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A chronological timeline of milestones, releases, and community events for the oxDNA ecosystem.
oxDNA release timeline
A decade of major releases across the oxDNA ecosystem, from the original coarse-grained DNA model to the latest Python interface. The numbers in brackets link to the matching entry in the references below.
- 2023
oxpy 216
The latest oxDNA release: a Python-based interface that makes simulations easier to set up, run and analyse.
- 2022
Nanobase 162
A public repository for DNA and RNA nanostructures, providing curated designs and metadata for the community.
- 2021
oxDNA.org 139
A public webserver for coarse-grained simulations of DNA and RNA nanostructures.
- 2020
oxView & OAT 103
Interactive browser-based visualisation, editing and simulation of large DNA and RNA nanostructures, together with the OxDNA Analysis Tool (OAT).
- 2019
tacoxDNA 93
A user-friendly web server for running oxDNA simulations, lowering the barrier to entry for non-specialists.
- 2018
oxDNA in LAMMPS 65
A port of the oxDNA model to the LAMMPS molecular dynamics engine, broadening accessibility and integration with other simulation tools.
- 2015
Salt-dependent oxDNA 32
Introduces improved structural properties and explicit salt dependence, making the model quantitatively predictive for ionic-strength effects.
- 2015
oxDNA on GPUs (CUDA) 25
GPU-accelerated implementation of oxDNA, enabling orders-of-magnitude speed-ups over the original CPU code.
- 2014
oxRNA 17
A nucleotide-level coarse-grained model of RNA, extending the oxDNA framework to RNA duplexes, hairpins, and strand displacement.
- 2011
Initial oxDNA 3
The original coarse-grained DNA model. Introduces the structural, mechanical and thermodynamic framework that underpins the entire ecosystem.
References
The papers referenced from the timeline above. The reference numbers match those used on the publications page.
- 3.T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011) — Structural, mechanical and thermodynamic properties of a coarse-grained DNA model (arXiv)
- 17.P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 140, 235102 (2014) — A nucleotide-level coarse-grained model of RNA (arXiv)
- 25.L. Rovigatti, P. Šulc, I. Reguly, F. Romano, J. Comput. Chem., 36, 1-8 (2015) — A comparison between parallelization approaches in molecular dynamics simulations on GPUs (arXiv)
- 32.B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye, J. Chem. Phys. 142, 234901 (2015) — Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA (arXiv)
- 65.O. Henrich, Y.A. Gutierrez-Fosado, T. Curk, T.E. Ouldridge, Eur. Phys. J. E 41, 57 (2018) — Coarse-Grained Simulation of DNA using LAMMPS (arXiv)
- 93.A. Suma, E. Poppleton, M. Matthies, P. Šulc, F. Romano, A.A. Louis, J.P.K. Doye, C. Micheletti, and L. Rovigatti, J. Comput. Chem. 40, 2586-2595 (2019) — tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami
- 103.E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang and P. Šulc, Nucleic Acids Res. 48, e72 (2020) — Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation (bioRxiv)
- 139.E. Poppleton, R. Romero, A. Mallya, L. Rovigatti and P. Šulc, Nucl. Acids Res. 49 W491–W498 (2021) — OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
- 162.E. Poppleton, A. Mallya, S. Dey, J. Joseph, P. Šulc, Nucleic Acids Res. 50, D246–D252 (2022) — Nanobase.org: a repository for DNA and RNA nanostructures
- 216.E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc and L. Rovigatti, J. Open Source Softw. 8, 4693 (2023) — oxDNA: coarse-grained simulations of nucleic acids made simple