EAGER: A Standard Enabled Workflow for Synthetic Biology

University Of Utah, Salt Lake City UT

Investigators

Abstract

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, and system-level design tools to construct and analyze models of complete designs. Data standards enable the ready exchange of information within such a workflow. They allow repositories and tools to be connected from a diversity of sources. This workflow will leverage several data standards developed for systems and synthetic biology. This workflow will have a broader impact on several diverse communities of synthetic biology users. This project also will work with journals, especially ACS Synthetic Biology, to integrate this workflow into their data archival process, and it will provide training videos for authors to minimize the impact on them. Ultimately, this workflow should play a significant role in enabling synthetic biology to become a truly reproducible scientific endeavor. This standard enabled workflow will leverage a variety of data standards. These standards include the Synthetic Biology Open Language (SBOL), which can be utilized to describe and visualize genetic designs, the Systems Biology Markup Language (SBML), which can be used to create computational models, the Simulation Experiment Description Markup Language (SED-ML), which can describe simulation experiments, and the COMBINE Archive, which can combine these files into a single exchangeable document. Using these standards, a synthetic biology workflow will be constructed that includes multiple repositories, such as the Newcastle SynBioHub and the JBEI ICE Repository, and multiple software tools such as Benchling, SBOLDesigner, iBioSim, and Cello, among others. The intellectual merit of this project includes the following activities: --Integration and refinement of genetic part datasets from a variety of libraries, including, among others, the iGEM registry, MIT Cello transcriptional circuit library, and the Newcastle BacillOndex part library. --Improve SynBioHub's connections with remote repositories, such as Benchling, JBEI ICE, and SBOLme, as further sources for genetic design information. --Connection of software to form a synthetic biology workflow, including, among others, SBOLDesigner, iBioSim, and SynBioHub. --Application and validation of this workflow using as a driving example the genetic circuit design and computational modeling of communication circuits for multicellular spatiotemporal patterning.