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I want to publish the software package I've written for my graduate work along with a paper describing the package. So far I've been considering liberal licenses such as BSD.

However, I am now aware that publishing your code may involve an agreement to the journal's licensing terms (cmp. e.g. this question) or even transfer of copyright. All this is undesirable. Are there any obvious choices concerning the journal? My field is physics. Do you have experience founding a BSD-license style open source project and publishing an accompanying paper?

I am aware of Computer Physics Communications (unfortunately published by Elsevier), cmp. QuTiP as an example. Thanks for your suggestions!

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    $\begingroup$ IMHO publishing a paper and publishing your software are two different things. If you publish your software prior to your journal paper, then the code in your paper - if you list any code in your paper - is a simple citation, right? $\endgroup$ – Dohn Joe Apr 22 '14 at 10:27
  • $\begingroup$ @DohnJoe That's right - though I am not sure the re-licensing involved is okay for all journals of interest. $\endgroup$ – AlexE Apr 22 '14 at 10:34
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    $\begingroup$ In many cases, your institution is actually the rights owner of work you produce. You may or may not actually have the legal right to choose your license in the first place. $\endgroup$ – Doug Lipinski Apr 22 '14 at 14:44
  • $\begingroup$ @DougLipinksi, that's a good point. I was founded by my country's public research funding organization. I believe it is along their guidelines to publish codes, but of course I have to double-check. $\endgroup$ – AlexE Apr 22 '14 at 15:10
  • $\begingroup$ In most places, thesis work is not work for hire. Thus, you most likely own the code you wrote. But it never hurts to ask and get a reply from the administration a few months later. $\endgroup$ – Guido Kanschat Apr 25 '14 at 6:02
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The best way to do this to avoid these issues is to publish a paper about what your software package does and the problems it solves and cite your Github repo or website or whatever for access to the software. That way you don't need to give up your copyright on your code, and you can BSD/MIT/GPL it to your heart's content.

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