Compose Hub Labs Locally

Use a version-pinned public Hub Lab with your own local BioModule instances in one BioWorld. The dependency is resolved explicitly and stored only with the parent Lab.

Pin the Hub Lab

Declare the child in lab.yaml with an exact version:

children:
  - alias: medium
    package: your-namespace/nutrient-medium
    version: "1.1.0"

Add the matching archive checksum in the sibling biosimulant.lock:

lock_version: 1
dependencies:
  - package: your-namespace/nutrient-medium
    version: "1.1.0"
    artifact_sha256: "<64-character archive SHA-256 from Hub>"

Every package-backed child needs one matching lock entry. This checks the bytes of the downloaded .bsilab, preventing a changed artifact from being accepted under the same version.

Run it beside local code

from biosimulant import BioWorld
from biosimulant.hub import HubComposition
 
world = BioWorld(communication_step=0.1)
world.add_biomodule("controller", DoseController())  # Your local BioModule.
 
composition = HubComposition(world, lab_root="./lab")
composition.add("medium", "your-namespace/nutrient-medium@1.1.0")
composition.apply()
composition.setup()
world.run(duration=24.0)

apply() verifies and resolves the Hub Lab, then flattens it into the same world. setup() initializes both the resolved Lab and modules you added with world.add_biomodule(...). Add composition.connect(...) only when you know the child Lab’s exposed io ports and their signal types.

Dependency state

For a source Lab, payloads resolve into that Lab only:

lab/.biosimulant/dependencies/

The first resolution needs Hub access. Later runs reuse the verified local copy. Deleting the directory causes a clean re-resolution without changing any other Lab; ordinary packages exclude this operational state.

For a standalone archive, state is created beside the archive under .biosimulant/<archive-name>.dependencies/. Use a writable override when the archive directory is read-only:

biosimulant labs run dist/my-lab.bsilab --dependency-root /tmp/my-lab-state

Vendor an archival release

Normal releases retain the compact package references and lockfile. For a fully self-contained, offline archive, vendor every locked child:

biosimulant labs package ./lab --out dist --vendor-dependencies

Use this for archival, regulated, or air-gapped distribution; use normal package references while actively composing and developing a Lab.