Process Bigraphs and the Architecture of Compositional Systems Biology

Abstract

Building multiscale biological models requires the integration of independently developed submodels, which means moving shared variables between them and coordinating when each submodel runs. Existing tools typically address isolated biological mechanisms with specific numerical methods, rarely specify which variables each model reads and writes, how those variables are translated, and how model updates are synchronized. We present Process Bigraph, a framework for composing and simulating multiscale models. Process Bigraph generalize the architectural ideas previously used in the Vivarium software into a shared specification that describes process interfaces, hierarchical data structures, composition patterns, and orchestration patterns. The paper explains how the framework is organized and why it makes biological models easier to understand, reuse, and build on; the Supplementary Materials provides the formal specification. We introduce Vivarium 2.0 as an open-source implementation of the process bigraph framework. We demonstrate its utility with Spatio-Flux, a standalone library of microbial ecosystem simulations that combine kinetic equations, dynamic flux balance analysis, and different spatial processes. These simulations illustrated how the framework effectively integrates diverse biological processes, leading to emergent spatially organized population dynamics. Finally, we discuss implications for emerging multiscale modeling standards.

16 pages, 7 figures, Supplementary Materials available