Contact / obtain code and data
Thomas Ouldridge
Royal School of Mines Room 4.37
Department of Bioengineering
Imperial College London, South Kensington Campus
SW7 2AZ
t.ouldridge@imperial.ac.uk
We're happy to share all of our code and data with anyone who's interested; please email Tom for information.
General releases:
- We have uploaded a general package of introductory tutorials of oxDNA alongwith a primer on how to setup initial simulations.
- If you're interested in the oxDNA model, please head to this wiki. You'll find the model implemented with simulation code and plenty of documentation. oxDNA is also available as a LAMMPS package: https://doi.org/10.5281/zenodo.3543743.
- A compiler for our ACDC system of nucleic acid-based catalytic activation networks can be downloaded from here: https://doi.org/10.5281/zenodo.3838080
- For the adventurous, the code for our domain-level model of origami folding can be found here.
Code and data for specific publications:
Over the last few years we've been releasing all the raw data/processing scripts/code that is used to generate figures in our work. Typically, these files are uploaded to Zenodo. Please look for the link in the relevant paper. If you can't find what you're looking for, please get in contact. In adidtion:
- Code for the data and analysis of "Designing the Optimal Bit: Balancing Energetic Cost, Speed and Reliability" can be downloaded from here.
- Code for the data and analysis of "High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits" can be downloaded from here.