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Intro
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Talk Outline
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Industrial fermentation: nature's chemical plant
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The total design space for biology is enormous
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The Zymergen approach
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Microbial engineering: Building DNA
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Microbial engineering: Building microbes
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Testing microbes
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Custom software requirements
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Software for DNA Search: Our problem
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Our solution: Codon
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DNA Data Model
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DNA is annotated
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DnaSpecification Example
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Promoter swapping
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DnaSpecifications are ASTS
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ASTs let us preprocess structure
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How'd we do?
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The "Code trust" problem
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Lessons from Code trust
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The Simplified interface problem
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Lessons from "Simplified interface"
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The "Learning curve" problem
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Lessons from "The learning curve"
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The Super User problem
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Lessons from "super users"
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Conclusions
Description:
Explore a conference talk that delves into the innovative Codon Domain-Specific Language (DSL) developed by Zymergen for efficient genome design. Learn how this powerful tool enables scientists to specify large collections of DNA changes concisely, facilitating the creation of numerous test strains for improving industrial microbes. Discover the atheoretic model employed by Zymergen, which focuses on systematic searching for functional improvements rather than relying on incomplete mechanistic understanding. Gain insights into the flexible system designed by engineers, utilized by scientists, and interpreted by machinery, opening new possibilities in DNA design. The talk covers the challenges faced during Codon's development, including code trust, simplified interfaces, learning curves, and super user requirements. Understand how Codon has been successfully implemented in production for over a year, continually evolving to meet new use cases identified by scientists.

Designing 1000 Genomes in a Single Bound - The Codon DSL

Strange Loop Conference
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