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IPython Notebooks, dissertations, and scholarly publication

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IPython Notebooks, dissertations, and scholarly publication

mcburton
Hello,

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.

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. 

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]? 

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.

--
mcb 






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Re: IPython Notebooks, dissertations, and scholarly publication

Gabriel Becker
Matt,

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.

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]

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).

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.

The paradigm wherein documents are used to generate articles rather than  being the articles themselves is actually an extremely powerful one. It allows us to, potentially, move beyond the ability to regenerate results (repeatability) towards being able to reproduce research (reproducibility). To quote  AJ Rossini from an embarassingly long time ago [3]

The resulting document should provide a clear description of the paths taken during the analyses to produce the working dataset, descriptive, exploratory, and con firmatory analyses. This should describe results and lessons learned, both substantiative and for statistical practice, as well as a means to reproduce all steps, even those not used in a concise reconstruction, which were taken in the analysis

(emphasis mine).

That, however, is a discussion for another time (and has to a large extent already happened on this list with respect to IPython specifically).

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.

~G

[1] http://www.executablepapers.com/

[2] http://www.vistrails.org/index.php/Main_Page#Publishing_Reproducible_Results

[3] http://www.r-project.org/conferences/DSC-2001/Proceedings/Rossini.pdf


On Thu, Oct 17, 2013 at 1:55 PM, mcburton <[hidden email]> wrote:
Hello,

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.

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. 

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]? 

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.

--
mcb 






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--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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Re: IPython Notebooks, dissertations, and scholarly publication

Thomas Kluyver-2
In reply to this post by mcburton

I know someone wrote their thesis in sphinx - google sphinx thesis resource. You could probably integrate notebooks into that via nbconvert, though the output is then essentially static documents.

Thomas

On Oct 17, 2013 3:55 PM, "mcburton" <[hidden email]> wrote:
Hello,

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.

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. 

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]? 

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.

--
mcb 






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Re: IPython Notebooks, dissertations, and scholarly publication

Jason Moore
I wrote my dissertation as a Sphinx document: moorepants.github.io/dissertation. The source to generate most of the figures was included with the Sphinx source. The IPython notebook wasn't an option at the time, but I would have certainly considered it for distributing some of the calculations. There is a more formal package for using Sphinx for a thesis here: https://github.com/jterrace/sphinxtr. Notebooks could be integrated into the Sphinx output.


Jason
moorepants.info
+01 530-601-9791


On Thu, Oct 17, 2013 at 8:04 PM, Thomas Kluyver <[hidden email]> wrote:

I know someone wrote their thesis in sphinx - google sphinx thesis resource. You could probably integrate notebooks into that via nbconvert, though the output is then essentially static documents.

Thomas

On Oct 17, 2013 3:55 PM, "mcburton" <[hidden email]> wrote:
Hello,

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.

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. 

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]? 

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.

--
mcb 






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[hidden email]
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http://mail.scipy.org/mailman/listinfo/ipython-dev



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