Specification and simulation of multicellular genetic programs in E. coli and yeast, developed in Eric Klavins’ lab at UW (gro home page).
Analysis and design of nucleic acid molecules and multistranded systems, developed in Niles Pierce’s lab at Caltech (NUPACK home page).
Stochastic simulation of tile-based self-assembly, developed in Erik Winfree’s lab at Caltech (Xgrow home page).
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).
DNA Strand Displacement tool
Simulation of kinetics for multistranded nucleic acid systems at the secondary structure level. (DNA Strand Displacement tool)