spatio-flux 1.2.0

A demonstration of process composition rebuilding and extending COMETS by composing functional components

Spatio-Flux: A Reference Application for Compositional Multiscale Simulation

Spatio-Flux is a reference application for compositional multiscale biological modeling built using the Process-Bigraph framework. It demonstrates how independently developed models—metabolism, spatial transport, particle dynamics, and population restructuring—can be composed into a single executable simulation through typed interfaces and shared orchestration, rather than tightly coupled solvers.

Spatio-Flux serves as the primary worked example in
Process Bigraphs and the Architecture of Compositional Systems Biology by Agmon & Spangler (arXiv:2512.23754).

---

What Spatio-Flux is

Spatio-Flux is designed as a testbed and reference implementation, not as an optimized domain-specific simulator. Its purpose is to make model composition explicit and inspectable.

In particular, Spatio-Flux demonstrates how to:

• compose heterogeneous modeling paradigms (ODEs, dFBA, spatial fields, particles),
• couple mechanisms through shared, typed state rather than direct process calls,
• coordinate multi-timescale execution using reusable orchestration patterns,
• swap or recombine processes without modifying surrounding models.

---

Automated test suite

The heart of Spatio-Flux is its automated test suite, which exercises a wide range of composition patterns using reusable process families.

Covered examples include:

• Monod and dynamic FBA metabolism
• Hybrid microbial communities
• COMETS-style spatial dFBA
• Brownian and Newtonian particle systems
• Particle–field exchange adapters
• Event-driven division and boundary handling

Each test produces:

• a process-bigraph visualization of model structure,
• serialized schemas and state for inspection,
• and domain-specific plots or animations.

Live test report:
👉 https://vivarium-collective.github.io/spatio-flux/report/index.html

---

Reference composite

The figure below shows a representative “mega-composite” integrating metabolic, spatial, mechanical, and structural processes into a single process bigraph.

---

Example simulation

Motile particles carrying internal metabolic models interact with evolving spatial nutrient fields.

---

Ecosystem

Spatio-Flux is part of Vivarium 2.0, an open-source ecosystem for compositional modeling:

• bigraph-schema — typed hierarchical schemas
• process-bigraph — process and composite simulation interfaces
• bigraph-viz — visualization of bigraph structure and data flow
• spatio-flux — reference multiscale application and test suite

All components are open source:
https://github.com/vivarium-collective