BioCompose: Create, execute, and introspect reproducible composite simulations of dynamic biological systems.

This service utilizes separate containers for REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance.

Documentation:

The complete BioCompose documentation can be found here: https://bio-compose.readthedocs.io/en/latest/

Getting Started:

We recommend using poetry to install this tooling. Installation of this tooling can be performed using PyPI as such:

pip install bio-compose

Alternatively, the REST API can be accessed via Swagger UI here: https://biochecknet.biosimulations.org/docs

IMPORTANT NOTES:

• Poetry is used as the environment manager. Poetry uses a globally referenced configuration whose cache setup may lead to permission errors when running poetry install. In the event that such errors exist, run the following:

poetry config cache-dir ~/poetry-cache
mkdir -p ~/poetry-cache
chmod -R u+w ~/poetry-cache

# then install the project:
poetry install

• If you are using the jupyter notebooks found within /tests, you must link the environment (in this case poetry) to the notebook's kernel. Take the following steps to ensure such linking occurs:

# in the case of running (poetry config virtualenvs.in-project true), the env name will be .venv
poetry run python -m ipykernel install --user --name=$ENV_NAME --display-name "$ENV_NAME"

Smoldyn to Simularium conversion:

A convenient template notebook for converting the outputs of Smoldyn simulations to Simularium trajectories can be found here.