This is the dataset associated with our manuscript on FAIR Biomedical Research Software (FAIR-BioRS) guidelines [1]. As part of that effort, we conducted a literature review to identify actionable guidelines for making research software FAIR. The data collected in that review is available in the dedicated GitHub repository. This repository contains the Jupyter notebook used to analyze that review data. See the FAIR-BioRS Hub repository (https://git.luolix.topFAIR-BioRS/Hub) for a list of ressources related to the FAIR-BioRS guidelines, including the manuscript.
The overall code is structured according to the FAIR-BioRS guidelines using FAIRshare. The Python code in the Jupyter notebook main.ipynb follows the PEP8 guidelines. Functions are documented with docstring formatted following Google's style guide. All the dependencies are documented in the environment.yml file.
We recommend using Anaconda to create and manage your development environment and using JupyterLab to run the notebook. All the subsequent instructions are provided assuming you are using Anaconda (Python 3 version) and JupyterLab.
Clone the repo or download as a zip and extract.
Open Anaconda prompt (Windows) or the system Command line interface then naviguate to the code
cd .FAIR-BioRS-code
$ conda env create -f environment.ymlThe environment variables required are listed in the table below along with information on how to get them
| Name | Value or instructions for obtaining it | Purpose |
|---|---|---|
| GITHUB_ACCESS_TOKEN | GitHub documentation | Required (optionally) to run the code block related to counting the number of biomedical-related repositories on GitHub |
Each of them can be set in your conda environment as follows
$ conda activate <environment_with _JupyterLab>
$ conda env config vars set MY_VAR=value1 MY_OTHER_VAR=value2$ conda activate FAIR-BioRS-code
$ conda install ipykernel
$ ipython kernel install --user --name=<any_name_for_kernel>
$ conda deactivateLaunch Jupyter lab and naviguate to open the main.ipynb file. Make sure to change the kernel to the one created above (e.g., see here). We recommend to use the JupyterLab code formatter along with the Black and isort formatters to facilitate compliance with PEP8 if you are editing the notebook.
The Jupyter notebook makes use of files in the associated dataset GitHub repository. The code points directly to the relevant files online so it is not required to download them. The csv file in the input folder can also be called as input to avoid re-running some time consuming code-block.
Outputs of the code include tables displayed directly in the notebook and plots displayed in the notebook but also saved as files. These saved plot files are included in the output folder here.
This work is licensed under MIT. See LICENSE for more information.
Use the GitHub issues for submitting feedback or making suggestions. You can also work the repository and submit a pull request with suggestions.
If you use this code, please cite the associated manuscript referenced in the FAIR-BioRS Hub and also cite the repository as:
Patel, Bhavesh, Soundarajan, Sanjay, Ménager, Hervé & Hu, Zicheng. (2023). Code: FAIR Biomedical Research Software (FAIR-BioRS) manuscript [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6468963