neurocurator 0.4.3

Application to perform curation of neuroscientific literature.

Getting Started | Releases | Status

NeuroCurator

Desktop application to perform systematic and collaborative curation of neuroscientific literature.

This is a Graphical User Interface (GUI) for the Python package NeuroAnnotation Toolbox (NAT).

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

With NeuroCurator, annotations are: - traceable, - reusable across projects, - structured with controlled vocabularies.

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Getting Started

Requirements:

System side:

• Git 1.7.0+

• ImageMagick 6

• Python 3.4*

• Qt 4.8.7*

• Miniconda*

Python side:

• NAT

• PySide 1.2.4

• NumPy

• pandas

• Wand

*Miniconda is not required. It simplifies only temporary the installation: no need to compile Qt and to install manually Python 3.4. It also makes the installation easier on Windows (pandas).

Installation:

Instructions for macOS 10.13+, Ubuntu 16.04+, Windows 10+.

1 - Create a virtual environment with Python 3.4:

conda create -y --name nc python=3.4

2 - Switch to the virtual environment:

On macOS and Linux:

source activate nc

On Windows:

activate nc

3 - Install PySide 1.2.4 and Qt 4.8.7 fromconda-forge:

conda install -y pyside --channel conda-forge

4 - Install NAT:

On macOS and Linux:

pip install nat

On Windows:

conda install -y pandas
pip install beautifulsoup4 gitpython lxml numpy parse pyzotero quantities scipy wand
pip install nat --no-deps

5 - Install NeuroCurator:

pip install neurocurator --no-deps

Use

Launch NeuroCurator:

neurocurator

For the future uses: 1. enter the virtual environment: source activate nc or activate nc 2. launch NeuroCurator: neurocurator 3. use NeuroCurator 4. close NeuroCurator 5. exit the virtual environment: source deactivate or deactivate

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.