Software for lab work: repurposing qPCR machines and making complex mixes
qslib: software that adapts the Applied Biosystems QuantStudio 5 qPCR machine for use as a general-purpose programmable temperature control and fluorescence measurement device.
alhambra-mixes: a tool for designing complex, hierarchical mixes of many different combinations of many components, and many different concentrations.
DNA sequence designer: SST-sequence
SST-sequence-design is a DNA sequence design and analysis tool for designing single-stranded DNA tiles.
Written in python by Damien Woods, David Doty and Erik Winfree, it was used to design DNA sequences for the following 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].
Since then, things have moved on! See Dave Doty’s nuad software below that uses much of the same thermodynamic principles as SST-sequence-design but allows specification of much more general DNA systems and has an easier to program interface.
Software that we contribute to and use
DNA sequence designer: nuad
nuad, or NUcleic Acid Designer, and named after Maigh Nuad, the Irish-language word for Maynooth, is a Python library that we use to design DNA sequences. A user writes a python program that specifies thermodynamic-based energy constraints on a DNA nanostructure design, and invokes the library to find suitable DNA sequences. Development is led by Dave Doty (UC Davis Molecular Computing group), with occasional contributions, and extensive wet-lab testing, by members of our group.
GUI-based design of DNA nanostructures: scadnano
scadnano.org is a browser-based GUI for design of DNA nanostructures. Developed and maintained by the UC Davis Molecular Computing group, with extensive wet-lab testing by our group. There is also an associated python scripting library. scadnano has a similar look and feel to cadnano (https://cadnano.org/), by the Douglas lab at UCSF. See the following publication for details:
David Doty, Benjamin L Lee, Tristan Stérin. scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures. DNA26: The 26th International Conference on DNA Computing and Molecular Programming, LIPIcs 174:9:1–9:17, 2020
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