Reference
API reference for the Biosimulant Python library.
Looking for step-by-step instructions? See the How-To Guides for task-oriented walkthroughs like creating a BioModule, composing simulations, and packaging models.
Installation
pip install "biosimulant @ git+https://github.com/Biosimulant/biosim.git@<ref>"Optional extras:
pip install "biosimulant[ui] @ git+https://github.com/Biosimulant/biosim.git@<ref>"For curated model packs, see the companion repo: github.com/Biosimulant/models
Architecture
┌─────────────────────────────────────────────────────────────┐
│ BioWorld │
│ (Orchestrator + Event Queue) │
│ │
│ Events: STARTED → TICK* → FINISHED │
└─────────────────────────────┬───────────────────────────────┘
│
┌────────────────────┼────────────────────┐
│ │ │
▼ ▼ ▼
┌─────────────────┐ ┌─────────────────┐ ┌─────────────────┐
│ BioModule │ │ BioModule │ │ BioModule │
│ (Neuron Pop) │ │ (Monitor) │ │ (Metabolism) │
│ │ │ │ │ │
│ in: current │ │ in: spikes │ │ in: params │
│ out: spikes │──│ │ │ out: species │
└─────────────────┘ └─────────────────┘ └─────────────────┘
│ │
└─────────────── BioSignals ──────────────┘API Reference
- BioModule API: Base interface for all composable simulation components.
- BioWorld API: Central orchestrator: lifecycle, events, scheduling.
- WiringBuilder API: Declarative composition: add modules and connect ports.
- BioSignal & Metadata: Message passing between modules.
Schemas
- model.yaml Schema: BioModule manifest format reference.
- lab.yaml Schema: Composed simulation manifest format reference.
Tools & Extensions
- Visualization Contract: Standard format for module visualization output.
- Domain Packs: Pre-built modules for neuroscience and ecology.
- SimUI: Python-declared web interface for local simulations.