Process Bigraphs and the Architecture of Compositional Systems Biology

TL;DR

This paper introduces Process Bigraphs, a framework for composing and simulating multiscale biological models with clear interfaces, hierarchical data, and orchestration, demonstrated through the Vivarium 2.0 implementation and Spatio-Flux application.

Contribution

It presents Process Bigraphs as a novel formal framework for multiscale biological model composition, enhancing clarity, reuse, and extensibility over existing tools.

Findings

Implemented Vivarium 2.0 as an open-source framework.

Demonstrated integration of kinetic ODEs, flux analysis, and spatial processes.

Improved model clarity and reusability in multiscale biological simulations.

Abstract

Building multiscale biological models requires integrating independently developed submodels, which involves sharing variables and coordinating execution. Most existing tools focus on isolated mechanisms and numerical methods, but rarely specify model interfaces: which variables are read or written, how they are translated, or how updates are synchronized. We present Process Bigraphs, a framework for composing and simulating multiscale biological models. Process Bigraphs generalize architectural principles from the Vivarium software into a shared specification that defines process interfaces, hierarchical data structures, composition patterns, and orchestration patterns. The paper describes the organization of the framework and explains how it improves model clarity, reuse, and extensibility; formal definitions are provided in the Supplementary Materials. We introduce Vivarium 2.0 as an open-source implementation of the Process Bigraph framework and demonstrate its utility with Spatio-Flux, a standalone library for microbial ecosystem simulations that integrate kinetic ODEs, dynamic flux balance analysis, and spatial processes. We conclude by discussing implications for emerging standards in multiscale modeling. Availability and implementation: Vivarium 2.0 is an open-source suite of libraries including: (1) bigraph-schema for hierarchical, JSON-based data typing; (2) process-bigraph for defining process interfaces and executing composite simulations; (3) bigraph-viz for interactive visualization of system structure and data flow; and (4) spatio-flux, the reference application used in this work. Detailed descriptions are provided in the Supplementary Materials. All software is available at https://github.com/vivarium-collective