Spatio–Flux Test Suite Report

About / Overview

Explore the Spatio–Flux test suite

This page is a catalog of executable compositions built with the Process Bigraph protocol. Each entry below is a self-contained simulation that demonstrates how distinct modeling concerns—metabolism, spatial transport, particle dynamics, and structural change—can be composed through explicit interfaces and shared state.

Rather than presenting biological conclusions, the goal of this test suite is to make model structure visible and inspectable. Clicking into a simulation lets you see how it is built: which processes are present, how they are wired to state, and how different process families combine to form more complex behaviors.

Bigraph structure

Inspect a rendered process–bigraph showing state variables, processes, and their read/write dependencies.

Interactive state

Browse serialized state trees to explore spatial fields, particles, and intermediate variables.

Dynamics & behavior

View plots and animations illustrating spatial gradients, particle motion, growth, and division.

Composition documents

Download the machine-readable process–bigraph documents that define each simulation.

Scroll down to explore individual compositions, or use the Contents section to jump to a simulation.

Spatio–Flux process families

Think of these as lego bricks for multiscale simulation. Each family does one thing well—metabolism, transport, motion, coupling, or structural change— and complex behaviors emerge by composing families rather than extending any single process.

Family	Color	Processes	Role
Metabolic processes	Metabolism	`DynamicFBA` `MonodKinetics` `SpatialDFBA`	Turns nutrients into growth. Computes uptake, secretion, and biomass production either at individual sites or across spatial grids by operating on substrate fields and biomass variables.
Field transport	Transport	`DiffusionAdvection`	Makes space matter. Updates dissolved species fields via diffusion and advection, so local metabolic activity can influence distant regions over time.
Particle movement	Movement	`BrownianMovement` `PymunkParticleMovement`	Moves agents through continuous space. Brownian motion provides stochastic movement; Newtonian motion adds mass, velocity, inertia, friction, and elastic interactions.
Particle–field coupling	Coupling	`ParticleExchange`	Bridges discrete and continuous. Mediates bidirectional exchange between particle-local state and spatial fields, syncing internal particle chemistry with nearby lattice values.
Structural and boundary processes	Rewrite	`ParticleDivision` `ManageBoundaries`	Changes the population. Rewrites the particle store by creating, removing, or relocating particles in response to conditions like growth thresholds or boundary crossings.

Vivarium 2.0 ecosystem

Spatio–Flux is a reference application in the Vivarium 2.0 software suite: an open-source ecosystem for building, executing, and visualizing Process–Bigraph compositions.

bigraph-schema — Defines a compositional type system and hierarchical data structures using JSON-based schemas. Provides the type engine, schema compilation, state validation, and type-specific update operators used in process–bigraph delta semantics.
process-bigraph — The dynamic core. Defines typed Process and Composite abstractions, event scheduling, global time management, and orchestration logic for executing process–bigraph documents.
bigraph-viz — Parses process–bigraph documents and renders their structure as inspectable graphs.
spatio-flux — A domain-specific application repository implementing concrete process families for metabolism, spatial fields, particle dynamics, and particle–field coupling, with an extended test suite of executable compositions.

References

Total sim time: 454.96s Generated: 2026-01-03T18:43:25

How to read the bigraph visualization

Each diagram is a map of a composite simulation: what state exists, what processes run, and how data flows between them.

1) Nodes

Circles are state (variables or structured stores). Boxes are processes (update rules that run on a schedule).

2) Edges

Edges show read/write dependency: a process reads state to compute updates, and writes deltas back into state.

3) Hierarchy

Big nodes often contain nested nodes. That nesting reflects the hierarchical state tree (e.g., collections, sub-stores, or typed substructures).

4) A quick way to scan

Start by locating the main stores (large circles), then follow edges into the processes that touch them. The “story” is the loop: state → process → state.

Tip: If a diagram feels busy, focus on one store (fields or particles), then trace only the processes connected to it. The report sections below let you compare structure (bigraph), serialized state (JSON viewer), and behavior (plots/GIFs) side-by-side.

monod_kinetics

Field-only baseline: Monod uptake/growth on a well-mixed substrate pool (no spatial lattice, no particles). Use to sanity-check kinetics + mass balance.

Runtime: 0.56 seconds

Spatio–Flux Test Suite Report

Explore the Spatio–Flux test suite

Bigraph structure

Interactive state

Dynamics & behavior

Composition documents

Spatio–Flux process families

Vivarium 2.0 ecosystem

References

1) Nodes

2) Edges

3) Hierarchy

4) A quick way to scan

monod_kinetics

monod_kinetics_state.json

monod_kinetics_viz.png

monod_kinetics.png

ecoli_core_dfba

ecoli_core_dfba_state.json

ecoli_core_dfba_viz.png

ecoli_core_dfba.png

ecoli_dfba

ecoli_dfba_state.json

ecoli_dfba_viz.png

ecoli_dfba.png

yeast_dfba

yeast_dfba_state.json

yeast_dfba_viz.png

yeast_dfba.png

community_dfba

community_dfba_state.json

community_dfba_viz.png

community_dfba.png

dfba_kinetics_community

dfba_kinetics_community_state.json

dfba_kinetics_community_viz.png

dfba_kinetics_community.png

spatial_many_dfba

spatial_many_dfba_state.json

spatial_many_dfba_viz.png

spatial_many_dfba_timeseries.png

spatial_many_dfba_video.gif

spatial_dfba_process

spatial_dfba_process_state.json

spatial_dfba_process_viz.png

spatial_dfba_process_model_grid.png

spatial_dfba_process_timeseries.png

spatial_dfba_process_video.gif

diffusion_process

diffusion_process_state.json

diffusion_process_viz.png

diffusion_process_video.gif

brownian_particles

brownian_particles_state.json

brownian_particles_viz.png

brownian_particles_mass.png

brownian_particles_particles_traces.png

brownian_particles_snapshots.png

brownian_particles_video.gif

br_particles_kinetics

br_particles_kinetics_state.json

br_particles_kinetics_viz.png

br_particles_kinetics_mass.png

br_particles_kinetics_particles_traces.png

br_particles_kinetics_snapshots.png

br_particles_kinetics_video.gif

br_particles_dfba

br_particles_dfba_state.json

br_particles_dfba_viz.png

br_particles_dfba_mass.png

br_particles_dfba_snapshots.png

br_particles_dfba_timeseries.png

br_particles_dfba_video.gif

comets_diffusion

comets_diffusion_state.json

comets_diffusion_viz.png

comets_diffusion_snapshots.png

comets_diffusion_timeseries.png

comets_diffusion_video.gif

comets_br_particles_kinetics