Software for labwork: 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-design
SST-sequence-design is a DNA sequence design and analysis tool for designing single-stranded DNA tiles.
- SST-sequence-design on github
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 thermodynaamic principles as SST-sequence-design but allows specification of much more general DNA systems and has an easier to program interface.
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