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Abit about my background first: I'm currently undertaking a PhD but have previously worked in healthcare for around 4-5 years. During this time I developed a suite of code to produce results from clinical sequencing data (a NGS pipeline plus filtering steps).

Recently while looking for example PhD theses to use as the basis for my own write up I came across a recent PhD thesis that contained a reference to a github account, which contained code I had written.

The code in the repo is over 97% direct copy of code that I had produced while working in my previous employment - the remaining 3% appears to be a cut and paste of lines from my original pipeline into a popular pipeline management system.

edit I should note here that this remaining 3% had previously been submitted by another ex-colleague as part of an external qualification - for which I was the internal assessor, this person claimed sole authorship at the time.

edit I should have noted that development of this code started a year before entering the employment that I mentioned, as part of a postgraduate qualification that I completed, submitted ironically - along with prototypes of the discussed code - to the same university. Just to clarify the IP issue, the university in question assigns ownership to the student in these cases.

There is no direct reference to my own Github repo which contains the original code (with GNU public license) and no acknowledgment of my authorship (I am mentioned indirectly as a maintainer of the code elsewhere in the thesis). I had no knowledge that the author of thesis was using my code as part of their thesis.

The author of the thesis was in the same department as me, however was at no point involved in the development of the code while I was present. They have since submitted and passed their PhD and are now employed as a PostDoc in the same department.

I can show continuous development of the code over a period of 4 years previously via my Github logs. The author of the thesis has only a single commit and no history in the github logs.

The person in question has essentially written a PhD chapter based on analysis of sequencing data that I did. The code is just part of the story, since the person also claimed that in addition to writing the code they used the code to produce the results in that chapter. They didn't - since I know that I ran the batches in question (this was around 2 years of work).

What steps should I take (if any)!

  • Comments are not for extended discussion; this conversation has been moved to chat. – StrongBad Mar 6 at 16:25
  • You say "no direct reference to my own Github repo", and then "I am mentioned indirectly as a maintainer of the code". I don't understand how they can do the latter without giving a direct reference. Do you mean their repo has no direct reference, or that they imply you are maintaining their repo? Or perhaps that they mention your repo without in the text without formally citing the link? – A Simple Algorithm Mar 6 at 16:39
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    One important thing remains unclear to me after reading this: Who holds the copyright on this code? Depending on your relationship with the Uni at the time you started developing it, they might either hold copyright on it, or at least certain rights of use and storage. Copyright on code developed/added while you were employed commercially may well belong to your employer at the time. If you hold the CR, you could simply relicense it to the Uni, and that would solve most legal issues. If the Uni owns it, they can do what they want. – T.E.D. Mar 6 at 19:00
  • ...if your employer owns it, then licenseing and enforcement is their problem, and issues should be referred to them (and I sure hope it was put online and licensed GPL with their permission...) If multiple parties own it, then likely the GPL will have to be stuck to, unless all parties can agree to a relicence. – T.E.D. Mar 6 at 19:02
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This is a tricky one. It probably sounds like academic plagiarism, but your licensing concerns are probably not going to resolve the problem at the core of this. There's two sides to this, the academic (plagiarism) side and the commercial (licensing) side. They're almost entirely separate, so I'm going to break them up.


Academic/Plagiarism Claim

The code in the repo is over 97% direct copy of code that I had produced while working in my previous employment...

Without attribution, this is plagiarism, and may be grounds to have the PhD rescinded, but this would be a serious procedure as it's likely to have life-altering affects on the PhD student in question. You'd need to be 100% sure of what you're doing and the validity of your claims going into this. Even if the case was black and white (which I don't think this one necessarily is), the student's University isn't going to take rescinding a PhD lightly as it reflects badly on them.

Additionally, it sounds like there is a some attribution within the work:

The indirect mention of my name is as a maintainer not the sole developer

...which might well be sufficient for the University to write this off as a referencing error, maybe requiring the student to make a small addendum to their thesis.

The code is just part of the story, since the person also claimed that in addition to writing the code they used the code to produce the results in that chapter. They didn't - since I know that I ran the batches in question (this was around 2 years of work).

If you can prove it, the experiments that they claim to have run, that you performed while under the employ of their department are probably your strongest leg to stand on here. But you'd have to have good evidence, and be able to show they haven't run the experiments themselves. If yours were not published previously, and they've generated the data themselves using your code, this may well be null and void.


Commercial/Licensing Claim

The licensing perspective of this is completely separate to the plagiarism side - if the work was published as GPL, they can basically do what they like with it, without attribution, provided that any code based upon it remains GPL. This bit is important, as it's probably where you have a leg to stand on, based on this comment:

although the person has also removed the GPL from the repo, which I thought was against the license terms

That is absolutely in breach of the terms, which is why most industrial entities won't touch GPL code with a bargepole (due to what's commonly called "license bleed").

Based on this, you might have a valid claim to get their repo pulled, but that's not going to solve your actual problem.

Again, from the comments:

...I feel that the supervisor (who used to be my boss)...

I understand this to mean that the PhD student in question is supervised by your old boss, which means you had a contract with their institution. Depending on the contract you had with them, they could therefore own all the rights to it regardless, making your initial GPL license in breach of your contract with them without prior stated agreement. This wouldn't affect the legitimacy of your plagiarism complaint, as that's a genuine academic concern, but might affect how the department deals with your request.

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    +1 I think this answer is most on the right track -- it's not a question of whether they cited OP or obeyed license terms, it's a question of whether they misrepresented the amount of work they had performed to fraudulently obtain a PhD. Going to the ombudsman and/or the student's advisor with your concerns is probably the only path forward, though I would be surprised if anything came of it (sadly). – cag51 Mar 6 at 2:14
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    The GPL clearly states: "You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program." See also: opensource.stackexchange.com/a/4582 – Pharap Mar 6 at 9:53
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    Thanks for the information @n00dle, seems to be a good summary of the points from other posts as well. Guess the best I can do is to raise the issue with the academic in charge of plagiarism and ask for a review. Given the supervisors status within the department and the ex-student's qualification, a slap on the wrist will be the best I can hope for - but at least it will mean that they can't claim to have produced the code themselves in the future. – Pasted Mar 6 at 9:54
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You want to accuse a peer of plagiarism on the basis of the following (emphasis added):

I came across a recent PhD thesis that contained a reference to a github account, which contained code I had written...There is no direct reference to my own Github repo which contains the original code (with GNU public license) and no acknowledgment of my authorship (I am mentioned indirectly as a maintainer of the code elsewhere in the thesis).

You've stated that the accused has acknowledged you and, as stated in a comment, "GPL(v2,v3) does not require attribution," so the accused was not required to reference your Github repository from their own.

This doesn't seem like plagiarism.

Nonetheless, as noted by Abion47, I appreciate that the OP feels they have been wronged and the OP wants to understand what happened. This could perhaps be achieved with a little digging, e.g., by emailing the accused and asking questions, by sitting down with accused, ... For such a strategy to work, the OP must enter the dialogue without any pre-assumptions of guilt: Listen to the accused, hear their story.


Response to comments by the OP:

The indirect mention of my name is as a maintainer not the sole developer

This seems like a minor quibble over the accused's word choice.

Please note my emphasis on sole developer of the original code

The accused has not claimed to be the developer of the code (at least, that's not mentioned in the original question).

The mention is in a different chapter and is not in the Github repo

If the mention is in an earlier chapter, then that surely suffices (code has been attributed to you, the owner), otherwise, well, it should have been, but that's easily explained away (e.g., due to changing the order of chapters). Regarding Github, we've established that you didn't require a mention.


Response to comments regarding maintainer vs. developer:

I'm shocked that this answer is [highly rated]. Being mentioned as a "maintainer" is nowhere near the same thing as being the sole developer. We can talk about technicalities all day, but the other student is clearly being deceptive.

and

I agree with the others in the comments here complaining about it--this person is certainly being dishonest by referring to the actual author as the "maintainer".

Wikipedia offers the following definitions:

  • A software developer is a person concerned with facets of the software development process, including the research, design, programming, and testing of computer software.

  • A software maintainer...is usually one or more people who build source code into a binary package for distribution, commit patches, or organize code in a source repository

I appreciate that software developer is the more appropriate term. However, the accused's first language mightn't be English and the accused (presumably) isn't an expert in software engineering (they work in clinical sequencing).

I really do not think that using maintainer as opposed to developer is a big deal. I certainly would not make a plagiarism case on the basis of a misused term.

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Talk to your advisor.

Talk to the other student's advisor, with the support of your own. Or even have your own advisor make the complaint to the other.

Complain to GitHub.

But, most important, make sure that your own advisor will agree that this other, seemingly prior, work doesn't prejudice your own degree.

As to publishing, I'm pretty sure that the code supports your work, rather than being the essence of your work. If that is the case, as is normal, then the issue of plagiarism shouldn't affect your own ability to publish your own results.

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    Thanks @Buffy - have taken this to my supervisor(s) but they were reluctant to become involved due to the plagiarism being of work I did prior to my PhD.. and the reputation of the offenders supervisor. Which is fair enough and I completely understand. I could make a complaint directly however I feel that the supervisor (who used to be my boss), would ignore my complaint. The other recourse may be to get an impartial review by someone outside the department (say in computer science), then go on their recommendation. – Pasted Mar 5 at 14:05
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    What complaint can be made to GitHub? – user2768 Mar 5 at 16:09
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    GitHub's Terms of Service state "You agree that you will not under any circumstances upload, post, host, or transmit any content that ... infringes on any proprietary right of any party, including patent, trademark, trade secret, copyright, right of publicity, or other rights." 1/2 – shoover Mar 5 at 16:20
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    Also "you will only submit Content that you have the right to post; and that you will fully comply with any third party licenses relating to Content you post." 2/2 – shoover Mar 5 at 16:20
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    @shoover OP's code was put on Github under the GPL license, which allows anyone to take and use the code without requiring attribution. As such, there are no proprietary rights to infringe upon. – Abion47 Mar 5 at 21:01
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Do nothing.

You provided some code that somehow ended up online.

That person has been the profit of your code, but I am sure a lot of what they did was more than just some code.

Be more generous.

If someone had used my code for successful research I would be pleased!

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    The person in question was working in the same department as myself and has essentially written a PhD chapter based on analysis of sequencing data that I did. The code is just part of the story, since the person also claimed that in addition to writing the code they used the code to produce the results in that chapter. They didn't - since I know that I ran the batches in question (this was around 2 years of work). I would question whether you would be as pleased to have a colleague use your work without attribution - it is kind of a core principle of science to recognize others work! – Pasted Mar 5 at 14:37
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    Ok, please adapt your question to account for the extra information in this comment. I agree with you, but at the same time, my code would only end up on a website after I have something published. Then you would have a much more valid arguement and It would be much easier to prove. – user22485 Mar 5 at 14:42
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    Thanks @zarina I'll add the additional details in - didn't want to put too much detail in the question, since the person in question is now an active researcher. – Pasted Mar 5 at 14:48
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    @Pasted "since the person also claimed that in addition to writing the code they used the code to produce the results in that chapter" If they directly claimed they wrote the code that needs to be added in to the question. Also if they directly claimed to have done work you actually did, that also needs to be added into the question. – Murphy Mar 5 at 18:07
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If code was produced under another employment then this question is not mainly about academic plagiarism but rather about potentially theft of intellectual property from this company. Either by you if you used it without being allowed to by your previous employer or by this other student who hadn't asked neither this company nor you.

  • The initial pipeline and filtering code was produced as part of a postgraduate qualification that I undertook before entering employment with that particular employer. Since that time the code has further been developed, although I maintained associate status with my old university. Note that the postgraduate qualification was self funded. The code and concepts pre-date my employment, although data from that employer was used as part of the development process. There was no explicit discussion of IP rights, or any contracts signed. – Pasted Mar 6 at 13:50
  • @Pasted ok then I guess I misunderstood the situation. – mathreadler Mar 6 at 14:19
  • I guess I can flip this on it's head and ask since the code was developed and working prior to my employment, and it's essential for the main revenue generation of the department, should they be giving me a portion of these revenues! Certainly my ex-employer had specific guidelines that stated this. – Pasted Mar 6 at 14:51

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