Dear Dr. Ashendel,
as one of the major contributors to both the MediaWiki software and the
(rather sparse) biochemistry texts on wikibooks, I understand the
problem you describe, as well as the solution you propose.
There is currently a way to use wiki pages (within the same wiki) as
modules. This template function was not designed to be used for this,
but it should work reasonably well. For example, writing "{{:Protein}}"
in a wiki page will display the text from the [[Protein]] page of this
wiki at the respective position.
A similiar mechanism is possible for images that are stored on wikimedia
commons [1]. "[[Image:Cell.jpg]]" will look on the local wiki for this
image, and if none is found, it will try the commons instead.
As both images and texts can be reused (with limits, though), it is
already be possible to write [[Proteins (brief)]], [[Proteins (long)]],
etc., and include these in other pages. (Modules would be more
fine-grained than "Proteins", of course).
Furthermore, this mechanism can be used to generate a (simple) stable
version. All articles that should belong in a book (for example) are
included on a single page in the desired order. The page that results
could be considered a "frozen" version for the time being, can be
printed into a virtual PDF printer, or saved as HTML (with some minor
modifications on HTML and CSS for offsite use).
There is a wiki-to-XML parser under development by others and myself. It
will, among other things, greatly improve export functions, e.g., to
OpenOffice XML. If you happen to know someone familiar with the Bison
parser generator who is willing to help on this, it would be greatly
appreciated.
It would be my pleasure to work with you on at least a demonstration on
wikibooks. It might be a good idea to set up a relatively narrow field
(e.g., protein structure/folding) as modules on several levels, then
generate a set of chapters and presentation-like pages by including them
through the template mechanism.
Yours,
Magnus Manske
[1]
http://commons.wikimedia.org