Team:BostonU/Project Overview

From 2013.igem.org

(Difference between revisions)
 
(26 intermediate revisions not shown)
Line 1: Line 1:
 +
{{Template:BU2013}}
<html>
<html>
-
<head>
+
<br><br>
-
<title>BostonU iGEM Team: Welcome</title>
+
-
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+
-
<script src="http://cdn.jquerytools.org/1.2.5/full/jquery.tools.min.js?foo"></script>
+
-
<style type="text/css">
+
-
/*hide default igem banner and reformat style into blank slate*/
+
-
#globalWrapper {width: 100%;}
+
-
#top-section {width: 100%; height:30px; border:none;}
+
-
#p-logo {display:none;}
+
-
#search-controls {display:none;}
+
-
#menubar a {color:#000000;}
+
-
#menubar a:hover{text-decoration:none; color:#52749C;}
+
-
.left-menu {background-color:#FFFFFF; margin:0px 0px 0px 0px; padding:0;}
+
-
.left-menu ul {background-color:#FFFFFF; margin:0; padding:0;}
+
-
.right-menu ul li a {background-color:#FFFFFF;}
+
-
.printfooter {display:none;}
+
-
#footer-box {border:none;}
+
-
#catlinks {display:none;}
+
-
.firstHeading {display:none;}
+
-
#content {width: 100%; border:none;}
+
-
#bodyContent {border:none;}
+
-
/*actual content styles*/
+
<h2>Abstract</h2>
-
body {width: 800px; margin:auto;}
+
-
#bu-wellesley_wiki_content {height:auto; line-height:100%;}
+
<body>
-
/*#bu-wellesley_wiki_content a {color:#69d01d;}*/
+
<h7><p>
-
#bu-wellesley_wiki_content a:hover {text-decoration:none; color:#3d3f3c;}
+
In order for synthetic biologists to be able to use automation technologies, we need a well-characterized library of basic biological components that can then be used to design more complex systems. MoClo is a one-pot digestion-ligation assembly technique developed by <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016765">(Weber et al., 2011)</a>, which enables faster and more efficient construction of genetic circuits compared to BioBricks, the current iGEM standard. With our project, we are proposing that iGEM teams replace the inefficient BioBricks cloning method with MoClo. We have expanded our library of basic MoClo DNA Parts and characterized devices using various promoter-5' Untranslated Region combinations via flow cytometry. We also are designing and implementing a standardized data sheet using Java and JavaScript in order to easily share our library and data with the community. Our MoClo library, characterization data, and data sheet tool fill an essential role in the implementation of automated synthetic biology protocols.</h7>
-
.navbar li {color: #ffffff;}
 
-
.navbar li a {color: #ffffff;}
 
-
.navbar li a:hover {background:#69d01d; color: #ffffff;}
 
-
/*only use for current page content header (i.e. Team, G-nomeSurferPro, etc)*/
+
<h2>Project Overview</h2>
-
H4 {
 
-
      font-family: Signika;
 
-
      text-transform: uppercase;
 
-
      text-decoration: none;
 
-
      text-align: left;
 
-
      color: #B22222;
 
-
      font-size: 20pt;
 
-
    }
 
-
H3 {
+
<p><center><img src="https://static.igem.org/mediawiki/2013/thumb/c/c5/Project_overview_bu.jpg/598px-Project_overview_bu.jpg" width="400px"></a></p>
-
      font-family: Signika;
+
-
      text-transform: none;
+
-
      text-decoration: none;
+
-
      text-align: left;
+
-
      color: #696969;
+
-
      font-size: 12pt;
+
-
    }
+
-
H7 {
+
-
      font-family: Signika;
+
-
      text-transform: none;
+
-
      text-decoration: none;
+
-
      text-align: left;
+
-
      color: #000000;
+
-
      font-size: 12pt;
+
-
    }
+
-
H8 {
 
-
      font-family: Signika;
 
-
      text-transform: none;
 
-
      text-decoration: none;
 
-
      text-align: left;
 
-
      color: #B22222;
 
-
      font-size: 12pt;
 
-
    }
 
-
H6 {
+
<h7><p>Synthetic biology exists more as a form of art than a reproducible, well-defined production chain. From laboratory to laboratory, the experiments vary in procedure, characterization, and yield. The main product of synthetic biology — engineered organisms, are available only to the highly-experienced researcher and are not without the costs of timely preparation and low product yield. Consequently, the lack of standardization across the field has impeded the product from ever reaching a wide industry audience. More recent engineering efforts in the assembly of gene circuits has provided a pathway to a modular view of genetic parts. Termed the Modular Cloning Assembly Method (MoClo), this novel single-pot reaction protocol is a time-efficient, two-enzyme system for DNA assembly <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016765">(Weber et al., 2011)</a>. Before MoClo can reach its full potential across research and industry interests, the synthetic biology community needs a standardized and well-characterized library of MoClo parts for <i>Escherichia coli</i> to enable protocol automation and informed device designing. The 2013 Boston University iGEM Team seeks to bridge this gap in the product development chain by building a standard library and characterizing the parts via flow cytometry. To further efforts to develop foundational advancements for synthetic biology, we are taking a multi-faceted approach and working at several aspects and levels of design automation by:</p>
-
      font-family: Signika;
+
<p>
-
      text-transform: none;
+
<ul>
-
      text-decoration: none;
+
<li>expanding a library of basic Level 0 MoClo parts by cloning from BioBrick parts and making new parts</li>
-
      text-align: left;
+
<li>building a library of composite Level 1 and 2 devices to characterize promoter-5' Untranslated Region combinations and demonstrate the library's usefulness</li>
-
      color: #B22222;
+
<li>providing feedback on Clotho 2.0 software tools including the EugeneCAD language to a team of developers in the <a href="http://wiki.bu.edu/ece-cidar/index.php/Main_Page">CIDAR Lab</a></li>
-
      font-size: 13pt;
+
<li>working with the <a href="https://2013.igem.org/Team:Wellesley_Desyne">Wellesley Desyne</a> team to develop an easy-to-use visualized programming language to wrap around Eugene</li>
-
          font-width: 300;
+
<li>continuing the <a href="https://2012.igem.org/Team:BostonU/DataSheet">Datasheet project from the 2012 BostonU team</a> by finalizing a format for sharing information with <a href="https://2013.igem.org/Team:Purdue">Purdue Biomaker's iGEM Team</a> and programming a web app to generate the standardized datasheets</li>
-
    }
+
</ul>
 +
</p>
-
H9 {
+
<p>This year's work on these projects bring us closer to a more complete MoClo/Clotho platform for designing devices with software, constructing more complex devices in the wet laboratory by hand or with a liquid-handling robot, and sharing characterization data.</p>
-
      font-family: Signika;
+
</h7>
-
      text-transform: none;
+
</body>
-
      text-decoration: none;
+
-
      text-align: left;
+
-
      color: #B22222;
+
-
      font-size: 14pt;
+
-
    }
+
-
 
+
</html>
-
</style>
+
-
 
+
-
<link rel="stylesheet" type="text/css" href="http://static.tumblr.com/bepcnvc/YKnm67emn/team.css">
+
-
<link href='http://fonts.googleapis.com/css?family=Signika:300,400' rel='stylesheet' type='text/css'>
+
-
 
+
-
<style type="text/css">@import "http://cs.wellesley.edu/~hcilab/iGEM_wiki/css/videobox.css";</style>
+
-
 
+
-
</head>
+
-
<body class="basiclayout">
+
-
<div id="bu-wellesley_wiki_content">
+
-
 
+
-
<div id="igemlogo">
+
-
<a href="https://2013.igem.org/Main_Page"><img src="https://static.igem.org/mediawiki/2012/1/13/Igemwhite_back.png" alt="iGEM 2012 main page" style="position: absolute; top: 10px; left: 10px;"width="90"></a>
+
-
</div>
+
-
 
+
-
<p  style="text-align:center;"><a href="https://2013.igem.org/Team:BostonU"><img src="https://static.igem.org/mediawiki/2013/2/2c/Marsh.png" width="800px" length="200px"></a></p>
+
-
 
+
-
<ul id="nav">
+
-
<li><a href="#">Our Team</a>
+
-
<ul>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Team">Team</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Social">Summer Fun</a></li>
+
-
</ul>
+
-
</li>
+
-
<li><a href="#">Project</a>
+
-
<ul>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Project_Overview">Project Overview and Abstract</a></li>
+
-
                        <li><a href="https://2013.igem.org/Team:BostonU/MoCloChara">Introduction to MoClo and Characterization</a></li>
+
-
 
+
-
+
-
                        <li><a href="https://2013.igem.org/Team:BostonU/QS">Quorum Sensing</a></li>
+
-
                        <li><a href="https://2013.igem.org/Team:BostonU/HK">Histidine Kinase</a></li>
+
-
                        <li><a href="https://2013.igem.org/Team:BostonU/ML">MoClo Library</a></li>
+
-
                        <li><a href="https://2013.igem.org/Team:BostonU/DataSheet">Data Sheets App</a></li> 
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Methodology ">Methodology Overview</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Results ">Results Summary</a></li>
+
-
</ul>
+
-
</li>
+
-
<li><a href="#">Achievements</a>
+
-
<ul>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Data">Data Collected</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Parts">Parts Submitted</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/MoClo">MoClo Kit</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Gold">Medal Fulfillment</a></li>
+
-
 
+
-
</ul>
+
-
</li>
+
-
 
+
-
<li><a href="#">Notebook</a>
+
-
<ul>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Protocols">Protocols</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Clotho">Clotho and Eugene</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/PR">Pigeon and Raven</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/NotebookQS">Quorum Sensing Notebook</a></li>
+
-
                        <li><a href="https://2013.igem.org/Team:BostonU/NotebookHK">Histidine Kinase Notebook</a></li>
+
-
                        <li><a href="https://2013.igem.org/Team:BostonU/NotebookML">MoClo Library Notebook</a></li>
+
-
                        <li><a href="https://2013.igem.org/Team:BostonU/TroubleShooting">Trouble Shooting</a></li>
+
-
</ul>
+
-
</li>
+
-
+
-
 
+
-
<li><a href="#">Considerations</a>
+
-
<ul>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/NEGEM">New England iGEM Regional Meeting</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Human Practices">Human Practices</a></li>
+
-
<li><a href="https://2013.igem.org/Team:BostonU/Safety">Safety</a></li>
+
-
 
+
-
</ul>
+
-
 
+
-
<li><a href="#">Acknowledgements</a>
+
-
<ul>
+
-
                    <li><a href="https://2013.igem.org/Team:BostonU/Collaborations">Collaborations</a></li>
+
-
                    <li><a href="https://2013.igem.org/Team:BostonU/Acknowledgements">Acknowledgements</a></li>
+
-
 
+
-
                </ul>
+
-
</li>
+

Latest revision as of 01:15, 28 September 2013



Abstract

In order for synthetic biologists to be able to use automation technologies, we need a well-characterized library of basic biological components that can then be used to design more complex systems. MoClo is a one-pot digestion-ligation assembly technique developed by (Weber et al., 2011), which enables faster and more efficient construction of genetic circuits compared to BioBricks, the current iGEM standard. With our project, we are proposing that iGEM teams replace the inefficient BioBricks cloning method with MoClo. We have expanded our library of basic MoClo DNA Parts and characterized devices using various promoter-5' Untranslated Region combinations via flow cytometry. We also are designing and implementing a standardized data sheet using Java and JavaScript in order to easily share our library and data with the community. Our MoClo library, characterization data, and data sheet tool fill an essential role in the implementation of automated synthetic biology protocols.

Project Overview

Synthetic biology exists more as a form of art than a reproducible, well-defined production chain. From laboratory to laboratory, the experiments vary in procedure, characterization, and yield. The main product of synthetic biology — engineered organisms, are available only to the highly-experienced researcher and are not without the costs of timely preparation and low product yield. Consequently, the lack of standardization across the field has impeded the product from ever reaching a wide industry audience. More recent engineering efforts in the assembly of gene circuits has provided a pathway to a modular view of genetic parts. Termed the Modular Cloning Assembly Method (MoClo), this novel single-pot reaction protocol is a time-efficient, two-enzyme system for DNA assembly (Weber et al., 2011). Before MoClo can reach its full potential across research and industry interests, the synthetic biology community needs a standardized and well-characterized library of MoClo parts for Escherichia coli to enable protocol automation and informed device designing. The 2013 Boston University iGEM Team seeks to bridge this gap in the product development chain by building a standard library and characterizing the parts via flow cytometry. To further efforts to develop foundational advancements for synthetic biology, we are taking a multi-faceted approach and working at several aspects and levels of design automation by:

  • expanding a library of basic Level 0 MoClo parts by cloning from BioBrick parts and making new parts
  • building a library of composite Level 1 and 2 devices to characterize promoter-5' Untranslated Region combinations and demonstrate the library's usefulness
  • providing feedback on Clotho 2.0 software tools including the EugeneCAD language to a team of developers in the CIDAR Lab
  • working with the Wellesley Desyne team to develop an easy-to-use visualized programming language to wrap around Eugene
  • continuing the Datasheet project from the 2012 BostonU team by finalizing a format for sharing information with Purdue Biomaker's iGEM Team and programming a web app to generate the standardized datasheets

This year's work on these projects bring us closer to a more complete MoClo/Clotho platform for designing devices with software, constructing more complex devices in the wet laboratory by hand or with a liquid-handling robot, and sharing characterization data.

Retrieved from "http://2013.igem.org/Team:BostonU/Project_Overview"