I am not getting academic credit for code I have written for my PhD, when it was later used in other research. Should I complain?

Question

During my PhD, I developed a data analysis code. My PI encouraged its development, expecting it to stay within the research group. The code was used in some published papers and gained attention when doing benchmarks for a Huge Science Collaboration (HSC).

As I left academia, I handed over the code to others in the PI's group, notably to X, who placed it in a private git repository. My understanding was that, as a courtesy -- and as I was forced by PI to do with others -- I would be offered authorship on papers using the code, a courtesy I would have declined the first time and would not have expected again, since citing my papers or acknowledging me would suffice. However, despite an agreement for a public release and a science paper using the code led by X that has not been published yet, I was often minimally acknowledged or not mentioned in subsequent papers using the code.

X moved to a new research group and published a paper using the code. Recently, HSC papers have cited only X's paper as the main reference for the code, downplaying my contributions, with the code still being private. After complaining, some corrections were made, but issues persist.

I feel my main scientific contribution, as well as for others who worked on the code, is not being properly credited. And I find unfair that, without a science paper on the code, only X's paper is cited. Am I overreacting? Or in the wrong? What are my possible outcomes?

Answer 1

What you are describing is a difficult situation, because a couple of written or unwritten rules are in conflict:

1. Those who made intellectual contributions to a piece of research should get the contribution.
2. Students or postdoc that are leaving a group should not (and should not be able to) block the scientific work of the rest of the research group.
3. If you made a building block to be used in scientific work, you get credit for it by being cited - your software being used in some work does not give you the right to demand authorship of the paper.
4. Writing software is not automatically an intellectual contribution.

Additionally, it looks like the whole issue was not handled very well.

From your question it looks like you never wrote a proper scientific paper on your software. If you had, your scientific paper could just be cited in all papers using your software, and you would not be an author of the papers in which your software is used. Then all rules above would have been satisfied.

Because you never wrote a paper on your software, there is now a conflict. You can't expect to be in the author list of every paper using your software just because it was not public, because that would mean that by not publishing your paper on the software, you get authorship on many papers essentially for free. At the same time, you can't expect your former group to not use your software, because then you would be blocking their work. Most likely you also got funding from the PI (if not, on the legal level, this may be different).

At the same time, it's certainly bad style that your contribution was forgotten in some cases - you should have been mentioned in the acknowledgements. After a few years of not publishing the paper about your software, you shouldn't be surprised to be forgotten, however.

A different issue is that X is still using your software after leaving the PI's group. If you got funding from the PI, then there may be the expectation that your PI has unlimited usage rights of the software, including sub-licensing it to X - which may have implicitly or explicitly happened, especially if X continued to work on it.

Now what are the possible solutions apart from "forget it"?

1. Ask X if she/he wants to co-author a paper on the software with you. If you don't have enough time to write it completely on your own now, perhaps that is an option?
2. Publish a short paper on your software, so that you can still find enough time to write it. It doesn't need to explain everything, but enough to be citable. Do so with the knowledge of the PI and X, so that in future papers, they can cite you correctly.

(I'm happy to update my answer if I forgot possibilities).

Note that rules 3 and 4 above may come in minor variations in some fields of research. In computer science, for instance, it is quite common to propose new algorithms that crucially depend on some other existing work — still, the authors of the existing work do not get authorship for the new work. Only if the existing work (which could come implemented in the form of a tool or library) needs to be modified in intellectually non-trivial ways, the authors of the existing work are typically invited to also be authors for the new work. Rule number 4 is addressed by some academic conferences having "tool papers" to allow researchers taking the time to write complex scientific software getting some publication credit for it.

Answer 2

At least conceptually, it does not seem right that you can expect perpetual co-authorship for papers to which you did not contribute in ways other than having developed a code years ago. The right approach to getting credit is getting cited, not being a co-author on work to which you did not concretely contribute.

The way to address this is to write a paper about the software that others can then cite. It should be written by all those who have contributed to the code by now, and since you started the software, it's not unreasonable that you would be first author. Such a paper can be a lot of work, but it doesn't have to be: the Journal of Open Source Software (JOSS) publishes citable papers that require fairly minimal work.

Answer 3

My career has primarily been in computational physics. I have done seven projects in this field. Four of them have been published and three have not. In all cases, there has been some form of written documentation. For the three that have not been published, to the best of my knowledge, I have not even had an acknowledgment. In all three cases, there has been at least a reasonable reason for this, if not perfect, and I am quite happy that either the work has been used or that I have had the opportunity to learn and add to my credentials. I have had a 15 year career in computational physics, which I love, and am quite proud of this and it has been the true joy of my life. I hope you can enjoy your career so thoroughly too, and be proud that your work has made a difference.

The great news, and what makes me feel a lot better about all of this, is that I have a great CV and resume following all of this, and several documents documenting the work I have done. What you can do, if there is any confusion over what work you did, is describe it on your LinkedIn profile and resume and CV. As others have suggested, you can either publish something on it or write documentation for it. You can document it in the github archive itself, you can make the documentation publicly available somewhere such as a website. Github itself has a website, or maybe your university has one you can edit, or there are some free website services available. Another iffy possibility is that maybe you can write an quasi-formal document and post it somewhere like Research Gate (maybe, depending how unofficial it is-- my unofficial thesis-- unusually extensive general exam document due to transferred classes-- for my third Masters in astrophysics is there). A lot of these options might work even if the code isn't public, depending how vague or clear the documentation is. You may or may not need your former collaborations approval to publish.