Team:BostonU/Chimera

From 2014.igem.org

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

Project Chimera

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).

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. At the start of our project, we were able to attend IWBDA 2014 and began learning about ways that other researchers incoporate software tools into the wet lab process.

The Chimera Workflow The Chimera 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. 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 assembly agnostic tools. 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. 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.

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