Team:BostonU

From 2014.igem.org

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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.
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         <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.
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           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>
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           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. 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>
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           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.
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           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.  
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          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>
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          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>
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          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>
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Revision as of 16:12, 28 July 2014



chimera - an optimized synthetic biology workflow
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.

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. We will supplement the CIDAR MoClo basic parts library (built by the 2012 and 2013 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 Registry of Standard Biological Parts.

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 Tools for flow cytometry.

 
 


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