[Bioc-devel] Compendium tools?

[M. Edward (Ed) Borasky]

I'm just starting to experiment with the compendium concept, and I'm
looking for tools to make the job easier. It turns out that the current
version of LyX, 1.3.6, can read the "Rnw" files in the existing
compendia on the web site at

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

For those not in the know, there are two major "WYSIWIG" TeX editors,
TeXmacs and LyX. I have both. TeXmacs is a tad more powerful and LyX is
a tad easier to use, but on the whole they are of comparable utility.
TeXmacs can insert R, Maxima and other sessions directly into a document
but doesn't read and write files in "Noweb" format directly. LyX doesn't
have sessions but can read and write "Noweb" format. Both have their own
native formats but can import and export LaTeX directly and can create
PDF output.

I had some minor glitches with the bibliography section in LyX, but
that's most likely just a lack of knowledge of Bibtex conventions on my
part. So:

1. Is anyone else on this list working with tools for editing compendia
other than the usual text editors like vi and emacs?

2. Are there other tools I don't know about?

3. For bonus points, is anyone working on integrating the compendium
concept with the Rpad concept to create living documents that are
"active" and "beautiful" in the TeX/Metafont sense? For example, I'm
building a smallish queuing theory model, and I'd like to be able to
have the user open up a web site in Rpad, define a model and execute it,
then save off the PDF as a finished document.

4. Is the plural of "compendium" really "compendia"?  :) 

I'm on the TeXmacs mailing list, and there have been some discussions
recently about enhancing it for literate programming. I'm not on the LyX
mailing list, but I will probably join now after my "discovery". By the
way, as usual, all this magic works seamlessly in Linux but there are a
few seams on Windows. TeXmacs is part of the standard CygWin
distribution but can't get to Windows-side tools for sessions. And it's
been a while since I tested LyX on a Windows system but I remember quite
a few issues, even with CygWin.

-- M. Edward (Ed) Borasky http://linuxcapacityplanning.com

-- 
M. Edward (Ed) Borasky

http://linuxcapacityplanning.com