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

Codenano

Codenano is a browser-based tool for designing DNA nanostructures.

Our blog post gives an overview of codenano's features. The source is on github.

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:

The whole project is written in Rust.

Pijul was featured in the following software conferences: