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:
- Code to generate all the setup files and the analysis files used in our recent paper A Primer on the oxDNA Model of DNA can be downloaded from https://zenodo.org/record/4809769.
- Code to generate the plots in "Edge-effects dominate copying thermodynamics for finite-length molecular oligomers" can be downloaded from here: https://doi.org/10.5281/zenodo.3901184.
- Initialization files, output data and processed data for the oxDNA simulations from "Modelling DNA-strand displacement reactions in the presence of base-pair mismatches" can be downloaded from here: https://doi.org/10.5281/zenodo.3655218.
- Raw data, processed data and processing scripts for the experimental data presented in "Handhold-mediated strand displacement: a nucleic acid-based mechanism for generating far-from-equilibrium assemblies through templated reactions" can be downloaded from here: https://doi.org/10.5281/zenodo.3832588.
- Raw and processed data, from both simulations and experiment, for the paper "Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement" can be donloaded from here: https://doi.org/10.5281/zenodo.3731499. Also included are scripts used to process and fit the experimental data.
- Code to reproduce the figures in "Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration" can be found here: https://doi.org/10.5281/zenodo.2656526.
- Code for the simulations in Coarse-grained modelling of strong DNA bending II: Cyclization can be downloaded from https://doi.org/10.5281/zenodo.1753767
- Code for data generation and analysis in Biochemical Szilard engines for memory-limited inference can be downloaded from https://zenodo.org/record/2536384
- 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.