https://github.com/dhimmel/biorxiv-licenses

The licensing of bioRxiv preprints
https://github.com/dhimmel/biorxiv-licenses

biorxiv creative-commons licensing preprints publishing satoshi-village science

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The licensing of bioRxiv preprints

• Host: GitHub
• URL: https://github.com/dhimmel/biorxiv-licenses
• Owner: dhimmel
• License: other
• Created: 2016-11-28T01:00:52.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2017-06-14T14:42:14.000Z (over 7 years ago)
• Last Synced: 2024-05-02T06:00:18.113Z (8 months ago)
• Topics: biorxiv, creative-commons, licensing, preprints, publishing, satoshi-village, science
• Language: Jupyter Notebook
• Homepage: http://blog.dhimmel.com/biorxiv-licenses/
• Size: 5.4 MB
• Stars: 8
• Watchers: 4
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE-BSD.md

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README

        
# Exploring which licenses authors choose for their bioRxiv preprints

[![Latest Zenodo DOI](https://zenodo.org/badge/74924525.svg)](https://zenodo.org/badge/latestdoi/74924525)

This repository analyzes the licensing of [_bioRxiv_](http://biorxiv.org/ "The

Preprint Server for Biology") preprints. The _bioRxiv_ data was generated Omnes

Res for [PrePubMed](http://www.prepubmed.org/) — a search engine for biomedical

preprints.

The findings from this analysis are summarized in a blog post titled [The

licensing of _bioRxiv_ preprints](http://blog.dhimmel.com/biorxiv-licenses/

"Satoshi Village"), which analyzes preprints through but not past November 2016.

## Binder

[![Binder](http://mybinder.org/badge.svg)](http://mybinder.org:/repo/dhimmel/biorxiv-licenses)

Click the badge above to launch this repository in binder, which allows you to

interact with the jupyter notebooks. Note that the mybinder.org build may be

outdated. You can [rebuild it

here](http://mybinder.org/status/dhimmel/biorxiv-licenses). Binder uses the

[`environment.yml`](environment.yml) in this repository to create a custom Docker image

with the environment for this analysis. If binder fails to load, check the [system status](http://mybinder.org/status/) and [gitter](https://gitter.im/binder-project/binder) before opening an issue here.

## Environment

This repository uses [conda](http://conda.pydata.org/docs/) to manage its environment as specified in [`environment.yml`](environment.yml).

Install the environment with:

```sh

conda env create --file=environment.yml

```

Then use `source activate biorxiv-licenses` and `source deactivate` to activate or deactivate the environment.

## Notebooks

The analysis is performed by running the following notebooks:

+ [`1.download.ipynb`](1.download.ipynb) retrieves _bioRxiv_ data from PrePubMed.

+ [`2.create-figure-data.ipynb`](2.create-figure-data.ipynb) creates JSON data

files for vega-lite.

+ [`3.impact.ipynb`](3.impact.ipynb) investigates the impact of the [blog post](http://blog.dhimmel.com/biorxiv-licenses/) on author license choices.

[`execute.sh`](execute.sh) automates running the analysis for command line

usage.

## License

This repository is dual licensed as [BSD 3-Clause](LICENSE-BSD.md) and [CC0

1.0](LICENSE-CC0.md), meaning any repository content can be used under either

license. This licensing arrangement ensures source code is available under an

[OSI-approved License](https://opensource.org/licenses/alphabetical), while

non-code content — such as figures, data, and documentation — is maximally

reusable under a public domain dedication.