Team:BostonU

From 2014.igem.org

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Latest revision as of 03:24, 18 October 2014

Chimera

an optimized characterization workflow for synthetic biology

Abstract

The Joy of Cloning: Chimera, a Recipe for Integrating Computational Tools with Experimental Protocols
If BU can clone it, so can you! With a pinch of wet lab work and a dash of computational tools, we have developed a new recipe called Chimera that will help fellow synthetic biology cloners in the creation of their genetic devices! Chimera utilizes bio-design automation software tools with experimental protocols and builds upon a thoroughly characterized library of MoClo parts. This recipe, or workflow, integrates software tools to reduce human error and to structure the way device designs are chosen, assembled, and tested. To demonstrate that this workflow can be used by any level of cloner (beginner, intermediate, and advanced), we will highlight how we used Chimera to create:

individual genetic parts (namely tandem promoters, fusion proteins, and different backbones),

transcriptional units assembled from individual parts (with both new and previously made MoClo parts), and

a complex genetic device (our goal is a priority encoder).

Click here to explore our project!

Our Sponsors

@@ Line 32: / Line 32: @@
 	<li><a href="">PROJECT</a>
 <ul>
 			<li><a href="https://2014.igem.org/Team:BostonU/Chimera">Overview</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/Encoder">Priority Encoder</a></li>
 <li><a href="https://2014.igem.org/Team:BostonU/MoClo">MoClo Assembly Method</a></li>
                          <li><a href="https://2014.igem.org/Team:BostonU/Backbones">Low Copy Backbones</a></li>
 <li><a href="https://2014.igem.org/Team:BostonU/ProjectTandemPromoters">Tandem Promoters</a></li>
         <li><a href="https://2014.igem.org/Team:BostonU/FusionProteins">Fusion Proteins</a></li>
-<li><a href="https://2014.igem.org/Team:BostonU/FlowCytometry">Flow Cytometry</a></li>
+       <li><a href="https://2014.igem.org/Team:BostonU/Repressors">Repressor Proteins</a></li>
+            <li><a href="https://2014.igem.org/Team:BostonU/Multiplexing">Multiplexing</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/Software">BioDesign Automation Tools</a></li>
+            <li><a href="https://2014.igem.org/Team:BostonU/Future">Future Work</a></li>
 	  </ul>
 </li>
@@ Line 44: / Line 49: @@
 	        <li><a href="https://2014.igem.org/Team:BostonU/Data">Data Collected</a></li>
 			<li><a href="https://2014.igem.org/Team:BostonU/Parts">Parts Submitted</a></li>
-             <li><a href="https://2014.igem.org/Team:BostonU/Workflow">Workflow</a></li>
+             <li><a href="https://2014.igem.org/Team:BostonU/Workflow">Chimera Workflow</a></li>
-<li><a href="https://2014.igem.org/Team:BostonU/Encoder">Priority Encoder</a></li>
+            <li><a href="https://2014.igem.org/Team:BostonU/ChimeraExample">Chimera Example</a></li>
              <li><a href="https://2014.igem.org/Team:BostonU/Medals">Medal Fulfillment</a></li>
-            <li><a href="https://2014.igem.org/Team:BostonU/Future">Future Work</a></li>
 	  </ul>
@@ Line 56: / Line 60: @@
 			<li><a href="https://2014.igem.org/Team:BostonU/Protocols">Protocols</a></li>
                          <li><a href="https://2014.igem.org/Team:BostonU/BackbonesNotebook">Backbones</a></li>
-                         <li><a href="https://2014.igem.org/Team:BostonU/TandemPromoters">Tandem Promoters</a></li>
+                         <li><a href="https://2014.igem.org/Team:BostonU/TandemPromoters">Tandem Promoters and Repressors</a></li>
                          <li><a href="https://2014.igem.org/Team:BostonU/FusionProteinsNotebook">Fusion Proteins</a></li>
 	  </ul>
@@ Line 63: / Line 67: @@
      <ul>
 <li><a href="https://2014.igem.org/Team:BostonU/Collaborations">Collaborations</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/Measurement">Measurement Track</a></li>
 <li><a href="https://2014.igem.org/Team:BostonU/Safety">Safety</a></li>
 <li><a href="https://2014.igem.org/Team:BostonU/Interlab">Interlab Study</a></li>
@@ Line 92: / Line 97: @@
    <br>
    <br>
-    <header1>chimera -
+<header1>Chimera</header1><h3>an optimized characterization workflow for synthetic biology</h3>
-    </header1>
+<maincontent><br>
-    <header3>an optimized synthetic biology workflow</header3><br>
+<table width="100%" border="0" cellspacing="0" cellpadding="0">
-    <header2><br>
-    </header2>
-    <maincontent><table width="100%" border="0" cellspacing="0" cellpadding="0">
        <tr>
-         <th colspan="2" scope="col">Currently in synthetic biology, the creation of novel genetic circuits revolves around a familiar design-build-test cycle. As an increasing number of laboratories become involved in designing newer and more sophisticated constructs, the lack of standardization in production and characterization inhibits workflow efficiency and, by extension, growth of the field. The 2014 Boston University iGEM team seeks to employ a formalized and optimized workflow supported by new bio-design automation applications, with the aim of benefiting synthetic biologists seeking to more efficiently design, build, and characterize complex constructs.
+         <td colspan="2" scope="col">
-          <br><br>
+<h3>Abstract </h3>
-          Advancements in bio-design automation (or BDA) have allowed for the implementation of a variety of software and automation tools that help improve the efficiency in a synthetic biology laboratory. We will take a novel approach to the design-build-test cycle by using software tools to formalize our workflows, thus making us one of the first BDA iGEM teams. We will supplement the <a href="http://cidarlab.org/" target="_blank">CIDAR</a> MoClo basic parts library (built by the <a href="https://2012.igem.org/Team:BostonU" target="_blank">2012</a> and <a href="https://2013.igem.org/Team:BostonU" target="_blank">2013</a> BU iGEM teams) with hybrid promoters, fusion proteins, and a variety of new destination vectors. With these modular parts, we will build complex constructs using our formalized workflow, in addition to providing comprehensive characterization data for all new parts and improving data for existing parts in the <a href="http://parts.igem.org/Main_Page" target="_blank">Registry of Standard Biological Parts</a>. <br><br>
+<strong>The Joy of Cloning: Chimera, a Recipe for Integrating Computational Tools with Experimental Protocols </strong><br>
-          Our BDA approach will include utilizing various software tools throughout the design-build-test cycle in our wet lab work, including <a href="http://eugenecad.org/" target="_blank">Eugene</a>, <a href="http://cidarlab.org/raven/" target="_blank">Raven</a>, and the <a href="https://synbiotools.bbn.com/" target="_blank">TASBE Tools</a> for flow cytometry.
+If BU can clone it, so can you! With a pinch of wet lab work and a dash of computational tools, we have developed a new recipe called <a href="https://2014.igem.org/Team:BostonU/Workflow">Chimera</a> that will help fellow synthetic biology cloners in the creation of their genetic devices! Chimera utilizes <a href="https://2014.igem.org/Team:BostonU/Software">bio-design automation software tools</a> with experimental protocols and builds upon a thoroughly characterized library of <a href="https://2014.igem.org/Team:BostonU/MoClo">MoClo</a> parts. This recipe, or workflow, integrates software tools to reduce human error and to structure the way device designs are chosen, assembled, and tested. To demonstrate that this workflow can be used by any level of cloner (beginner, intermediate, and advanced), we will highlight how we used Chimera to create:<br>
-        </tr>
+<p class="tab"><li> individual genetic parts (namely <a href="https://2014.igem.org/Team:BostonU/ProjectTandemPromoters">tandem promoters</a>, <a href="https://2014.igem.org/Team:BostonU/FusionProteins">fusion proteins</a>, and <a href="https://2014.igem.org/Team:BostonU/Backbones">different backbones</a>), </p>
-      <tr>
+<p class="tab"><li> transcriptional units assembled from individual parts (with both new and previously made MoClo parts), and </p>
-        <th colspan="2" scope="col">  <p>&nbsp;</p></th>
+<p class="tab"><li> a complex genetic device (our goal is a <a href="https://2014.igem.org/Team:BostonU/Encoder">priority encoder</a>).</p>
-        </tr>
+<br><br><strong><a href="https://2014.igem.org/Team:BostonU/Chimera">Click here to explore our project!</a></strong></td></tr></table>
-      <tr>
+</maincontent>
-        <th scope="col">&nbsp;</th>
-        <th scope="col"></th>
+</div></div>
-        </tr>
-      </table>
-  </maincontent></div></div>
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