Biological simulations are among the most information-dense artifacts in science. They also tend to be among the hardest to share. Simularium was built to change that.
Most computational biology tools run on specialized hardware, require specific software, and demand a certain fluency to operate. The result is that a simulation is often accessible only to the person who ran it — which limits collaboration, peer review, and public communication of findings.
From file to browser
Simularium defines an open file format that simulations from diverse tools can be exported to, and a web viewer that renders them interactively — step through time, filter agents, change visual encoding, examine individual molecules. No install. Just a link.
The paper was published in Nature Methods in 2022, with a team spanning the Allen Institute and collaborating institutions. The viewer is open source and actively used by researchers sharing models that would previously have required a live demo to communicate.