Team:BostonU

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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

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-<ul>
-	        <li><a href="https://2014.igem.org/Team:BostonU/Team">Team</a></li>
-			<li><a href="https://2014.igem.org/Team:BostonU/Fun">Fun</a></li>
-	  </ul>
    </li>
 	<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/Backbones">Backbones</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/MoClo">MoClo Assembly</a></li>
+       <li><a href="https://2014.igem.org/Team:BostonU/Repressors">Repressor Proteins</a></li>
-<li><a href="">Flow Cytometry</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>
 	<li><a href="">ACHIEVEMENTS</a>
 <ul>
-	        <li><a href="">Data Collected</a></li>
+	        <li><a href="https://2014.igem.org/Team:BostonU/Data">Data Collected</a></li>
-			<li><a href="">Parts Submitted</a></li>
+			<li><a href="https://2014.igem.org/Team:BostonU/Parts">Parts Submitted</a></li>
-             <li><a href="">Workflow</a></li>
+             <li><a href="https://2014.igem.org/Team:BostonU/Workflow">Chimera Workflow</a></li>
-             <li><a href="">Medal Fulfillment</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>
 	  </ul>
    </li>
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 	  <ul>
        		<li><a href="https://2014.igem.org/Team:BostonU/Training">Training</a></li>
-			<li><a href="">Protocols</a></li>
+			<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>
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 	<li><a href="">CONSIDERATIONS</a>
      <ul>
-<li><a href="">Collaborations</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/Collaborations">Collaborations</a></li>
-<li><a href="">Safety</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/Measurement">Measurement Track</a></li>
-<li><a href="">Interlab Study</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/Safety">Safety</a></li>
-<li><a href="">NEGEM</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/Interlab">Interlab Study</a></li>
-            <li><a href="">Human Practices</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/NEGEM">NEGEM</a></li>
+<li><a href="https://2014.igem.org/Team:BostonU/HumanPractices">Policy and Practices</a></li>
 	  </ul>
-<li><a href="">ACKNOWLEDGEMENTS</a>
+<li><a href="https://2014.igem.org/Team:BostonU/Acknowledgements">ACKNOWLEDGEMENTS</a>
    </li>
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-    <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">
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-         <th colspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/0/02/DBTcycle_bu14.png" width="400" height="270" alt="Chimera Workflow" style="float:right" style= "margin-left:10px">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 design-build-test 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. Using basic parts from the <a href="http://cidarlab.org/" target="_blank">CIDAR</a> MoClo 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), 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 Eugene, Raven, and the TASBE flow cytometry tool.
+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>
-          <br><br>
+<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>
-          The design of our genetic devices will be facilitated by <a href="http://eugenecad.org/" target="_blank">Eugene</a>, a language specifically designed for the description of genetic networks. Eugene allows for a very efficient design process for new parts by providing an exhaustive list of possible transcriptional units that can be made with available genetic parts, while following a set of rules to ensure the viability of the final designs. <br><br>
+<p class="tab"><li> transcriptional units assembled from individual parts (with both new and previously made MoClo parts), and </p>
-          The building process will be facilitated by <a href="http://cidarlab.org/raven/" target="_blank">Raven</a>, a web-based tool that generates an assembly plan for genetic devices. Our team plans to build devices using the MoClo method employed by previous BU iGEM teams, in addition to multiplexing in order to build many variations on one design in an efficient one-pot reaction. <br><br>
+<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>
-          We will use flow cytometry in conjunction with the <a href="https://synbiotools.bbn.com/" target="_blank">TASBE Tools</a> to test the functionality of new constructs and enhance the documentation available for existing parts in the Registry. Additionally, we will contribute several new parts and their characterization data to the Registry including hybrid promoters, fusion proteins, and a variety of new vectors.&nbsp;</th>
+<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>
-      <tr>
-        <th colspan="2" scope="col">  <p>&nbsp;</p></th>
+</div></div>
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