Amyris Genotype Specification Language published

[Michal Galdzicki]

Congrats Darren, Mike and the rest of the Amyris team!

Genotype Specification Language

Erin H. Wilson, Shiori Sagawa, James W. Weis, Max G. Schubert, Michael Bissell, Brian Hawthorne, Christopher D Reeves, Jed Dean, and Darren Platt*

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.

http://pubs.acs.org/doi/abs/10.1021/acssynbio.5b00194 

-Mike

[Ernst Oberortner]

I’d like to join Mike to congratulate the Amyris team!

Easy to read and understand, clearly defined language, its operators, and abstraction levels!

I fully agree with the statement “ that moving users away from working directly with DNA sequences and toward more abstract representations will require transparency, time, and trust”

Building up trust is, as I'm experiencing it every day, the biggest challenge!

Best,

Ernst

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[Cesar Rodriguez]

Darren,

Thanks for sharing GSL with the community.  Look forward to reading the paper!

Cesar

[Da Pl]

Thanks everyone! Great to be able to share that finally.  We are in the process of depositing the source code for the compiler into github.  We are cleaning it up and making it build better on non windows platforms, but hoping interested parties will be able to do cool things with it and help us evolve it further.  SBOL 2 generation is also currently work in progress but planning to have that finished up this year.   Hope you enjoy the paper and let us know if you have questions or ideas for making it better.  

Darren

p.s. if you're really interested in hacking the compiler, you should get a head start and take a crash course on F# (http://fsharp.org)

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[Da Pl]

If anyone is in SF Tuesday evening and curious about GSL, I will be giving a talk to the F# meetup in the evening.   It's more programming language crowd, but everyone welcome.   The source code for GSL is getting cleaned up to remove dependencies and ensure a clean cross platform build, but still but we are hoping to get into the Amyris github soon.  Here's the meetup link  http://www.meetup.com/sfsharp/events/228954768/ 

We are also starting work on SBOL 2.0 generation, so good things coming,

Darren

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