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I am considering publishing a Mathematica notebook, used for analysis of some data, as a “supporting information” file alongside a research paper. What are the common practices for doing so, and what should I consider in making this choice? In particular, I am wondering:

  • Is the .nb format suitable, or should I transform it into a CDF?
  • Or is it better to include a PDF of the Mathematica notebook (thus readable by anyone), attaching the notebook itself inside the PDF (thus allowing Mathematica owners/users to use it directly)?
  • Do I need to audit/edit the content of the file to remove any metadata that could leak?
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Regarding citation, there are some (possibly obsolete) guidelines here. – b.gatessucks Nov 2 '12 at 15:27
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To be safe, why not provide both the CDF file and the notebook? – J. M.♦ Nov 2 '12 at 15:30
@J.M. I don't want to overload the supporting information with what would be duplicate information… I have meanwhile had the idea for another possibility (PDF), and thus edited the question. – F'x Nov 2 '12 at 15:38
@J.M. A CDF file can be opened in Mathematica and, in my experience, works just like a notebook in that context. What's the advantage of publishing both? I think I'd go with CDF so that anyone can read it. – Mark McClure Nov 2 '12 at 15:55
@Mark, some of the stuff John brought up here came to mind... – J. M.♦ Nov 2 '12 at 15:59
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