Team:BostonU/Chimera

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Latest revision as of 00:15, 18 October 2014

Project Chimera

Synthetic biology research revolves around design-build-test cycles for the production of genetic devices. An effective process often depends on protocol robustness and a thorough understanding of individual genetic components. Currently, limited software integration and part characterization represent significant stymying factors to the growth of the field, particularly as researchers endeavor to construct increasingly complex devices with behavior that is difficult to predict.

We seek to strengthen the traditional design-build-test cycle by developing a workflow that utilizes bio-design automation software tools and builds upon a thoroughly characterized library of parts. Our group was motivated to start this project through our participation in the 6th International Workshop on Bio-Design Automation, at which important questions about software integration into wet lab experiments were discussed. Our goal is to bridge the gap between software tools and the wet lab to design a more efficient synthetic biology experimental process.

The Chimera Characterization Workflow
The Chimera characterization workflow is intended to facilitate the predictive design of complex genetic regulatory networks. It employs a design-build-test engineering approach made unique by the inclusion of the following computational tools: Eugene and Pigeon for designing, Raven for assembling, and the TASBE Tools for testing genetic constructs. Depending on the researcher's knowledge of device design and assembly, the Chimera workflow can be adjusted in its reliance on the computational tools employed.
This is a graphic depiction of where the software tools Eugene, Pigeon, Raven, and TASBE Tools enter into the classic design-build-test engineering cycle. We also have a Share branch to reflect sharing our data with the iGEM community on the Registry Pages and also through the Synthetic Biology Open Language (SBOL) sharing capabilities.	The end goal of the Chimera workflow is to collect high quality quantitative characterization data from genetic devices that can then be used to inform the users on which parts are reliable for use in more complex devices. Currently, this workflow uses flow cytometry as a means of measuring functionality of genetic devices due to the use of the TASBE tools, which allows users to easily process flow cytometry data. When it comes to the design and build aspects of this workflow, Chimera is unbiased when it comes to which assembly method the user selects thanks to Eugene and Raven, which are tools agnostic to assembly method.
A desired genetic device behavior and an idea of the parts required are all a researcher needs to begin using Chimera. Once these characteristics have been targeted, the workflow can be used to guide a researcher to building their intended device more efficiently. The following is a general outline of the Chimera workflow. An example of BU 2014's test case can be found on our workflow page, in which we test the functionality of Chimera by using it to assemble a priority encoder.

Our Sponsors

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-         <th scope="col">The lack of standardization. this will become an increasingly significant stymying factor to the growth of the field as more laboratories continue to share resources and data. We seek to strengthen the traditional design-build-test cycle fundamental to synthetic biology with a formalized workflow defined by bio-design automation software tools and built upon a thoroughly characterized library of parts.</th>
+         <td scope="col">Synthetic biology research revolves around design-build-test cycles for the production of genetic devices. An effective process often depends on protocol robustness and a thorough understanding of individual genetic components. Currently, limited software integration and part characterization represent significant stymying factors to the growth of the field, particularly as researchers endeavor to construct increasingly complex devices with behavior that is difficult to predict.<br><br>
-<th scope="col"><img src="https://static.igem.org/mediawiki/2014/7/75/DVL1_AE_BU14.png" width="300" height="300" alt="DVL1AE" style="float:right" style= "margin-left:10px"><br><br><capt><br>Plasmid map of a MoClo Level 1 destination vector with original pMB1 origin of replication, LacZ fragment, and designed primers for backbone extraction.</capt></th>
+We seek to strengthen the traditional design-build-test cycle by developing a workflow that utilizes bio-design automation software tools and builds upon a thoroughly characterized library of parts. Our group was motivated to start this project through our participation in the <a href="https://2014.igem.org/Team:BostonU/HumanPractices">6th International Workshop on Bio-Design Automation</a>, at which important questions about software integration into wet lab experiments were discussed. Our goal is to bridge the gap between software tools and the wet lab to design a more efficient synthetic biology experimental process.</td>
+<td scope="col"><img src="https://static.igem.org/mediawiki/2014/d/d9/Chimera_plasmid_BU14.png" height="300" width="300" alt="ChimeraPlasmid" style="float:right" style= "margin-left:10px"><br><br><capt></capt></td>
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+    <table width="100%" border="0" cellspacing="15" cellpadding="0">
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-<th colspan="2" scope="col"><br><h2>June</h2></th>
-</tr>
+      <tr>
+        <td colspan="2" scope="col">
+<h3>The Chimera Characterization Workflow</h3></td></tr>
+      <tr>
+        <td colspan="2" scope="col">
+The Chimera characterization workflow is intended to facilitate the predictive design of complex genetic regulatory networks. It employs a design-build-test engineering approach made unique by the inclusion of the following computational tools: <a href="http://eugenecad.org/">Eugene</a> and <a href="http://pigeoncad.org/">Pigeon</a> for designing, <a href="http://ravencad.org/">Raven</a> for assembling, and the <a href="https://synbiotools.bbn.com/">TASBE Tools</a> for testing genetic constructs. Depending on the researcher's knowledge of device design and assembly, the Chimera workflow can be adjusted in its reliance on the computational tools employed.</td></tr>
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-<th colspan="2" scope="col"><h3>Week of June 23</h3></th>
+<td scope="col">
+<center><img src="https://static.igem.org/mediawiki/2014/1/1a/BU14_DBTcycle.png" width="450"></center>
+<center><capt>This is a graphic depiction of where the software tools Eugene, Pigeon, Raven, and TASBE Tools enter into the classic design-build-test engineering cycle. We also have a Share branch to reflect sharing our data with the iGEM community on the Registry Pages and also through the Synthetic Biology Open Language (SBOL) sharing capabilities.</capt></center></td>
+<td scope="col">
+The end goal of the Chimera workflow is to collect high quality quantitative characterization data from genetic devices that can then be used to inform the users on which parts are reliable for use in more complex devices. Currently, this workflow uses flow cytometry as a means of measuring functionality of genetic devices due to the use of the TASBE tools, which allows users to easily process flow cytometry data. <br><br>When it comes to the design and build aspects of this workflow, Chimera is unbiased when it comes to which assembly method the user selects thanks to Eugene and Raven, which are tools agnostic to assembly method.</td>
 </tr>
+      <tr>
+        <td colspan="2" scope="col">
+A desired genetic device behavior and an idea of the parts required are all a researcher needs to begin using Chimera. Once these characteristics have been targeted, the workflow can be used to guide a researcher to building their intended device more efficiently. The following is a general outline of the Chimera workflow. An example of BU 2014's test case can be found on our <a href="https://2014.igem.org/Team:BostonU/Workflow">workflow</a> page, in which we test the functionality of Chimera by using it to assemble a priority encoder.<br><br><br>
-<tr>
+<center><img src="https://static.igem.org/mediawiki/2014/2/26/BU14_Overview_PhaseI_II_III.png" width="100%"></center>
-        <th colspan="2" scope="col">The backbones that would have their origin replaced were selected and new origins were selected. DVL1 with "A" and "E" MoClo fusion sites and DVL2 with "A" and "F" fusion sites were initially chosen, as they are the most commonly used MoClo level 1 and 2 destination vectors, respectively (See <a href="https://2014.igem.org/Team:BostonU/MoClo">MoClo</a> for more information on our assembly method). The general plan to replace the backbones was formulated, which comprised of:<br><br>1. Using PCR to extract the backbones without their high-copy origins from their full destination vectors, and to extract the lower-copy origins from their respective plasmids.<br>2.Performing a restriction digest on the backbone and origin fragments to have compatible sticky ends.<br>3. Ligating the origins to the destination vectors.<br>4. Transforming into E. Coli, purifying the plasmid DNA, and sequencing for confirmation.<br><br>The PCR primer design added restriction sites for the MfeI restriction enzyme, which would give the ends of each of the amplified fragments compatible 4bp overhangs suitable for ligation. (Detailed primer design available <a href="https://static.igem.org/mediawiki/2014/c/c6/Primer_Design_6-23_BU14.xls">here</a>).<br><br>
-•	Struck out devices with low copy origins for PCR on plates with appropriate antibiotic.<br>
-•	Prepared liquid cultures, incubated, and miniprepped.<br>
-•	Received primers, diluted.
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+ <br><br><br>
+</td>
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