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In a paper I developed some theory; some of the applications require extensive computations that are not part of the paper. I wrote a Mathematica notebook. I want to publish a PDF and .nb version somewhere to refer to from the paper. seems a good choice, but they won't accept the .nb file. I do not want to put this through peer review. Where to publish it?

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I think Doron Zeilberger just uploads them to his personal website and links to them in his papers. You might try that. – Qiaochu Yuan Mar 7 '10 at 1:58
A recent paper of mine had a good bit of code associated with it. We published the paper in a relevant journal to what the code produced(In this case JKTR) and put the entire code base up on one of the coauthors webpages. I think this is pretty standard, I have seen at least 3 other papers handle this the same way. The same method works well when you have really fancy diagrams that don't go well into the journal. – B. Bischof Mar 7 '10 at 2:22
up vote 29 down vote accepted

You should upload the notebook along with the sources of the actual article to the arXiv, of course.

The official (but rather hard to find) advice on this from the arXiv is to place your code in a directory called /aux/. (This is problematic for windows users.)

You can see an example of this in my recent paper on the extended Haagerup subfactor. A footnote in the text of the article explains that the code is available along with the source download. It would also be appropriate to use the comments field in an arxiv submission to explain that source code is available in the /aux/ directory.

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Thanks for helpful information. Where did you find this piece of advice? – Boris Bukh Mar 7 '10 at 10:22
Initially via email correspondence with the arxiv administrators, concerning a paper that broke the size limits because of embedded source code. Until very recently, there was a web page that showed an email conversation between someone at the arxiv and some library, talking about plans for future special handling of the /aux/ directory. This seems to have vanished, however. – Scott Morrison Mar 7 '10 at 17:41

The problem with storing the files on your personal website is that it is not clear how long that website will remain valid. What happens if you move to a new institution and your old account gets deactivated? The arXiv solution pointed out by Scott Morrison is better.

Here is another possibility: Some journals that publish an electronic version in addition to (or instead of) a paper version will allow you to include ancillary files with the electronic version of an article. If you'll excuse the self-promotion, see this journal's website, for example.

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Yes! Please be careful, I have seen papers who cite websites... and by the time the paper is published the link is broken. – Douglas S. Stones Mar 7 '10 at 8:04
Also, the LMS Journal of Computation and Mathematics allow attachments too. – Douglas S. Stones Mar 7 '10 at 8:04
I have published papers with references of the form [8] Link available at "publications" part of my website (currently [insert current location of website]). The links to the relevant files are right next to the links to the paper on my website. If my website moves its http address will move but its structure will stay largely the same, and I credit the reader with being able to use google. – Kevin Buzzard Mar 7 '10 at 9:43
@Douglas: I must confess that I am guilty myself of publishing an article that now refers to a non-existent webpage. – Bjorn Poonen Mar 8 '10 at 3:17

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