Citation Guidelines for Bilayers

[rajavishah]

We need to determine how users should cite Bilayers. Initially, we considered using a DOIs array in the spec file. Adding DOIs should be needed for wrapper and the wrapped tool.

Key Points - How to find Citations:

1. Check for CITATION Files:

   • First, look in the GitHub repository for CITATION, CITATION.md, or CITATION.cff files to find citation information of any tool.

2. Published Papers:

   • If the tool has a published paper, link to it for citation. These can often be found in the GitHub repo or through a quick search.

3. Citing Interfaces:

   • Ensure that interfaces, like Jupyter or Gradio, are also cited. Refer to their respective CITATION.cff files or other citation guidelines provided.

4. Zenodo Archiving:

   • If no published paper exists, check if the repository has been archived on Zenodo, which generates a DOI for citation purposes. This is less common but worth checking.

Key Points - How to attach citations at config.yaml level?

1. Along with DOIs, we want to put a one-liner description. We would put everything under citations:

   citations:
     Jupyter:
        - name: "Jupyter"
          doi: 10.1109/MCSE.2007.53
          description: "Interactive, code-driven documents for data analysis and visualization"
   
     Gradio:
        - name: "Gradio"
          doi: 10.48550/arXiv.1906.02569
          description: "A simple web interface for deploying machine learning models"
   
     Algorithm: 
        - name: "Cellpose"
           doi: 10.1038/s41592-020-01018-x
           description: "Deep Learning algorithm for cell segmentation in microscopy images"