Getting Started | Upgrade | Releases | Status

NeuroAnnotation Toolbox (NAT)

Python module to use the annotations created with NeuroCurator, for example in a Jupyter notebook.

This framework has been described in details in the following open-access paper: https://doi.org/10.3389/fninf.2017.00027.

NAT provides the necessary functions and utilities to:

• reliably annotate the neuroscientific literature,
• curate published values for modeling parameters,
• save them in reusable corpora.

Getting Started

Installation

After having installed the requirements:

pip3 install nat

Before, you might want to create a dedicated environment with conda:

conda create --name nat_env python=3.7
conda activate nat_env

Requirements

• Python 3.5+
• Git 1.7.0+ (GitPython)
• Miniconda (optional)

Python dependencies

• Beautiful Soup 4
• GitPython
• lxml
• NumPy
• pandas
• parse
• dateutils
• Pyzotero
• quantities
• requests
• SciPy

Upgrade

pip3 install --upgrade nat

If you have used conda, activate the environment before:

conda activate nat_env

Releases

Versions and their notable changes are listed in the releases section.

Status

Created during 2016.

Ongoing stabilization and reengineering in the branch refactor-architecture.

The branch refactor-architecture is not intended to be used by end-users.

New features, bug fixes and improvements are done on the reengineered code sections.

When a reengineered code section is stable, it's merged into the branch master and a release is published.