My colleague and I have developed a software tool intend to release it open-source. This tool is specifically for tasks in bioinformatics but we think it would be helpful for the wider community. Our institution will permit us to release it provided we get appropriate credit.

Thus we wish to publish it in peer-review. Is peer-review publication of bioinformatics software available? If so what is required to publish it?

  • $\begingroup$ Yes. academic.oup.com/bioinformatics ? $\endgroup$ – zx8754 Feb 5 '20 at 7:34
  • $\begingroup$ A Bioinformatics journal publication will require some results to demonstrate broad application $\endgroup$ – M__ Feb 5 '20 at 12:53
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    $\begingroup$ @MichaelG. I'm aware of this and I don't think our tool is a good fit for that so I'm looking into other options. Answers for the benefit of others are okay of course. This is quite a broad question. $\endgroup$ – Tom Kelly Feb 6 '20 at 7:07
  • $\begingroup$ As another alternative: SoftwareX is a journal for research-level software. That said, I have published software paper (see: TIGRE toolbox) on a journal of my field (not bioinformatics), rather than a software journal. $\endgroup$ – Ander Biguri Feb 6 '20 at 17:22

There are whole journals based primarily around publishing open source tools. The primary example of that is "Bioinformatics", where a lot of the open-source tools are published. We've also had luck publishing in the Nucleic Acids Research yearly special webservers issue, since we make Galaxy wrappers around our tools.

You can also publish on tools in venues like Nature Methods, but it's vastly more difficult to get in there if your paper is purely on a tool and it's not something game-changing like salmon or kallisto.

Regarding what's actually needed to publish a tool, you will typically need the following:

  • Decent documentation. I ask for this as a reviewer and am asked about it when I submit things.
  • Easy installation. No one wants to spend two hours trying to compile your tool, so make sure there's a conda package or at least a docker container for it.
  • Test data. Without this your reviewers and users will likely not be happy since they won't be able to try it out on something small.

For the actual submission you'll tend to need comparisons to other tools. I'm generally not a big fan of this, but you will find that some reviewers will demand it (assuming there are other tools that do something similarish to yours).


Yes, there is even a journal dedicated to this: The Journal of Open Source Software

Here the software itself is peer reviewed and a decent documentation and tests are required. Since the submission and review process is based on GitHub, publishing there is straightforward if your code is on GitHub already.

Note: I am not affiliated with this journal, I just published two software packages there a while ago.


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