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https://github.com/bluebrain/neurocurator

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

https://github.com/bluebrain/neurocurator

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 5 committers (80.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.0%) to scientific vocabulary

Keywords

annotation-framework curation literature-review modeling-parameters neuroscience python qt

Keywords from Contributors

literature-mining
Last synced: 5 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 16
  • Watchers: 8
  • Forks: 4
  • Open Issues: 72
  • Releases: 0
Archived
Topics
annotation-framework curation literature-review modeling-parameters neuroscience python qt
Created almost 10 years ago · Last pushed over 4 years ago

https://github.com/BlueBrain/neurocurator/blob/master/ 

[Getting Started](#getting-started) |
[Upgrade](#upgrade) |
[Releases](#releases) |
[Roadmap](#roadmap) |
[Status](#status)

**For the Annotation Viewer or the integration with the [OpenMinTeD](
https://openminted.eu) platform, please refer to this [branch](
https://github.com/BlueBrain/neurocurator/blob/annotation_viewer/ANNOTATION_VIEWER.md).**

# NeuroCurator

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

This is a Graphical User Interface (GUI) for the Python module
[NeuroAnnotation Toolbox (NAT)](https://github.com/BlueBrain/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.

---

## Getting Started

### Installation

After having **installed the [requirements](#requirements)**:

```bash
pip3 install neurocurator
```

You might want to install NeuroCurator in a dedicated `conda` environment:

```bash
conda create --name neurocurator_env python=3.7
conda activate neurocurator_env
pip install neurocurator
```

To launch NeuroCurator:

```bash
neurocurator
```

#### Requirements

  - [Python 3.5+](https://www.python.org/downloads/)
  - [Git 1.7.0+](https://git-scm.com/downloads) (NAT)
  - [ImageMagick **6**](http://docs.wand-py.org/en/latest/guide/install.html) (Wand)
  - [Miniconda](https://conda.io/miniconda.html) (optional)

#### Python dependencies

  - [NAT](https://pypi.org/project/nat/)
  - [PyQt5](https://pypi.org/project/PyQt5/)
  - [NumPy](https://pypi.org/project/numpy/)
  - [pandas](https://pypi.org/project/pandas/)
  - [Wand](https://pypi.org/project/Wand/)

## Upgrade

```bash
pip3 install --upgrade neurocurator
```

If you have used `conda`, activate the environment before:

```bash
conda activate neurocurator_env
```

## Releases

Versions and their notable changes are listed in the [releases section](
https://github.com/BlueBrain/neurocurator/releases/).

## Roadmap

**Ongoing**

1. Stabilize NeuroCurator and NAT (Software Architecture).
2. Split NAT into nat-core, nat-analytics and nat-server (separation of scope).

**TODO**

1. Integrate fully the [Annotation Viewer](
https://github.com/BlueBrain/neurocurator/blob/annotation_viewer/ANNOTATION_VIEWER.md)
into NeuroCurator.
2. Semi-automate the Knowledge Extraction process.

**Done** (latest first)

* Make the annotations publishable into a [Blue Brain Nexus](
https://bluebrain.github.io/nexus/) instance.
* Remove legacy dependencies in NeuroCurator (Qt 4 and Python 3.4).
* Integrate OpenMinTeD annotations into the literature curation framework.
* Visualize NeuroCurator and OpenMinTeD annotations directly on PDFs.
* Make NeuroCurator easily installable, especially by scientists.

Updated on 04.10.18.

## 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.

Owner

  • Name: The Blue Brain Project
  • Login: BlueBrain
  • Kind: organization
  • Email: bbp.opensource@epfl.ch
  • Location: Geneva, Switzerland

Open Source Software produced and used by the Blue Brain Project

GitHub Events

Total
  • Fork event: 1
Last Year
  • Fork event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 160
  • Total Committers: 5
  • Avg Commits per committer: 32.0
  • Development Distribution Score (DDS): 0.369
Top Committers
Name Email Commits
Christian O'Reilly c****y@e****h 101
Pierre-Alexandre Fonta p****a@e****h 51
christian-oreilly c****y@g****m 5
Elisabetta Iavarone e****e@e****h 2
Ben Morrice b****e@e****h 1
Committer Domains (Top 20 + Academic)
epfl.ch: 4

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 96
  • Total pull requests: 4
  • Average time to close issues: 3 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 0.84
  • Average comments per pull request: 1.25
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • pafonta (69)
  • christian-oreilly (14)
  • srjimenez (10)
  • davidcsterratt (2)
  • awakenting (1)
Pull Request Authors
  • christian-oreilly (2)
  • MFSY (1)
  • 9999years (1)
Top Labels
Issue Labels
bug (37) enhancement (36) high priority (11) medium priority (10) design / architecture (8) devops / infrastructure (8) new feature (5) won't fix (4) need review (3) documentation (1) with workaround (1) question (1) on hold (1)
Pull Request Labels
bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 11 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 2
pypi.org: neurocurator

Application to perform curation of neuroscientific literature.

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 11 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 14.8%
Dependent repos count: 21.7%
Forks count: 22.6%
Average: 24.7%
Downloads: 54.2%
Maintainers (2)
chore pafonta
Last synced: 6 months ago

Dependencies

setup.py pypi
  • PyQt5 *
  • nat >=
  • numpy *
  • pandas *
  • wand *