Automation of Genetic Design - DELS Microsite...

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Our funders: Automation of Genetic Design National Academy of Sciences Industrialization of Biology Workshop February 17, 2014 J. Christopher Anderson Assistant Professor, Bioengineering 512E EBB, UC Berkeley [email protected] http://andersonlab.qb3.berkeley.edu

Transcript of Automation of Genetic Design - DELS Microsite...

Page 1: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Our funders:

Automation of Genetic Design

National Academy of Sciences

Industrialization of Biology Workshop

February 17, 2014

J. Christopher Anderson

Assistant Professor, Bioengineering

512E EBB, UC Berkeley

[email protected]

http://andersonlab.qb3.berkeley.edu

Page 2: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Synthetic

Biology

Today

Page 3: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Automated

Synthetic

Biology

Page 4: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic
Page 5: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

synbiotrails.org Coming June 11th!

Page 6: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Act Ontology

Page 7: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Exhaustively compute the biosynthetically reachable space Enumerate all paths to each reachable chemical Rank those pathways for plausibility Provide linkage to the DNA sequences (parts) that encode each enzyme

Page 8: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

True

Page 9: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

The L0-L2 Reachable Space

Page 10: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Filtering the Reachable Space

Page 11: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Filtering the Reachable Space

Page 12: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Validation of an L2 target: Tylenol

Page 13: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic
Page 14: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Known Prediction Holes

Expression in foreign host Chemical modifications Multiple subunits Kinetic parameters Membrane/organellar localization Spontaneous reactions Volatile products

Page 15: Automation of Genetic Design - DELS Microsite Networknas-sites.org/synbioroadmap/files/2014/04/3.-Anderson-Chris.pdf · This tutorial will guide you through the basics of genetic

Big-Picture Bottlenecks

Intellectual property / freedom to operate Biosafety/biosecurity checks Regulatory analysis Target coordination Polyketides/Non-ribosomal peptides Polysaccharides Complex lipids Genetic circuits