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Someone published a paper whose supplementary material contains source code. Can I include part of that code (I would mark it as copied in the source and the manuscript) in my own code, which is intended for the supplementary material of my own paper?
If not (or at least not automatically), who would I have to contact to ask for permission, the journal or the author of the other paper?
If the published code is licensed, follow the terms of the license. This website sums up in a concise way what the most common open source licenses allow you to do or not.
If you cannot find a license, or if you are sure there is none, then by default you have almost no right to do anything with it (in most countries, no license means all rights reserved to the author). You still have the right to contact the corresponding author of the article, or the author of the code (if they are not the same person, and if you can find the contact info of the author of the code), and request permission to reuse their code, or even better ask them to explicitly attach the license of their choice to their code. Then, follow the license terms.
Ask the author. First, possibly, they made this code available elsewhere, e.g., Github, and you can reference that place, instead of saying that you copied the code from a journal article. Second, if what you do is copy over parts of someone else's code it into your code, there's a chance that the author would object to that, and would instead propose a cleaner way to re-use their work.
But it is a good question, what happens to the rights on the code that is submitted to a journal as supplementary material. I don't know.
