oxView

Simulation output is only useful if someone can actually look at it. Before a browser-based option existed, inspecting an oxDNA trajectory meant installing a desktop viewer, wrangling file formats, and losing the ability to just send a colleague a link.

oxView renders DNA/RNA nanostructures directly in WebGL: load a topology and configuration, scrub through a trajectory frame by frame, select and edit individual strands — extend, nick, or ligate them — and export the result. Through oxServe, it can also drive a live oxDNA simulation on a connected server and stream the results back over a WebSocket in real time, so relaxing a freshly designed structure becomes an interactive loop instead of a submit-and-wait job.

My contributions have centered on the parts of oxView that talk to oxDNA itself: keeping the viewer in step with engine-side changes like non-singular masses and newer CUDA backends, and — more recently — an oxView LLM mode built by fine-tuning the Qwen model, so structure generation, relaxation, simulation, and analysis can be driven through natural-language prompts instead of the GUI.

For a field where the design–simulate–redesign loop used to require real computational expertise, oxView collapses most of that loop into a browser tab. It's the shared interface referenced in the paper describing oxView, oxCloud, and nanobase as one connected ecosystem for simulating, analyzing, and sharing nucleic acid nanostructures.