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When writing a manuscript for a scientific article, I often wonder what software I should cite or acknowledge, and how.

The first problem is to make a choice which software to cite. On the one hand, there is no way to cite all software, as this would mean to cite my whole software stack (Linux, GNU tools, emacs, git, ...). On the other hand, not citing any software is not fair, either. Furthermore, some software explicitly asks to be cited, some software doesn't. Also, some software is really crucial to the results, some isn't. Another important aspect is that citing software is not only about giving credit to the authors of the software, but also to give other scientists hints on what software they might want to use. So, he choice which software to cite is a problem.

The second problem is how to cite the software. Some (scientific) software does provide a classical scientific article that can be cited. However, in this case, no URL to the software is given. Others do not have an associated article. How do I cite these? I have seen people that cite the manual of a software, others just give the URL. What is the way to go?

Another aspect is where to cite the software. Some software can be cited in the course of the articles text, but when it comes to more fundamental software, other places may be more appropriate.

Are there any good ideas out there on any of these aspects?

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    I was going to put a bounty to request a canonical answer, but it appears "How to cite and describe software" by Mike Jackson at the Software Sustainability Institute already provides a thorough answer to this question that considers many options: software.ac.uk/so-exactly-what-software-did-you-use – Abe Oct 16 '15 at 16:10
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After some thought on the matter, my own approach in my next manuscript will probably go like this:

  1. Which: To choose which software to cite, I would try to answer the following questions:

    • Is there a scientific article that can be cited and are the authors of the software asking to be cited?

    • Was this specific software relevant to the results of the manuscript? If there are plenty of alternatives to the software and you use it merely because you knew it, this is probably not a reason to cite it. But if I used and profited from the specific features of a software, then it is probably worth citing it.

    • Do I explicitly want to give credits to the software? Maybe I found the software very good to use and I want to tell other scientists to use it, then I would cite it.

  2. How: If there is a scientific article, I cite it in the classical way. However, I would also cite a URL of the software, as this makes it significantly easier for a reader to find the software. Otherwise, cite the URL. Citing the manual doesn't make sense to me, the only reason to do so would be to give explicit credits to an author.

  3. Where: If I can cite a software in the course of the text, I do so, otherwise, I would make an appropriate paragraph in the Introduction or Acknowledgements.

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A few additional thoughts to your answer:

Otherwise, cite the URL.

cite also the version.

Citing the manual doesn't make sense to me, the only reason to do so would be to give explicit credits to an author.

  • sometimes the manual is a normal book, so this allows you to cite it in analogy to the "there is a paper" strategy.
  • manuals usually have the version of the software in their name.
  • maybe a practical historical reason: BibTeX has an entry type @MANUAL (since at least 25 years), so for BibTeX users manuals are an easy way to cite the software.

otherwise, I would make an appropriate paragraph in the Introduction or Acknowledgements.

I use a paragraph "software" in the materials & methods section

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An variant of this question was asked today: Whether to cite software. Here is my answer about "whether."

Yes, cite key software that you use! Citing the work of software developers, by their name, is important to some careers. I'm a faculty member at a major research university, and we do a lot of "counting papers" and "counting citations" when it comes to promotion/pay/tenure cases. (I don't fully approve of how we do this, but that's irrelevant here.) Since open-source software is often not carefully cited, this really discourages aspiring junior faculty (and grad students) from working on it.

If they have written a paper about the software, by all means cite that. Our systems are quite good at tracking citations of academic papers (at least, citations in other academic journals). Otherwise, cite by name + web site.

You are also helping your readers, by being clearer about your methods, and giving them a place they can look if they want to pursue your techniques further.

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