Dallas B. Warren wrote:
FYI, MediaWiki is the one used by Wikipedia (plus the one that use /
know).  There are others.

In terms of integration with a Joomla site, I don't think there is
anything very good that works with MediaWiki.  Was one floating around
awhile ago, a component, but it didn't do a very good job (wiki is
displayed inside an iframe, so URL doesn't change on browser) and I
don't think it has been developed further.  There may be a better wiki
software now that integrates with Joomla better, if that is what you
want to do, just check the Joomla site.

I googled a bit for wikis that work with Joomla (e.g. http://extensions.joomla.org/component/option,com_mtree/task,listcats/cat_id,1812/Itemid,35/), and found OpenWiki http://projects.j-prosolution.com/projects/os-projects/project-openwiki.html (formerly JD-Wiki) and thought it looked good. It's a Joomla integration of the standards-compliant DocuWiki, whose feature list is here http://wiki.splitbrain.org/wiki%3Afeatures

I followed some other links to a wiki-comparison wiki at http://www.wikimatrix.org. This contains a feature where you can select features that you want in your wiki and it'll give you a table of compliant wikis and you can whittle them down further. Whoever on the GROMACS team will make this choice should probably do this process themselves :-) After filtering for what I thought we'd want, the resulting candidates are listed here http://www.wikimatrix.org/compare/DokuWiki+Giki+MoinMoin+Perspective+PmWiki+ProWiki+PukiWiki+wxWikiServer+yawiki

The only features DocuWiki lacks that I think might be desirable is WYSIWYG editing and MediaWiki-syntax compliance. I wouldn't want WYSIWYG, but some people would rather not maintain documents with markup inside it. MediaWiki seems to have more market share than DocuWiki, but the syntax examples for DocuWiki look straightforward and accessible.

Mark
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