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I wrote a software package called rna-pdb-tools. Hmm.. but now I have a problem. Is it?

Furthermore, rna-pdb-tools were used to curated structures submitted to the RNA-Puzzles, https://github.com/mmagnus/RNA-Puzzles-Normalized-submissions) facilitating the comparison of structural models.

or was used?

Or I should say "software rna-pdb-tools was used" or "package rna-pdb-tools was used" but "rna-pdb-tools were used"?

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    Both will work. The (software package) "rna-pdb-tools" was used. The (tools in) "rna-pdb-tools" were used. The second part of the Q: that depends on whether you are referring to the package or the tools specifically -- if you think it doesn't matter, then better use the singular to refer to the package.
    – Kris
    Mar 20, 2018 at 12:29
  • Yeah, this is what I thought. In Polish (my native language) I would say the same, depends on the form used, name alone or xxx rna-pdb-tools. Mar 20, 2018 at 12:30
  • Like: "Microsoft Windows is a group of several graphical operating system families, all of which are developed, marketed, and sold by Microsoft..." en.wikipedia.org/wiki/Microsoft_Windows Mar 23, 2018 at 13:19

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Because "rna-pdb-tools" is a software package (singular), the verb should be "was." However, I would use "Furthermore, the rna-pdb-tools package was used to...."

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One thing to note re Chris's comment is that you wouldn't use the definite article "the" when eliding. It should be in the optional brackets.

As a software engineer I prefer the shortest version and to use the plural in this case when the name makes number clear. As another edit you should use "to curate" rather than curated for the infinitive.

In formal literature it also helps to add emphasis to the package name with italicisation and/or add a footnote giving a reference/link to your package or info thereabout.

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