Via First Author, I see that BioMed Central has added the ability for authors to include extra web material with a paper:
... to make it possible to upload collections of files that can be conveniently navigated in the web browser - essentially a miniature website associated with the article. This functionality has now been added to the BioMed Central publication system.
The BioMed Central homepage offers instructions for uploading these ‘mini-websites’ as a ZIP file. Readers of the published article will have a choice of whether to download the ZIP file to view locally on their own machine, or alternatively they can follow a link to view the contents of the ZIP file via the BioMed Central website...
There's a link there to an article about butterflies, with some extra material in HTML.
This sounds like something that ICE could do really well. ICE has lets you create “mini-websites” complete with internal navigation with an export to ZIP. The ZIP files exported by ICE are actually IMS packages, designed to slot into learning management systems, but they work as stand alone websites. You can see examples at the USQ open courseware site, see the automatically generated navigation at the left? This could be a good way to package materials. You can tie just about anything together into a package using ICE, and we're working hard right now to make sure that there are tools to help embed data visualizations into documents as seamlessly as possible.
I'm working on a paper at the moment about exporting HTML from word processors. One of the things I've been doing is documenting some of the issues with the built-in HTML export in widely available software pacakages. I was just going to link to the blog, but one idea would be to include all these blog posts and a set of sample documents as a package to go along with the paper. Whether or not a publisher would be set up to take it is another matter.
Another packaging mechanism that might be useful given tools to support it would be METS pacakages. We saw first hand at our repository interop workshop how APSR developed an Australian METS profile for packaging journals, to enable automated depost from a journal management system into a repository. But who knows how to make a METS package? Apart from geeks like the ICE team, or some speical repository-rats1, that is. BioMed Central's choice of ZIP is sensible. No fancy metadata required, just make sure your ZIP has an entry point named index.html. But it could do more if it knew how to deal with IMS content packages or a METS profile as well.
To submit such a 'mini-website' as an additional material file, all you need to do is to ensure that the homepage is named index.html, and sits in the root folder of the content you wish to submit. Then convert the folder hierarchy into a ZIP archive, and upload this ZIP file using the regular manuscript submission system, which will recognize and process it automatically. Full guidelines are provided in each journal's Instructions for Authors (example).
1 Dorothea Salo, “A Messy Metaphor,” Caveat Lector , Blog, January 9, 2006, http://cavlec.yarinareth.net/archives/2006/01/09/a-messy-metaphor/