Software tools
As part of our research efforts, we develop tools for computer simulation, analysis and visualization. Most of the tools that we develop can be found on our
github account.
OxDNA and OxRNA
We codevelop oxDNA simulation package. The package is hosted on
sourceforge repository, and documentation is provided on
dna.physics.ox.ac.uk
ANM-oxDNA/oxRNA
An extension of oxDNA/oxRNA models that also allows you to represent proteins. It can be downloaded
here, for examples of use check this
tutorial.
oxDNA/oxRNA simulation analysis
A new set of Python tools for automated analysis of large nanostructure simulations. The scripts with documentation and examples are provided
here.
oxView.org
A new tool for interactive visualization, editing and analysis of DNA and RNA nanostructures. Very fast, user-friendly and platform independent. Runs in
any web-browser with JavaScript support.
Check it out!
Online services
oxDNA.org
A new
server for simulation analysis and simulations of nucleic acid nanostructures. It is equipped with 8 NVIDIA RTX 2080Ti GPUs and free to use.
nanobase.org
A repository
server for deposition of DNA, RNA and protein-DNA hybrid nanostructure designs, with the incentive to provide a resouce where all nanostructures can be shared in a common format.
Tutorials
Most of our tools are fully documented on our
github account. Also check out
oxDNA tutorial youtube channel.
Outreach
Nano Building Game:
An outreach
game designed to illustrate principles of designed systems for self-assembly
