From: Alex Gutteridge <alexg@...>
Date: 2007-03-16T09:29:22+09:00
Subject: Re: [slightly OT] New O'Reilly book features Matz

On 16 Mar 2007, at 00:04, Yukihiro Matsumoto wrote:

> In message "Re: [slightly OT] New O'Reilly book features Matz"
>     on Thu, 15 Mar 2007 15:47:48 +0900, "M. Edward (Ed) Borasky"  
> <znmeb@cesmail.net> writes:
>
> |programming". It was intended to get the programmer to create the
> |documentation hand in hand with the code. However, literate  
> programming
> |has evolved into a concept I find very appealing -- so called
> |"reproducible research." As practiced by the bio-informatics  
> community
> |in the R language, the core concept is something called a  
> compendium. A
> |compendium is a software package, which contains all of the code and
> |data required to reproduce the research, including the tools to write
> |the paper. The way it's done in R, and the way it could be done in  
> Ruby,
> |the author creates a collection of source and data files. The  
> literate
> |programming process of _weaving_ produces the document -- in the  
> case of
> |R, this includes running R scripts that do the analysis, create the
> |figures, and so on.
> |
> |I think what I really would like to see is some combination of
> |test/behavior driven development and reproducible research. In short,
> |the programmer develops the tests, the software *and* the  
> documentation
> |concurrently.
>
> Interesting idea.  Where can I find more information for compendium
> (in R)?
>
> 							matz.
>

There are some example compendiums here:

http://www.bioconductor.org/docs/papers/2003/Compendium

and this paper is a good introduction:

http://www.bepress.com/bioconductor/paper2/

> "M. Edward (Ed) Borasky" <znmeb@cesmail.net> writes:
> I am actually hacking away on a project called Rameau to bring  
> reproducible research to Ruby -- more the other way around,  
> actually -- to apply the pragmatic automation of Ruby to the  
> processes of reproducible research. I haven't spent too much time  
> on it recently, but I'll assume neither you nor Matz is interested  
> in volunteering to join it when I get more of it laid down and  
> start looking for help. :)

Ed: I'd be interested in playing/helping with Rameau - have you  
released anything yet?

Alex Gutteridge

Bioinformatics Center
Kyoto University