<div dir="ltr"><div><div><div><div><div><div><div>Matt,<br><br></div>Disclaimer: I'm not on the IPython core team and I don't claim to represent the views of the team or any particular member therein. I am, however, doing my thesis on systems for creating, processing, and displaying documents which capture and convey the research process for data analytic research, so I've thought about this topic a bit.<br>
<br></div>The concept of executable journal articles and repeatability (I use this term instead of "reproducibility" for a very specific reason which I will get to later length permitting) in "in silico" research is an exciting one which has been getting a good amount of attention lately [1] [2]<br>
<br>IPython has quite a bit of potential in this arena but IMO more as a submission format and downloadable form for papers rather than the default viewing mechanism for them. One reason that I say this is that while the availability of the exact code used to run the analysis described in a paper is *extremely* important, in many contexts its actually pretty detrimental for every single line of code to appear in an article as it is being read (this does not include some situations where the intended purpose is to teach coding or which require full display of the code for other reasons). <br>
<br></div>nbconvert gives us a way around this by allowing us to generate a concise static view containing only the text and code we actually want to show (ie an article pdf/HTML page), but we lose the interactivity. Furthermore, if we want to distribute the ipynb and allow people to run it then generate the static article view themselves (we do), we need to distribute the nbconvert filter as well, which loses us the "everything contained in a single file" benefit.<br>
<br>The paradigm wherein documents are used to <i>generate</i> articles rather than <i>being</i> the articles themselves is actually an extremely powerful one. It allows us to, potentially, move beyond the ability to regenerate <i>results</i> (repeatability) towards being able to reproduce <i>research</i> (reproducibility). To quote AJ Rossini from an embarassingly long time ago [3]<br>
<br><div style="margin-left:40px"> <span style="font-family:arial,helvetica,sans-serif">The resulting document</span><span style="font-family:arial,helvetica,sans-serif"> should provide a clear description of the paths taken during the analyses to pro</span><span style="font-family:arial,helvetica,sans-serif">duce the working dataset, descriptive, exploratory, and con firmatory analyses. This</span><span style="font-family:arial,helvetica,sans-serif"> should describe results and lessons learned, both substantiative and for statistical</span><span style="font-family:arial,helvetica,sans-serif"> practice, as well as <b>a means to reproduce all steps, even those not used in a concise</b></span><b><span style="font-family:arial,helvetica,sans-serif"> reconstruction, which were taken in the analysis</span></b></div>
<br></div>(emphasis mine).<br><br></div>That, however, is a discussion for another time (and has to a large extent already happened on this list with respect to IPython specifically).<br><br></div>Getting back to the more immediate subject, I think its great that you're thinking of having your thesis be a notebook. I think there are a large number of benefits to doing so even if you end up needing to use nbconvert to generate a concise "readable" version for publication or submission to your committee.<br>
<br></div>~G<br><div><div><br><div><div><div>[1] <a href="http://www.executablepapers.com/" target="_blank">http://www.executablepapers.com/</a><br><br>[2] <a href="http://www.vistrails.org/index.php/Main_Page#Publishing_Reproducible_Results" target="_blank">http://www.vistrails.org/index.php/Main_Page#Publishing_Reproducible_Results</a><br>
<br>[3] <a href="http://www.r-project.org/conferences/DSC-2001/Proceedings/Rossini.pdf">http://www.r-project.org/conferences/DSC-2001/Proceedings/Rossini.pdf</a><br>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Oct 17, 2013 at 1:55 PM, mcburton <span dir="ltr"><<a href="mailto:mcburton@gmail.com" target="_blank">mcburton@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>I am on a panel discussion tomorrow morning talking about "digital dissertations" (broadly construed) and I was going to bring up the IPython Notebook as not only a platform for interactive computing, but the Notebook specifically as an emerging genre of scholarship in and of itself.</div>
<div><br></div><div>We have already seen published Notebooks being used for teaching programming[1], as supplementary materials for a book[2], and even as a platform for the book itself[3]. I toying with ways to similarly integrate the notebook into my dissertation (most likely as supplementary material on Github due to institutional formatting constraints). But it would be interesting to ruminate about the possibility of submitting a Notebook (or set of Notebooks) to my committee. </div>
<div><br></div><div>I was wondering if there is anyone on this list who has similarly explored, if only in your imagination, the IPython Notebook as a platform for dissertations or, to be even more provocative, as a platform for scholarly publishing more generally[4]? </div>
<div><br></div><div>I've been spreading the IPython Notebook gospel in various conversations about new modes scholarly communication/publishing and people get very excited. I'd love to hear what folks on ipython-dev think.</div>
<div><br></div><div>--</div><div>mcb </div><div><br></div><div><br></div><div>[1] <a href="http://peak5390.wordpress.com/2013/09/22/how-ipython-notebook-and-github-have-changed-the-way-i-teach-python/" target="_blank">http://peak5390.wordpress.com/2013/09/22/how-ipython-notebook-and-github-have-changed-the-way-i-teach-python/</a></div>
<div><br></div><div>[2] <a href="https://github.com/ptwobrussell/Mining-the-Social-Web-2nd-Edition" target="_blank">https://github.com/ptwobrussell/Mining-the-Social-Web-2nd-Edition</a></div><div><br></div><div>[3] <a href="http://camdavidsonpilon.github.io/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/" target="_blank">http://camdavidsonpilon.github.io/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/</a></div>
<div><br></div><div>[4] <a href="https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks#-reproducible-academic-publications" target="_blank">https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks#-reproducible-academic-publications</a></div>
</div>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Gabriel Becker<br>Graduate Student<br>Statistics Department<br>University of California, Davis<br>
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