Digital Tools

Software 

Transforming Ideas into Digital Realities

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 libraryscadnano 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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Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Innovation Council and SMEs Executive Agency (EISMEA). Neither the European Union nor the granting authority can be held responsible for them.

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