  We present a new technique for rapid modeling and construction of
scientifically accurate mesoscale biological models. Resulting 3D models are
based on few 2D microscopy scans and the latest knowledge about the biological
entity represented as a set of geometric relationships. Our new technique is
based on statistical and rule-based modeling approaches that are rapid to
author, fast to construct, and easy to revise. From a few 2D microscopy scans,
we learn statistical properties of various structural aspects, such as the
outer membrane shape, spatial properties and distribution characteristics of
the macromolecular elements on the membrane. This information is utilized in 3D
model construction. Once all imaging evidence is incorporated in the model,
additional information can be incorporated by interactively defining rules that
spatially characterize the rest of the biological entity, such as mutual
interactions among macromolecules, their distances and orientations to other
structures. These rules are defined through an intuitive 3D interactive
visualization and modeling feedback loop. We demonstrate the utility of our
approach on a use case of the modeling procedure of the SARS-CoV-2 virus
particle ultrastructure. Its first complete atomistic model, which we present
here, can steer biological research to new promising directions in fighting
spread of the virus.

Quantitative Methods