[Bioc-devel] Question on GPL2 license copyright

Levi Waldron |w@|dron@re@e@rch @end|ng |rom gm@||@com
Fri Jul 29 14:46:01 CEST 2022

Dear Ji-Ping and all, here are some more thoughts of my own on software
licensing and ethics, in case they are helpful. I separate out questions of
software licensing and code reuse from academic conduct/misconduct:

Software licensing and code reuse: I think it's fair to say that the
emphasis of the GPL license is on ensuring the freedom of anyone to copy,
modify, and redistribute the software, and on not allowing anyone to
restrict that freedom on derivatives - not on ensuring attribution,
although GPL does maintain copyright and requires anyone copying or
modifying and distributing to prominently display the original copyright
notice and to indicate which files have been modified and when. There are
situations where direct code copying is really advantageous to users, as a
few examples, to incorporate code from another package without requiring
all of that package's dependencies, to incorporate code from packages not
in CRAN or Bioconductor or unpackaged code, or to fix compilation / linking
problems. In other instances where it's not beneficial to users, it's still
allowed by the license and within the spirit of the GPL license.

Academic conduct/misconduct: if someone copies your code and claims it as
their own work without attribution, that could represent plagiarism and
academic misconduct, even if it would be allowed by the software license.
For example, code under a completely public domain license like CC0 that
surrenders copyright, or writing that is too old to be protected by
copyright, must be attributed and not claimed as your own. That is normally
the realm of journals and universities to adjudicate and take action on.
The Bioconductor project isn't currently equipped to adjudicate matters of
academic integrity, and as far as I know, no other distributor of
open-source software tries to do it either.

On the other hand, benchmarking against an old version of your software may
be misleading and not very fair, but probably not misconduct or even
incorrect if they stated the software version they benchmarked against. I
would think the available remedy is a rebuttal letter/editorial, or
publishing updated benchmarking with the new version of your software. I've
experienced unfair and inaccurate characterizations of my own work too, but
ended up deciding that the most effective way forward was just to continue
trying to improve my own product and to communicate its value, because I
think most users decide what software to use based on their own experience
and understanding of what the software can do for them, rather than on what
competitors say about each other.

I hope that this experience won't discourage you from submitting to
Bioconductor, especially since these same issues exist no matter where you
publish your software.



Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035


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