airavata-cerebrum 0.1.3

Apache Airavata Cerebrum : Integrated Data-driver Modeling for Computational Neuroscience

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

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