oxCloud

Running oxDNA well requires knowing quite a bit that has nothing to do with DNA nanotechnology: how to write a relaxation protocol, how to request a GPU node, how to keep an eye on a multi-day job. That's a real barrier for the experimentalists who most need simulation feedback before committing lab time to a design.

oxCloud packages the full oxDNA workflow — relaxation, equilibration, production, and analysis — into a single hosted pipeline, so a user submits a structure and gets back a relaxed, analyzed trajectory without ever writing an input file or a SLURM script by hand. It's the infrastructure layer connecting design tools upstream to oxView for visualization downstream.

The public face of this work is the GPU-backed simulation server at oxdna.org, which runs on a shared bank of NVIDIA GPUs and is free to use — the same idea at the center of the oxCloud platform, aimed at making simulation a routine step in nanostructure design rather than a specialist's task.