viva-amici
Citation: No publication identified in inspected sources
A process-bigraph bridge that compiles Antimony or SBML models into AMICI per-model C++/SWIG extensions and integrates them with SUNDIALS CVODES, exposing time-stepped and one-shot simulation processes plus exponential-decay, Lotka-Volterra, and MAPK cascade composites.
How this model is classified mathematically and dynamically.
- Model class
- Formalism
- Determinism
- Deterministic
- Time dynamics
- Discrete
- Spatial
- Non-spatial
- Multiscale
- No
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 |
|---|---|---|---|
| interval | 0.5 | time unit | Per-step integration window. |
| k | 0.2 | rate unit | First-order decay rate constant. |
| alpha | 1.1 | rate unit | Prey birth rate. |
| beta | 0.4 | rate unit | Predation rate. |
| d_gain | 0.1 | rate unit | Predator growth per prey eaten. |
| signal | 1 | dimensionless unit | Input signal driving KKK activation. |
| k1 | 0.05 | rate unit | Activation rate from signal to KKK. |
| k2 | 0.15 | rate unit | Activation rate from KKK to KK. |
| k3 | 0.15 | rate unit | Activation rate from KK to K. |
| rtol | 1e-8 | dimensionless unit | CVODES relative tolerance. |
Initial conditions
| Name | Value | Unit |
|---|---|---|
| model state stores | Species/state values supplied through the states port; examples include A=10, prey=10, predator=5, and KKK/KK/K=0. | dimensionless unit |
Outputs
| Name | Quantity | Unit | Format |
|---|---|---|---|
| state trajectories | Per-step state deltas emitted by AmiciProcess and collected by the RAMEmitter. | Not recorded | in-memory map |
| observables | Derived observable deltas such as predator/prey ratio, total population, downstream MAPK signal, and amplification. | Not recorded | in-memory map |
| demo report | Self-contained HTML report containing Plotly time-series charts, architecture diagrams, and the PBG document tree. | Not recorded | HTML |
Experiment protocol
The demo runs exponential decay for 20 time units, Lotka-Volterra for 40 time units, and MAPK cascade for 80 time units through fixed per-step intervals.
- Timestep
- 0.5 time unit
- Duration
- 40 time unit
- Observables
- statesobservables
Runtime environment, dependencies, and compute requirements.
- Language
- Python >=3.11
- Environment
- native
The first unique model source compiles a C++ extension and is reported as approximately 10 seconds in the README; later runs use the AMICI cache.
Compute requirements
- CPU cores
- 1
- GPU
- Not required
- Parallelism
- single
- Typical runtime
- 10 seconds
Dependencies
- runtime
- bigraph-schema >=0.0.60
- process-bigraph >=0.0.66
- amici >=1.0
- antimony >=2.13
- numpy
- bigraph-viz >=2.0.3
- pyyaml >=6.0
- jsonschema >=4.21
- jinja2 >=3.1
- pypdf >=4.0
- matplotlib
- plotly
- vivarium-workbench
- ninja
- optional
- pytest
- system
- C/C++ compiler toolchain
- SWIG
- CMake
- Ninja
- BLAS/LAPACK
- HDF5
Containers
- docker (Dockerfile)
Entry points
python demo/demo_report.pyRun the three AMICI-driven composite simulations and write the self-contained HTML demo report.
Tests
pytestpytest tests/
Artifacts stored with this model.
Identifiers and integrity.
- Metadata review
- Approved · 1da614bf-946a-4400-a0be-4fd0f1d00f74 · Oct 2026
- Contacts
- viva-amici authors · noreply@example.com
- Related
- Is derived fromurl:https://github.com/AMICI-dev/AMICI
- Is derived from
- External IDs
- url:https://github.com/vivarium-collective/viva-amici