Apache Airavata Cerebrum, an Integrated Neuroscience Computational Framework

Contents

• Introduction
• Key Features
• Installation
• Examples
• Contributing

Introduction

Airavata Cerebrum is an open-source framework that provides tools to simplify building whole brain models via integration of data collected from cellular-level brain atlases. Cerebrum modules allow for accelerated 'data to model' workflows that are flexible to update, and straight-forward to reproduce.

Key Features

• Integration of Brain Atlases: Transparently connect to publicly available cellular-level brain atlases via a single, accessible platform.
• Model Consruction Workflows: Workflows to collect/filter/combine data from different databases and construct whole brain scale models.
• Model Editor: Utilties for simple edits
• Open-Source Framework: Developing a user-friendly, open-source environment for neuroscience research.
• Streamlined Environment: A lightweight, efficient framework that is interactively accessible via jupyter/marimo notebooks.

Install Airavata Cerebrum

NOTE:: Some of the example notebooks provided at the github source repo might require additional dependencies. Please consult the documentation in the examples/README.md for the respective examples or the jupyter notebooks.

Airavata Cerebrum requires python v3.10 environment. It is currently tested only in the Linux operating system. To install from the source, we recommend creating a conda environment using miniforge as below:

conda config --add channels conda-forge
conda create -n cerebrum python=3.10 nodejs
conda activate cerebrum

To install Airavata Cerebrum from source into the environment created above, install from pypi using pip.

pip install airavata-cerebrum

Example Usage

The examples directory in our github repo contains a set of notebooks and scripts that demonstrate the capabilities of Cerebrum. Both the notebooks and standalone batch scripts instruct the use of Cerebrum in building/simulating large-scale neuroscience models. Please refer to examples/README.md for additional installation requirements to run the notebooks.

Contributing

Issues and PRs are welcome — especially from neuroscience researchers on real models. See CONTRIBUTING.md for software design, source layout, and dev setup. Bug reports and enhancement requests go in the issue tracker.

License

Apache 2.0