Plasmid assembly workflows are becoming increasingly complicated. Many projects require the development of large libraries of related genetic constructs. As a matter of fact, assembling these plasmid libraries can require a team of several scientists to generate hundreds or thousands of intermediates.  Unless the team is able to properly keep track of all these samples, the project success is unlikely.

Many projects include a number of bioinformatics steps that are an integral part of the research project. Scientists use various bioinformatics tools. However, they struggle to properly document this important aspect of their project. As a result, they keep track of their experimental work independently of the computational effort that supports their experiment.  For example, many scientists who are working with synthetic genes have lost track of the codon optimization algorithm used to design the gene.

The vision of this project is to model DNA manufacturing processes using extensible attribute grammars that capture the relationships between the structure and performance of synthesis processes. The power of this conceptual breakthrough will be demonstrated by specifying a domain-specific programming language that will allow end-users to define, analyze, and execute complex DNA manufacturing projects. The language will initially accommodate three classes of projects that represent a broad range of DNA synthesis needs: 1) insertion of a synthetic DNA fragment into an existing plasmid, 2) producing a library of plasmids that represents the combinatorial assembly of a given set of DNA building blocks and 3) editing the genome of yeast strains; an example of whole genome engineering.

This project is supported by the National Science Foundation (Awards #1832320 and #1241328).


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