FAIR Biomedical Research Software Guidelines
Minimal and actionable step-by-step guidelines for making
biomedical research software reusable in line with the FAIR4RS principles
About
The FAIR Biomedical Research Software (FAIR-BioRS) guidelines are a set of minimal and actionable step-by-step guidelines for making biomedical research software FAIR (Findable, Accessible, Interoperable, Reusable), in line with the FAIR Principles for Research Software (FAIR4RS Principles).
What are research software?
- Research software is any software created during the research process or for a research purpose. It can come in many format such as artificial intelligence (AI) models as Python scripts or data visualization tools as Jupyter notebooks. They are an essential aspects of biomedical research and therefore making them FAIR, i.e. optimally reusable is critical just like data.
How to make research software FAIR?
- The FAIR Principles for Research Software (FAIR4RS Principles) are reformulated versions of the FAIR Principles developed by the research software community specifically to make research software reusable.
What are the challenges?
- By design, the FAIR4RS Principles only provide a high-level framework for making software FAIR but do not provide practical instructions to do so. Therefore, making software FAIR requires an in-depth understanding of each of the FAIR4RS Principles, and finding out how to practically comply with them.
How do the FAIR-BioRS guidelines help?
- We established the FAIR Biomedical Research Software (FAIR-BioRS) guideline, which are clear, actionable, and step-by-step guidelines for making biomedical research software FAIR. Researchers can simply follow and implement the guidelines as they are developing their software to make it compliant with the FAIR4RS principles.
Development Approach
The FAIR-BioRS guidelines were developed in collaboration with researchers from UCSF and ELIXIR (E.U.). We first established a list of outstanding questions we identified for practically implementing the FAIR4RS Principles (e.g., How to obtain a unique identifier for software? How to include metadata? and so on). Then we combined literature review, community feedback, and our own assessment as developers of research software to established answers for these questions. Finally, we organized these answers as a set of step-by-step instructions that follow the typical sofware development process which became the FAIR-BioRS guidelines.
Funding
The FAIR-BioRS guidelines where conceived while working on a project funded through a supplemental award from the National Institute of Allergy and Infectious Diseases (NIAID). Besides some initial effort through this project for the first few months, the development of the guidelines has been done without any support, through the sole will of the project members to make it easier for our peers wanting to develop and share FAIR software.
Team Members
Research Partners
The FAIR-BioRS guidelines were developed in collaboration with Dr. Zicheng Hu (UCSF) and Dr. Hervé Ménager (Institut Pasteur, ELIXIR).
Timeline
December 2021 - Beginning of the idea
The need for actionable guidelines to make biomedical research software FAIR is identified.
December 2021 - April 2022 - First version
The first version of the guidelines is established based on literature review plus our own assessment.
April 2022 - August 2023 - Community feedback and improvements
Improvements are made through based on community feedback collected during conferences, webinars, and other means. Our most fruitful outreach effort was at the Biomedical Open Source Conference (BOSC) in 2022 and 2023, especially during the CoFest organized across two days before the conference.
September 2023 - Publication of the guidelines
The second versions of the guidelines are published in Nature Scientific Data.
September 2023 - Present - Promotion and development of user support tools
We continue to promote the guidelines. We are also developing user-support tools such as FAIRshare and codefair so that implementing the guidelines is seamless for researchers.
Impact
Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool
Citation
Patel, B., Soundarajan, S., Ménager, H., & Hu, Z. (2023). Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02463-x