[IPython-dev] [FWD] An interesting take on the Notebook Problem

Fernando Perez Fernando.Perez at colorado.edu
Fri Jul 15 19:27:42 EDT 2005

[Chris, note that ipytho-dev discards non-subscriber posts (too much spam). 
I've manually forwarded your message ]

> ------------------------------------------------------------------------
> Subject: An interesting take on the Notebook Problem
> From: Christopher Hart <christopher.e.hart at gmail.com>
> Date: Fri, 15 Jul 2005 13:05:02 -0400
> To: ipython-dev at scipy.net
> To: ipython-dev at scipy.net
> Hi,
> I've been lurking and casually reading the notebook discussion during
> the past month or so.  I'm quite excited about the progress that seems
> to be going on, and the ideas that are being flushed out.
> In the bioinformatics community the problem of recording ones analysis
> for both later inspection and sharing is a large problem.  This paper
> takes, although not precisely focused on the notion of an interactive
> notebook, might still be an interesting read to anyone involved in
> creating a notebook.  I think it highlights nicely some of the
> problems and the desires of at least one active community that would
> benefit greatly from a ipython notebook.  Personally, the particular
> implementation they provide doesn't appeal to me - but that's largely
> because I prefer (i)python ;)  Aside from the methods section - little
> actually knowledge of bioinformatics is a prereq for reading.
> Just thought I'd share....
> Robert Gentleman (2005) "Reproducible Research: A Bioinformatics Case
> Study", Statistical Applications in Genetics and Molecular Biology:
> Vol. 4: No. 1, Article 2.
> http://www.bepress.com/sagmb/vol4/iss1/art2
> """
> Reproducible Research: A Bioinformatics Case Study
> Robert Gentleman, Harvard University
> While scientific research and the methodologies involved have gone
> through substantial technological evolution the technology involved in
> the publication of the results of these endeavors has remained
> relatively stagnant. Publication is largely done in the same manner
> today as it was fifty years ago. Many journals have adopted electronic
> formats, however, their orientation and style is little different from
> a printed document. The documents tend to be static and take little
> advantage of computational resources that might be available. Recent
> work, Gentleman and Temple Lang (2003), suggests a methodology and
> basic infrastructure that can be used to publish documents in a
> substantially different way. Their approach is suitable for the
> publication of papers whose message relies on computation. Stated
> quite simply, Gentleman and Temple Lang (2003) propose a paradigm
> where documents are mixtures of code and text. Such documents may be
> self-contained or they may be a component of a compendium which
> provides the infrastructure needed to provide access to data and
> supporting software. These documents, or compendiums, can be processed
> in a number of different ways. One transformation will be to replace
> the code with its output -- thereby providing the familiar, but
> limited, static document. <p /> In this paper we apply these concepts
> to a seminal paper in bioinformatics, namely The Molecular
> Classification of Cancer, Golub et al (1999). The authors of that
> paper have generously provided data and other information that have
> allowed us to largely reproduce their results. Rather than reproduce
> this paper exactly we demonstrate that such a reproduction is possible
> and instead concentrate on demonstrating the usefulness of the
> compendium concept itself.
> """
> --chris

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