An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology

Ernst Oberortner; Robert Evans; Xianwei Meng; Sangeeta Nath; Hector Plahar; Lisa Simirenko; Angela Tarver; Samuel Deutsch; Nathan J Hillson; Jan-Fang Cheng

doi:10.1007/978-1-0716-0908-8_1

An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology

Methods Mol Biol. 2020:2205:3-18. doi: 10.1007/978-1-0716-0908-8_1.

Authors

Ernst Oberortner^{1

2}, Robert Evans^{3

4}, Xianwei Meng^{3

4}, Sangeeta Nath^{3

4}, Hector Plahar^{5

6}, Lisa Simirenko^{3

4}, Angela Tarver^{3

4}, Samuel Deutsch^{3

4}, Nathan J Hillson^{3

5

6

7

8}, Jan-Fang Cheng^{3

4}

Affiliations

¹ DOE Joint Genome Institute (JGI), Berkeley, CA, USA. eoberortner@lbl.gov.
² Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. eoberortner@lbl.gov.
³ DOE Joint Genome Institute (JGI), Berkeley, CA, USA.
⁴ Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁵ Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁶ Technology Division, DOE Joint BioEnergy Institute (JBEI), Emeryville, CA, USA.
⁷ DOE Agile BioFoundry, Emeryville, CA, USA.
⁸ TeselaGen Biotechnology, Inc., San Francisco, CA, USA.

PMID: 32809190
DOI: 10.1007/978-1-0716-0908-8_1

Abstract

Biological computer-aided design and manufacturing (bioCAD/CAM) tools facilitate the design and build processes of engineering biological systems using iterative design-build-test-learn (DBTL) cycles. In this book chapter, we highlight some of the bioCAD/CAM tools developed and used at the US Department of Energy (DOE) Joint Genome Institute (JGI), Joint BioEnergy Institute (JBEI), and Agile BioFoundry (ABF). We demonstrate the use of these bioCAD/CAM tools on a common workflow for designing and building a multigene pathway in a hierarchical fashion. Each tool presented in this book chapter is specifically tailored to support one or more specific steps in a workflow, can be integrated with the others into design and build workflows, and can be deployed at academic, government, or commercial entities.

Keywords: Bioengineering; Computer-aided design; Computer-aided manufacturing; DNA assembly; DNA synthesis; Software; Synthetic biology.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computer-Aided Design
Software
Synthetic Biology / methods*
Workflow