Open source, and FAIR Research Software in Proteomics

Important dates:

• 11/09 - the deadline for new contributions
• 11/11 - our target date for manuscript submission to the Journal of Proteome Research

Description

This repository is an effort from the proteomics community to write a critical view point about Open source (OS) in computational proteomics. We aim the following:

• Define the role of OS for the field (computational proteomics) and science in general.
• Define open source, the implications for the review process, and how to make clear for users, developers, journal reviewers and community what is open-source, what is not.
• We aim to define the role of OS in the development of FAIR (Findable, Accessible, Interoperable, and Reusable) research software in proteomics.
• We aim to define some important concepts for computational proteomics like distribution, licensing, and citation of software.
• We also want to explore other omics fields and how they are dealing with OS and FAIR software.

The tentative title of the manuscript is: "Open source, and FAIR Research Software in Proteomics." We plan to write the manuscript as a GitHub project where contributors could do Pull Requests (PR), issues to comment topics, point of views, etc. The manuscript is written in Markdown and converted to LaTeX using pandoc.

Code of Conduct

We strive to foster a welcoming, inclusive, and respectful community where everyone feels encouraged to participate and contribute. As contributors and maintainers, we are committed to upholding ethical standards to prevent conflicts, harassment, and discrimination. We ask all participants to communicate respectfully, avoid personal attacks, and be constructive in their feedback. Contributions should be made with honesty, empathy, and respect for differing perspectives. Read the full Code of Conduct.

Commenting and contributing

We welcome contributions from the community. If you would like to contribute, please open an issue or a pull request. We will review your contribution and provide feedback. We aim to be inclusive and collaborative, and we welcome all contributions that are in line with our goals.

• If you want to contribute to the manuscript, please do the following:
  • Fork the repository
  • Change the content manuscript.md
  • Submit a pull request
  • We will review your contribution and provide feedback
• If you want to discuss a topic, please open an issue.

NOTE: If, based on your contribution, you would like to be added as a co-author, please open an issue and provide your name and affiliation and a short description of your contribution or a link to the relevant issue and pull request.

Journal Submission

Our plan is to submit this manuscript as a Perspective piece in the Journal of Proteome Research as part of the "Special Issue on Software Tools and Resources". Although the original deadline for this issue was 10/31, we have secured an extension and plan to submit the manuscript on 11/11. Please make sure all of your contributions have been submitted as pull requests by 11/09 to ensure that there is enough time to incorporate them into the manuscript.

Disclaimer

The authors have no affiliation with any commercial entity mentioned in this article. The views described here reflect our own views without input from any third party organisation.