Team:BostonU

From 2014.igem.org

Revision as of 16:23, 16 October 2014

• TEAM
• PROJECT
  • Overview
  • Priority Encoder
  • MoClo Assembly Method
  • Low Copy Backbones
  • Tandem Promoters
  • Fusion Proteins
  • Repressor Proteins
  • Software Tools
  • Multiplexing
  • Future Work
• ACHIEVEMENTS
  • Data Collected
  • Parts Submitted
  • Chimera Workflow
  • Medal Fulfillment
• NOTEBOOK
  • Training
  • Protocols
  • Backbones
  • Tandem Promoters and Repressors
  • Fusion Proteins
• CONSIDERATIONS
  • Collaborations
  • Measurement Track
  • Safety
  • Interlab Study
  • NEGEM
  • Policy and Practices
• ACKNOWLEDGEMENTS

Chimera -

an optimized synthetic biology workflow

Abstract 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).

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 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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