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.
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Acknowledgments
This work was part of the DOE Joint Genome Institute (https://jgi.doe.gov) and Joint BioEnergy Institute (https://www.jbei.org) supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, and was part of the Agile BioFoundry (https://agilebiofoundry.org) supported by the US Department of Energy, Energy Efficiency and Renewable Energy, Bioenergy Technologies Office, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy. The views and opinions of the authors expressed herein do not necessarily state or reflect those of the US Government or any agency thereof. Neither the US Government nor any agency thereof, nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility or the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. The US Government retains and the publisher, by accepting the article for publication, acknowledges that the US Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US Government purposes.
We thank the DOE National Energy Research Scientific Computing Center (NERSC) (https://www.nersc.gov/) for hosting the JGI’s instances of the bioCAD/CAM tools described in this chapter (e.g.., DIVA/DeviceEditor/j5 , BOOST , BLiSS, SynTrack, and ICE).
Author Contributions: R.E., S.N., A.T., N.J.H. and J.F.C. are end-users of the bioCAD/CAM tools. N.J.H. developed and maintains j5. X.M. developed and maintains SynTrack. E.O. developed and maintains BOOST and the SynBioQC pipelines. H.P. developed and maintains DIVA/DeviceEditor and ICE. L.S. developed and maintains BLiSS and manages the JGI’s deployments of DIVA/DeviceEditor/j5, and ICE. S.N. designed and performed the pathway design workflow . All authors wrote, edited, and reviewed the manuscript.
Conflicts of Interest Statement: N.J.H. declares financial interests in the form of issued and pending patent applications related to the j5 software, and equity in TeselaGen Biotechnology, Inc.
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Oberortner, E. et al. (2020). An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology. In: Chandran, S., George, K. (eds) DNA Cloning and Assembly. Methods in Molecular Biology, vol 2205. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0908-8_1
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DOI: https://doi.org/10.1007/978-1-0716-0908-8_1
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