Contact / obtain code and data
Royal School of Mines Room 4.37
Department of Bioengineering
Imperial College London, South Kensington Campus
We're happy to share all of our code and data with anyone who's interested; please email Tom for information.
- 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.