/Project">Project</a> </li>
-
<li><b>Let us know by June 25 </b>if you will need an extension on the Preliminary Version, or your Preliminary Version will be significantly incomplete.</li>
+
<li><a href="https://2014.igem.org/Team:UCSD_Software/Parts">Parts</a> </li>
-
<li><b>June 30: </b>Submit the Preliminary Version of the <b>Safety Form</b>.</li>
+
<li><a href="https://2014.igem.org/Team:UCSD_Software/Modeling">Modeling</a> </li>
-
<li>Participate in Virtual Open Office Hours to ask questions and discuss safety topics (exact date to be determined).</li>
+
<li><a href="https://2014.igem.org/Team:UCSD_Software/Notebook">Notebook</a> </li>
-
<li><b>September 1:</b> Submit the Final Version of the Safety Form.</li>
+
<li><a href="https://2014.igem.org/Team:UCSD_Software/Safety">Safety</a> </li>
-
<li><b>October: </b> Wiki freeze (exact date to be determined)</li>
+
<li><a href="https://2014.igem.org/Team:UCSD_Software/Attributions">Attributions</a> </li>
-
<li><b>October 30 - November 3: </b>GIANT JAMBOREE!</li>
+
</ul>
</ul>
 +
</td>
</td>
-
</tr>
+
<td > </td>
-
 
+
<td width="45%">
-
 
+
-
 
+
-
 
+
-
<tr>
+
-
 
+
 +
<p>There are a few wiki requirements teams must follow:</p>
 +
<ul>
 +
<li>All pages, images and files must be hosted on the <a href ="https://2014.igem.org/Special:Upload">  2014.igem.org server</a>. </li>
 +
<li>All pages must be created under the team’s name space.</li>
 +
<li>As part of your documentation, keep the links from the menu to the left. </li>
 +
<li>Do not use flash in wiki code. </li>
 +
<li>The <a href="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png"> iGEM logo </a> should be placed on the upper part of every page and should link to <a href="https://2014.igem.org/Main_Page">2014.igem.org</a>.</li>
 +
</ul>
 +
<p>Visit the <a href="https://2014.igem.org/Wiki_How-To"> Wiki How To page </a> for a complete list of requirements, tips and other useful information. </p>
 +
</td>
 +
</tr>
 +
<tr> <td colspan="3"  height="15px"> </td></tr>
 +
<tr><td bgColor="#e7e7e7" colspan="3" height="1"> </tr>
</table>
</table>
-
</html>
+
<script>
 +
$(document).ready(function(){
 +
    //redirecting to other pages
 +
    $("#home").click(function(){
 +
      window.location.href="https://2014.igem.org/Team:UCSD_Software";
 +
    });
 +
    $("#team").click(function(){
 +
      window.location.href="https://2014.igem.org/Team:UCSD_Software/Teaml";
 +
    });
 +
    $("#officialTeam").click(function(){
 +
      window.location.href="https://igem.org/Team.cgi?year=2013&team_name=UCSD_Software";
 +
    });
 +
    /*$("#project").click(function(){
 +
      window.location.href="https://2014.igem.org/Team:UCSD_Software/Project";
 +
    });*/
 +
    $("#parts").click(function(){
 +
      window.location.href="https://2014.igem.org/Team:UCSD_Software/Parts";
 +
    });
 +
    $("#modeling").click(function(){
 +
      window.location.href="https://2014.igem.org/Team:UCSD_Software/Modelingl";
 +
    });
 +
    $("#notebook").click(function(){
 +
      window.location.href="https://2014.igem.org/Team:UCSD_Software/Notebook";
 +
    });
 +
    $("#safety").click(function(){
 +
      window.location.href="https://2014.igem.org/Team:UCSD_Software/Safety";
 +
    });
 +
    $("#attributions").click(function(){
 +
      window.location.href="https://2014.igem.org/Team:UCSD_Software/Attributions";
 +
    });
 +
   
 +
    });
 +
</script>
 +
</body>

Revision as of 04:58, 11 October 2014


SBiDer: Synthetic Biocircuit Developer

Abstract

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. The displayed circuit's literature reference, characterization data, and images of included devices can be viewed through the built-in table. Basic validation of the circuit performance is also provided within in the interface. 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.

Project Description

Problem Statement

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:

  1. building a comprehensive database that captures the behavior, composition, and interactions of existing genetic devices in the literature
  2. constructing and visualizing the network of all synthetic genetic circuits that can interact with one another
  3. devising algorithms to search this network for the set of genetic devices that can be used to construct a complex genetic circuit.
  4. Perform some basic validation via kinetic modelling.

Aim 1 - Building a Database

We will mine the scientific literature for existing genetic devices and then construct a database that captures device characteristics such as:

  • composition of devices
  • function
  • characterization data
  • literature reference
    • We will design our database by rigorously constructing an entity relationship diagram and then normalizing these relationships to construct tables for a relational database.

    Aim 2 - Constructing Network of Interacting Devices

    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

    Aim 3 - Searching the Network

    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

    Requirements

    Please be sure to keep these links, your audience will want to find your:

    There are a few wiki requirements teams must follow:

    • All pages, images and files must be hosted on the 2014.igem.org server.
    • All pages must be created under the team’s name space.
    • As part of your documentation, keep the links from the menu to the left.
    • Do not use flash in wiki code.
    • The iGEM logo should be placed on the upper part of every page and should link to 2014.igem.org.

    Visit the Wiki How To page for a complete list of requirements, tips and other useful information.

    Retrieved from "http://2014.igem.org/Team:UCSD_Software/Safety"