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Description of Files

This repository contains Eugene files specifying designs for the repressilator (Elowitz and Leibler), recombinase state machines (RSMs) (Roquet et al.) , and dual-feedback oscillator (Stricker et al.). In particular, one design is specified for the repressilator, eight designs are specified for 2 input, 5 state RSMs, three designs are specified for 3 input, 16 state RSMs, and six designs are specified for the dual-feedback oscillator. The vector backbone and input plasmids of the RSMs are not included. The RSM designs are unique, non-permuted variants, while the oscillator designs vary the order of the same three transcriptional units with alternating orientations.

Issues with Eugene

  1. The product function cannot be applied to composite devices (that is, devices containing other devices).

  2. A DnaComponent of type CDS (Sequence Ontology term SO:0000316) is exported by default whenever a part with a type unknown to Eugene is encountered. A more appropriate type would be engineered region (SO:0000804).

References

Michael B. Elowitz and Stanislas Leibler, ``A synthetic oscillatory network of transcriptional regulators,'' in Letters to Nature, vol. 403, pp. 335-338, 2000.

Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, and Timothy K. Lu, ``Synthetic recombinase-based state machines in living cells,'' in Science, vol. 353, 2016.

Jesse Stricker, Scott Cookson, Matthew R. Bennett, William H. Mather, Lev S. Tsimring, and Jeff Hasty, ``A fast, robust and tunable synthetic gene oscillator,'' in Nature, vol. 456, 2008.