bio-compose

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:

HIGH-LEVEL bio_compose API:

The primary method of user-facing interaction for this service is done through the use of a high-level "notebook" api called bio_check. A convenient notebook demonstrating the functionality of this service is hosted on Google Colab and can be accessed by clicking the above "Open In Colab" badge.

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

Smoldyn to Simularium conversion:

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

FOR DEVELOPERS:

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