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Software

Useful software members of our organization use or maintain.

MPP software

gro

Specification and simulation of multicellular genetic programs in E. coli and yeast, developed in Eric Klavins’ lab at UW (gro home page).

NUPACK

Analysis and design of nucleic acid molecules and multistranded systems, developed in Niles Pierce’s lab at Caltech (NUPACK home page).

Xgrow

Stochastic simulation of tile-based self-assembly, developed in Erik Winfree’s lab at Caltech (Xgrow home page).

caDNAno

Computer-aided design of DNA origami nanostructures, developed in William Shih’s lab at Harvard and Shawn Douglas’s lab at UCSF (caDNAno home page).

Useful software

DNA Strand Displacement tool

Simulation of kinetics for multistranded nucleic acid systems at the secondary structure level. (DNA Strand Displacement tool)