viva-simbio
A process-bigraph wrapper for simbio that represents chemical reaction networks using Antimony or reaction specifications, rebuilds Antimony through libantimony and libSBML, and integrates the resulting ODEs with simbio's LSODA solver. Species concentrations are exposed through shared stores and emitted as additive per-step deltas.
How this model is classified mathematically and dynamically.
- Model class
- Formalism
- Determinism
- Deterministic
- Time dynamics
- Discrete
- Spatial
- Non-spatial
- Multiscale
- Yes
Organisms, entities and processes this model represents.
- Organisms
- Not recorded
- Infectious agents
- Not recorded
- Health conditions
- Not recorded
- Biological processes
- Molecular entities
- Not recorded
- Proteins / genes
- Not recorded
The data this model consumes and produces when executed.
Parameters
| Name | Default | Unit | Meaning |
|---|---|---|---|
| antimony | Not recorded | Not recorded | Antimony model string; when non-empty it takes precedence over the reaction-spec path. |
| species | {} | concentration | Mapping from species name to initial concentration for the reaction-spec path. |
| reactions | [] | Not recorded | List of mass-action reaction specifications with reactants, products, and rate. |
| volume | 1 | Not recorded | Compartment volume for the reaction-spec path. |
| interval | 0.25 | second | Composite tick size; documented examples use 0.25 seconds for two oscillators and 0.5 seconds for the repressilator. |
| k2 | 3 | per second | Brusselator X-to-Y conversion rate; the documented default is 3.0. |
| k3 | 1 | per second | Brusselator autocatalytic feedback rate. |
| k_birth | 1.1 | per second | Lotka-Volterra prey birth rate. |
| k_predation | 0.4 | per second | Lotka-Volterra predation rate. |
| a | 10 | per second | Repressilator maximum transcription rate. |
Initial conditions
| Name | Value | Unit |
|---|---|---|
| concentrations | map[string,float] | concentration |
Outputs
| Name | Quantity | Unit | Format |
|---|---|---|---|
| concentrations | concentration | concentration | Not recorded |
| demo_report | Self-contained HTML report with Plotly time-series charts, metrics, Antimony models, and architecture diagrams. | Not recorded | HTML |
Experiment protocol
The demo runs three deterministic CRN oscillators with fixed composite intervals and gathers emitter snapshots. Demonstration durations are 25.0 s (Brusselator), 40.0 s (Lotka-Volterra), and 50.0 s (repressilator).
- Timestep
- 0.25 second
- Duration
- 25 second
- Observables
- species concentrationstime
Runtime environment, dependencies, and compute requirements.
- Language
- Python >=3.12
- Environment
- pip
The reusable library is primarily imported and composed by callers; the repository's self-launching model demonstration is demo/demo_report.py. The Docker image also starts vivarium-workbench serve for the workspace dashboard.
Compute requirements
- CPU cores
- 1
- GPU
- Not required
- Parallelism
- single
Dependencies
- runtime
- bigraph-schema >=0.0.60
- process-bigraph >=0.0.66
- viva-superpowers
- simbio >=1.1.0
- antimony >=2.15 (non-linux/aarch64); ==2.14.0 (linux/aarch64)
- python-libsbml >=5.20
- numpy
- optional
- pytest
- matplotlib
- plotly
- bigraph-viz
- vivarium-workbench
- system
- build-essential
- gcc
- g++
- python3-dev
Containers
- docker · docker.io/mismplatform/envbuild@sha256:d64230847b96cbfb2c92426c0931661c3066eb8b5d2272b09688fd7348f0b531 · docker.io
Image approved · envbuild-agent · Oct 2026
Entry points
python demo/demo_report.pyRun the Brusselator, Lotka-Volterra, and repressilator demonstrations and write an HTML report.
Tests
pytestpytest tests/
Artifacts stored with this model.
Identifiers and integrity.
- Metadata review
- Approved · 1da614bf-946a-4400-a0be-4fd0f1d00f74 · Oct 2026
- Contacts
- Eran Agmon · agmon.eran@gmail.com
- Related
- Is derived fromurl:https://github.com/dyscolab/simbio
- Is derived from
- External IDs
- url:https://github.com/vivarium-collective/viva-simbio