Just a curiosity following up on the notebook question:  Is there a standard practice to submitting journal articles with iPython notebooks?  We were looking to do the same with a few papers in our lab and wondered if this was common yet, if there were guidelines set forth by the journals to this regard, and if only certain journals accepted notebook as accompanying materials.

On Friday, January 24, 2014 7:01:39 PM UTC-5, Stefan van der Walt wrote:

On Fri, 24 Jan 2014 17:57:17 -0500, François Boulogne wrote:
> I think we should decide where and how we write codes, in the text with
> a snippet style and/or at the end with a full code.
> I don't know how it depends on the journal where you want to submit the
> paper. Have you reached a consensus about that?

If you want to show something specific, e.g. the simplicity of building a
pipeline, for which you need just 3-5 lines of code, then it should probably
go inline.  If it is a longer snippet, attach it at the end or perhaps think
whether it should be included at all.

We can very easily write an IPython notebook and simply reference that from
the paper for examples.

Stéfan