Write a short paper about your software

[lcolladotor]

Related to #3, I recommend writing a small application note about the software you are documenting here. The paper will be quite small and can have a structure like this:

• introduction: why people would need it and some problems that existed prior to this software
• results: what the software does without any code shown (you might want a schematic figure here)
• methods: anything you need to cite that allowed you to build your software
• discussion: some limitations, context for the software
• funding
• acknowledgments: early users, people who help proofread the docs, etc
• references: a small list

Two typical journals for this type of paper are Oxford Bioinformatics and F1000Research. See https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab152/6162880 and https://academic.oup.com/bioinformatics/article/36/16/4532/5861528 for two similar papers I was involved in recently as well as the spatialLIBD paper we are writing right now https://www.overleaf.com/read/tqvgjssdckqv. Check https://f1000research.com/gateways/bioconductor?selectedDomain=articles for some F1000Research papers others have written. Brenda @bpardo99 checked a few of these before starting the spatialLIBD one.

If you go with Oxford Bioinformatics, check the Application Note format (max 2 pages, 1 figure OR table) https://academic.oup.com/bioinformatics/pages/General_Instructions. The first time you submit the paper it does have to be <= 2 pages. Then in the review process you can expand to 3 (and pay the extra page charge). It'd be up to your team whether to pay the open access fees (I'm in favor of that but it's pricey, like in regutools we didn't have the budget for that).

Another potential journal, though it might not apply here given that your software is based on Matlab code, is the Journal of Open Source Software https://joss.theoj.org/.

Overall with this type of paper, the paper is really small. Most of the work goes into the documentation (if you really want others to use your software).

If you go with Oxford Bioinformatics, create an Overleaf account and use their template which will make it much easier for you https://www.overleaf.com/latex/templates/template-for-oxford-bioinformatics-journal-new-version/zjrmbrmtrytg. That's how we started the spatialLIBD paper. It's like Google Docs but for LaTeX. It's helpful to look at the main.tex from others to see any syntax issues. For citations, you'll need to use Bibtex, so check for example the document.bib for spatialLIBD (I recommend using lastnameYEAR and ordering your citations alphabetically in the .bib file; cc @abspangler13 @bpardo99). Once you are ready to pre-print the paper, I can help you a bit with adding a .cls file that strips out some of the Oxford Bioinformatics info such that you'll be ok uploading the resulting PDF to bioRxiv.