Our theoretical and experimental work is aided by custom software developed in-house.

SST-sequence-design

DNA sequence design and analysis tool for designing single-stranded DNA tiles. Written in python by Damien Woods, David Doty and Erik Winfree.

SST-sequence-design was used to design DNA sequences for the paper:

  • Damien Woods*, David Doty*, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, Erik Winfree. (*Joint first co-authors)
    Diverse and robust molecular algorithms using reprogrammable DNA self-assembly.
    Nature 567:366–372. 2019. [pdf].

Pijul

A patch-based version control system based on a new datastructure for asynchronous computing, itself suggested by a result from category theory.

Pijul is theoretically correct (i.e. provably satisfies a number of axioms), and fast. The project required us to write other libraries to achieve the theoretical complexity in actual programs:

  • Sanakirja, a fully transactional key-value store where tables can be forked in O(log n), where n is the number of bindings in the store.

  • Thrussh, an SSH library handling both the client side and server side of the SSH 2 protocol.

  • The Nest, a hosting platform for Pijul repositories.

The whole project is written in Rust.

Pijul was featured in the following software conferences: