Genetic Design Automation with GenoCAD

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Genetic Design Automation with GenoCAD

• Matt Lux
• Virginia Bioinformatics Institute
• Virginia Tech

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CAD and Biodesign?

• Needed for effective CAD in synthetic biology

• Abstraction

• Modular Components

• Guide Design

• Simulate Function

• Easy to Use

• Assist Implementation

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Abstraction Work at Parts Level
CCGATACTGTGAAATCTCCCGATGTGTGAAATCTCCCAATCGATACTGTG
AAATCTCCTCC
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Modular Components Parts Library

• MIT Registry
• Parts definitions
• Parts functions
• Parts interference

de Smit MH, van Duin J (1990) Secondary structure
of the ribosome binding site determines
translational efficiency a quantitative
analysis. Proc Natl Acad Sci U S A 87 7668-7672.
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Guide Design Syntactic Model

• Like English for us, DNA is a language for cells

DNA codes life.
Codes life DNA.
? ? ? ? ? ? ?
ACTGTGAAATCTCCCGATGGCCTT
CCCGATGACTGTGAGCCTTAATCT
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Simulate Function Semantic Model

• Meaning is more than just order

Subject
Object

• Implemented Using Attribute Grammar

Students drink coffee.
Coffees drink students.
Verb
ACTGTGAAATCTCCCGATGGCCTT
Prom ? Prom mRNA kt
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Easy to Use GenoCAD Design

• Web-based
• Professional interface
• Quick
• Flexible
• GenoCAD parts
• Registry parts
• Make your own parts

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Whats Next?

• Assist Implementation
• Guide synthesis procedures?
• Improve grammars
• Expand library
• Other organisms
• Yeast
• Mouse
• Plant (Arabidopsis)
• Of course, test!

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Acknowledgements

• - Patrick Cai
• - Jean Peccoud
• - Synthetic Biology Group

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Questions?