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Synthetic Biology Informatics Group

Software Engineers in the Synthetic Biology Informatics Group develop, deploy, and maintain software that support the DOE JGI’s Synthetic Biology Program. Representative software includes:

  1. Synthetic Biology Internal Review System, which supports the JGI’s Synthetic Biology Internal Review process
  2. DNA Synthesis Sequence Screening Pipeline, which screens all DNA sequences prior to synthesis in compliance with the Federal Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA
  3. SynTrack and associated tools, which track samples through the JGI’s Synthetic Biology pipeline as well as provide process automation support
  4. DOE JGI’s ICE (Inventory of Composable Elements) instance, which serves as an informatic repository of the JGI’s host strains, vectors, and DNA parts
  5. DOE JGI’s DIVA (Design, Implementation, Validation Automation) instance, which will serve as the community’s front end to the DNA Synthesis Program, provide access to DNA design tools, and enable users to track the progress of their designed constructs as they proceed through the construction process

Projects and Resources

Research Team

Nathan Hillson Lisa Simirenko
Nathan Hillson, leader Lisa Simirenko
[email protected]
510-486-6754		 [email protected]
More about Nathan

Selected Publications

  1. “The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology”, Nat Biotechnol. (2014)
  2. “The Plant Glycosyltransferase Clone Collection for Functional Genomics”, Plant J. (2014)
  3. “Cloud-Enabled Microscopy and Droplet Microfluidic Platform for Specific Detection of Escherichia coli in Water”, PLoS ONE (2014).
  4. “PR-PR Cross-Platform Laboratory Automation System”, ACS Synthetic Biology (2014).
  5. “j5 DNA Assembly Design Automation”, DNA Cloning and Assembly Methods (2014).
  6. “Development of a broad-host synthetic biology toolbox for ralstonia eutropha and its application to engineering hydrocarbon biofuel production”, Microbial Cell Factories (2013).
  7. “The Fusion of Biology, Computer Science, and Engineering – towards efficient and successful synthetic biology”, Perspectives in Biology and Medicine (2013).
  8. “PaR-PaR Laboratory Automation platform”, ACS Synthetic Biology (2012).
  9. “Design, Implementation and Practice of JBEI-ICE: An Open Source Biological Part Registry Platform and Tools”, Nucleic Acids Research (2012).
  10. “DeviceEditor visual biological CAD canvas”, Journal of Biological Engineering (2012).
  11. “j5 DNA Assembly Design Automation Software”, ACS Synthetic Biology (2012).
  12. “DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems”,Design and Analysis of Bio-molecular Circuits (2011).

Intellectual Property

  • Scar-Less Multi-Part DNA Assembly Design Automation. (2012) U.S. Patent Application US20120259607.
  • Microfluidic Platform for Synthetic Biology Applications. (2012) U.S. Patent Application US20120258487.