title: Genotype Specification Language.
abstract: We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: Erin H
authors.initials: EH
authors.lastname: Wilson
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: Shiori
authors.initials: S
authors.lastname: Sagawa
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: James W
authors.initials: JW
authors.lastname: Weis
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: Max G
authors.initials: MG
authors.lastname: Schubert
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Bissell
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: Brian
authors.initials: B
authors.lastname: Hawthorne
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Reeves
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: Jed
authors.initials: J
authors.lastname: Dean
authors.affiliation: Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States.
authors.forename: Darren
authors.initials: D
authors.lastname: Platt
mesh_terms: D004247:DNA / Q000235:genetics*; D005818:Genetic Engineering / Q000379:methods*; D005838:Genotype; D007802:Language; D012984:Software
chemical_list: D004247:DNA
keywords: DNA assembly; bio-design automation; programming language