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I was in a research group for my MSc. dissertation (computational work) during which I developed quite a bit of code that went on being used in a publication which I co-authored (no code was published at the time - I know how much of a bad practice this is, it was not dependent on me).

Now, without changing much of the code (I would say the bulk of the code remains unchanged), my advisor wants to make it publicly accessible as part of a new publication. My advisor does not want me to be one of the authors, claiming that I do not own the code and that the code is now owned by my advisor and by the institute where she works and where I did my MSc. dissertation work. The changes were done by people who are now members of this group.

For the sake of not going through too much trouble, I would be happy foregoing this whole situation, but as a matter of principle this really bothers me. I do not feel like I am in a position where this can hurt or affect me, but I fear it may happen to other people, too. What would be the usual thing to do? Is being confrontational about this worth it? Who actually owns the code in this situation and what would be the right thing to do?

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    Did the code have any scientific contribution (rather than just a particular implementation)? Then you have the right to co-authorship. The ownership of the code is a different issue. Typically rights to code at MSc level is owned by the university (but check the regulations, YMMV). Apart from the above, and unless the code is owned by you, you cannot stop them from using it, though. Jun 1 at 16:41
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    @CaptainEmacs the code contained a few different analyses using pre-existing methods as well as ways to aggregate and compare this information in a rigorous way (this last bit would be the novel part). I thought that ownership of the code would play a part here but thank you for clearing that up.
    – iliupersis
    Jun 1 at 16:49
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    @iliupersis The point being made by Captain Emacs doesn't have to do with what the code implements, but the source of the scientific contribution. Did you implement their ideas, or did you create ideas while working on their project? The distinction is subtle, but necessary to determine if you have publication rights. Also, your code was written in pursuit of a Master's which 99.99% of the time means there's an agreement that the University has a free license to do with it what they please, even if you also have a personal copyright. They likely "effectively" own it.
    – Edwin Buck
    Jun 1 at 18:12
  • @EdwinBuck ah ok, understood. My former advisor sent me a page for an analogous analysis and mentioned it could be an interesting addition to the work we were doing - that was the starting point of this analysis and then everything else was implemented/applied by me and added on top of this. So I ran with an idea they had forwarded me and expanded upon it. I hope this is clear enough
    – iliupersis
    Jun 1 at 18:25
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    @DanielHatton I didn't indicate the University would obtain the copyright, but rather that the University would have a free and clear license to do whatever they deemed permissible with the code. There are many cases where the copyright no longer confers control over a written work by a different person than the author, when that work is explicitly licensed to that different person with a very permissive license. If I write a program, and then license you to resell it, modify it, and rebrand it, then my copyright is effectively a name on the work only, not a means of control.
    – Edwin Buck
    Jun 2 at 2:13
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I'll leave aside the legal side of this, other than to say that I agree with other that the likely legal status is that the university owns the code that is not in the public domain.

Moving to the moral side of things. It is correct that if you developed a code base that is useful academically, you should be credited for this. But from your description in the original post it seems you have been - you were author on a paper that came out of your Master's work and that you developed the code for. At that point really the code should have been made public, even if it wasn't. At that point, by publishing, you relinquish your rights to exclusive use of the code (again, morally, not legally, and in all matters moral, only in my view). In theory anyone in the world should be able to use and build on your published work without including you as an author in the derived work (although they should cite your original publication). This includes your former advisor, and their future students and employees.

What complicates this is that is the advisor appears to have kept the code for their exclusive use so they can benefit - there is no moral case that they should benefit from exclusivity while you don't. Secondly, from what I can make out from what you say, they now do wish to make the code public (is this being forced by a journal they now wish to publish in?). If the code is made public in this second paper, but wasn't in the first, this will lead to that paper being cited if anyone reuses the code, and not you.

Given that the code was not made public with the first release, I think that ideal solution going forward would be for you to make the code public separately from the second paper with a license that identified you as the author and specifying that people wishing to use the code in academic work must cite your original paper. Your former advisor would then not include you as an author in their new paper, but would cite your original publication as the source of the code.

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  • Your solution is spot on, I think that will be the solution forward. Thank you for contributing, it really is a situation where publishing the code in the first publication would have save everyone a lot of trouble.
    – iliupersis
    Jun 2 at 11:39
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The answer is "it depends," but I'll throw out some US-oriented answers that apply to me as I know it at UT Austin under US NSF funding now. The usual thing to have done would to have published the original code along with the paper and/or your Master's thesis (depending on how long ago that was) under an NSF-approved open source license, assuming that NSF funded the work. That code is probably owned by the institution you worked for when you wrote it (depending on their policies). There may be ways around giving your code away even such a situation, but that's how I'd approach it if this were my situation. Other US funding agencies take a similar approach. I would hope that you'd want to work with your former advisor to make this code open source, anyway.

Any recent changes would also be published to the same open source repository as a part of the ongoing publication process for the code and its working community (even if that's just the grad students of the PI of the lab that originally developed it). You would be able to use this code wherever you are now and others out there would, too, as well as ongoing use by the original lab.

Ideally, you would have been part of an original publication or so-called "marker paper" about the methods in used in the code when the repository was made public, and your thesis might have served this purpose, though I think a journal paper or peer-reviewed conference paper would have been better. Your advisor is being quite stingy with academic credit by not wanting to include you in the authorship of a current paper with a contemporary repository release. I'd fight that tooth and nail if you don't need a working relationship with her anymore. Your former university probably has an intellectual property page describing who owns what, and I'd bet money in Vegas that it's not your former advisor. She may be due a substantial cut of any licensing revenue that the university generates, but that doesn't seem like the worry here. At my university, the ownership is predetermined by who funded the work and the contracts that conveyed that funding. There's a lot of "it depends" that need to be checked.

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  • Yeah, maybe checking with my former uni would not be too bad, I was trying to understand if there was a general guideline for this. I'll see. I agree that the code should have been released with the first publication but my former advisor was very keen on keeping it so it could be reused for future papers and similar analyses (I know poor of a practice this is but I was not really in a position where I could argue or call them out on their poor practices).
    – iliupersis
    Jun 1 at 18:28
  • Publishing the code doesn't prevent your advisor from doing future work with it nor future publication. If the marker paper is highly cited and the code becomes popular, then that's great. Just look at libraries like PETSc, deal.ii, etc., their authors make hay out of their popularity to bolster their grant proposals and to further the ongoing development of their libraries. The authors of these libraries are also among some of the heaviest ongoing users of their libraries with many publications Your advisor just doesn't understand scientific OSS. Lots of use by others expands citation counts!
    – Bill Barth
    Jun 9 at 15:28
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    I whole heartedly agree, believe me! Just a correction - former advisor*. But they are becoming more open to this and I am happy to see it happening
    – iliupersis
    Jun 10 at 12:02
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Legal aspects depend on jurisdiction, but in general the following are points to have in mind:

  • in most countries, computer programs are literary works that are protected by copyright. In that respect, it does not matter whether your code has any scientific contribution, the moment you create it you have author's rights.
  • there's no such thing as "owning the code". Author's rights include both copyright and untransferrable moral rights. The latter, in particular, includes the right of attribution, as well as the right to the integrity of the work. So, even if the copyright for your code belongs to the university, them publishing it without your name on it would be illegal.
  • there's a fair chance that you actually retain the copyright, unless you have withdrawn it explicitly, or, in some jurisdictions (US but not most of Europe), were paid to do the work. I don't think being a Master student withdraws any of your IP rights.

That's the legal aspect, but there's also a separate question of scientific integrity, which I would say is majorated by the IP law - in the sense that anything that breaches someone else's authors rights is a major scientific misconduct, but not conversely. For example, ideas are not protected by copyright, but using someone else's idea without attribution is a misconduct. What your advisor attempts to do seems to be a major ethical violation, regardless of the copyright status. If they publish anything not created by the authors, they must attribute it.

In practice, it is likely that your advisor has no idea about IP rights and such - she just assumes, as many commentators here, that students and junior faculty have no rights. So, if you want to stand your ground, it may be enough to write her an e-mail saying that you created the code, you believe you retain the copyright as you don't recall tranferring it, and as an author you object to them publishing it without your name on it. Of course, that might be quite a nuclear option in terms of your relationship with her.

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    "So, even if the copyright for your code belongs to the university, them publishing it without your name on it would be illegal." - I don't believe this is true in any jurisdiction. There may be academic codes that are broken, but not laws. If you write code for Microsoft, they don't have to name you when they distribute Windows.
    – Bryan Krause
    Jun 1 at 19:32
  • @BryanKrause, distributing Windows is rather different from publishing its source code, also I'm sure Microsoft contracts with developers contain all kinds of waivers. That said, the possibility to waive moral rights differ by jurisdiction (as you can see from the source), and I know of at least one jurisdiction (Russia) where such waiver would be null ans void. Of course, even if some programmers may sue Microsoft to put their names in credits, there's no point to that in practice.
    – Kostya_I
    Jun 1 at 20:37
  • Don't take legal advice from non-lawyers. Or even form casual contact with actual lawyers.
    – Buffy
    Jun 1 at 20:47
  • I feel like for a work to be protected by copyright you have to adequately license it; it doesn't come under copyright law on its own. But this was interesting contribution, thank you.
    – iliupersis
    Jun 2 at 11:41
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    @iliupersis, that is not true. See, for example, en.wikipedia.org/wiki/Copyright_registration.
    – Kostya_I
    Jun 2 at 13:06

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