Spatio-Flux
Citation: Process Bigraphs and the Architecture of Compositional Systems Biology
Spatio-Flux composes independently developed processes including metabolism, spatial transport, particle dynamics, and structural rewrites into executable simulations through typed interfaces and shared orchestration.
How this model is classified mathematically and dynamically.
- Determinism
- Hybrid
- Time dynamics
- Discrete
- Spatial
- 2D
- Multiscale
- Yes
Organisms, entities and processes this model represents.
- Organisms
- Infectious agents
- Not recorded
- Health conditions
- Not recorded
- Biological processes
- Proteins / genes
- Not recorded
The data this model consumes and produces when executed.
Parameters
| Name | Default | Unit | Meaning |
|---|---|---|---|
| total_time | 100 | second | Configured simulation duration |
| bounds | [10,20] | Not recorded | Spatial domain extent |
| n_bins | [8,16] | Not recorded | Two-dimensional grid resolution |
| field_diffusion_rate | 0.1 | Not recorded | Diffusion coefficient for fields |
| n_particles | 10 | Not recorded | Initial particle count |
| particle_diffusion_rate | 0.1 | Not recorded | Particle Brownian diffusion rate |
| particle_add_rate | 0.3 | Not recorded | Boundary particle addition rate |
| glucose_Km | 1 | Not recorded | Monod half-saturation parameter for glucose |
| glucose_vmax | 0.1 | Not recorded | Maximum glucose uptake rate |
Initial conditions
| Name | Value | Unit |
|---|---|---|
| initial_min_max | {"acetate":[0,0],"glucose":[10,10],"detritus":[0,0],"dissolved biomass":[0,0.1]} | Not recorded |
| particle_mass | [0.001,1] | Not recorded |
Data inputs
| Name | Format | Required | Purpose |
|---|---|---|---|
| SBML metabolic model | XML | Optional | COBRApy dFBA model input |
Outputs
| Name | Quantity | Unit | Format |
|---|---|---|---|
| state trajectories | Time-indexed process state including fields, biomass, and particles | Not recorded | JSON |
| structure artifacts | Serialized schemas and state plus process-bigraph diagrams | Not recorded | PNG |
| analysis charts | Domain-specific plots and animations | Not recorded | Not recorded |
Experiment protocol
A study loads a baseline composite, runs it for a configurable duration, flushes analysis outputs, and persists a trajectory in a per-study run store.
- Timestep
- 1 second
- Duration
- 60 second
- Observables
- process statefieldsbiomassparticles
Runtime environment, dependencies, and compute requirements.
- Language
- Python >=3.11,<3.13
- Environment
- native
Vivarium-style process/composite tiers are implemented through process-bigraph and pbg-superpowers; the canonical current runner is scripts/reproduce.py.
Compute requirements
- GPU
- Not required
- Parallelism
- multi-process
Dependencies
- runtime
- bigraph-schema >=1.4.3
- process-bigraph >=1.8.5
- bigraph-viz
- cobra
- highspy
- imageio
- ipython
- matplotlib
- pbg-superpowers >=0.16
- pymunk
- scipy
- optional
- build
- pytest
Containers
- docker · docker.io/mismplatform/envbuild@sha256:a3e1407ab5f4ed7ed7036f3a1835e0e2d8887265ffbe95dcf04a1ed55811976b · docker.io
Image approved · envbuild-agent · Oct 2026
Entry points
python scripts/build_report.pyBuild the HTML report
- --out
python scripts/reproduce.pyReproduce all 19 studies and build the report
- --only
- single study slug
- --out
- report output path
python spatio_flux/runners/run_study.py <SLUG>Run one study
- SLUG
- TIME
python scripts/build_all_figures.pyBuild figure assets
- --all
- --dry-run
- --only
- --force
- --promote
- --base
python scripts/build_paper_figures.pyStitch paper figure panels
- --study
python scripts/export_plos_tifs.pyExport PLOS TIFF figures
- --out
python scripts/export_figure_composites.pyExport figure composites
- --check
python scripts/sync_loom_views.pySynchronize loom views
- --promote
- --seed
- --id
python scripts/verify_reference.pyVerify reference studies
- --baseline
- --no-write
- --eval-only
- slugs
python scripts/scaffold_studies.pyScaffold studies
python scripts/build_fig07bcd_plots.pyBuild Fig. 7 plots
python scripts/build_fig08b_snapshots.pyBuild Fig. 8 snapshots
python scripts/build_figure1.pyBuild Figure 1
python scripts/build_figure2.pyBuild Figure 2
python scripts/build_figure7.pyBuild Figure 7
python scripts/build_figure8.pyBuild Figure 8
python scripts/build_figures_site.pyBuild figures site
- workspace
- output
python scripts/figure_pipeline.pyRun figure pipeline
python scripts/export_draft_composites.pyExport draft composites
python scripts/fig08_reference_gif.pyBuild reference GIF
python spatio_flux/experiments/compare_comets.pyCompare Spatio-Flux with COMETS
- --mode
- --ray-address
- --n-shards
- --solver
python spatio_flux/experiments/figure_A.pyRun Figure A experiment
python spatio_flux/experiments/figure_B.pyRun Figure B experiment
python spatio_flux/experiments/overview_fig.pyBuild overview figure
python spatio_flux/processes/dfba.pyRun dFBA process demonstration
python spatio_flux/processes/pymunk_particles.pyRun Pymunk particle demonstration
python tools/capture_baseline_doc.py <NAME>Capture a baseline composite document
- NAME
Tests
pytestpytest tests/
Artifacts stored with this model.
Identifiers and integrity.
- Metadata review
- Approved · 07ab255c-9ada-4d33-9f49-66cc6277d9f2 · Oct 2026
- External IDs
- url:https://github.com/vivarium-collective/spatio-flux