ReferencesOverview

Reference

Reference pages for the biosimulant Python runtime and its CLI. Use this page to pick the right interface, then follow the links for lifecycle and data-contract details.

Looking for step-by-step instructions? See the How-To Guides.

Installation

pip install "biosimulant>=0.0.26"

ExecutionPolicy, ExecutionContext, and the execute() hook need 0.0.26 or later. The local lab UI ships with the default install. The old ui extra was removed in 0.0.15.

To install from a Git ref instead of PyPI:

pip install "biosimulant @ git+https://github.com/Biosimulant/biosim.git@<ref>"
biosimulant labs serve ./my-lab

For curated model packs, see the companion repo: github.com/Biosimulant/models

Local runtime

Use the open-source runtime to build and run simulations on your machine or in your own CI:

from biosimulant import BioWorld
from biosimulant.hub import HubComposition
 
world = BioWorld(communication_step=0.1)
composition = HubComposition(world, lab_root="./lab")

BioWorld and BioModule are the core local composition interface. HubComposition explicitly resolves exact, lockfile-pinned Hub Labs into that same local world; it never turns a Python import into a network request.

Client and AsyncClient are separate. They submit a versioned Hub Lab as a managed run and need an API key. See the Developer API.

Architecture

┌─────────────────────────────────────────────────────────────┐
│                       BioWorld                               │
│           (Orchestrator + Event Queue)                       │
│                                                              │
│  Events: STARTED → STEP* → FINISHED                          │
└─────────────────────────────┬───────────────────────────────┘
                              │
         ┌────────────────────┼────────────────────┐
         │                    │                    │
         ▼                    ▼                    ▼
┌─────────────────┐  ┌─────────────────┐  ┌─────────────────┐
│   BioModule     │  │   BioModule     │  │   BioModule     │
│  (Neuron Pop)   │  │  (Monitor)      │  │  (Metabolism)   │
│                 │  │                 │  │                 │
│ in: current     │  │ in: spikes      │  │ in: params      │
│ out: spikes     │──│                 │  │ out: species    │
└─────────────────┘  └─────────────────┘  └─────────────────┘
         │                                         │
         └─────────────── BioSignals ──────────────┘
Package & PublishHow Biosimulant Works