Thinking about Open Notebook Science

A lot of water under the bridge since my last post. For the most part, my thesis proposal is coming up for defense later this month, and a lot of thinking and experimentation has followed. Right now, I am looking at Jean-Claude Bradley’s comments to this blog post on Open Notebook Science; those comments provide an opportunity for me to explain my latest thinking. I’ll take his three points and comment on each.

Use a wiki as the actual notebook with one experiment per page.

I agree with that. In fact, one experiment per page relates closely to Wikipedia’s one topic per page, and appears to express the notion of subject-centric federation as I see it. In fact, I am now using MediaWiki as the platform of choice.

Use a blog to discuss milestones and key problems to a more general scientific audience and link back to the experiments in the wiki.

I agree with that. Use blog posts to advertise conference papers and so forth.

Use a mailing list for external collaborations.

Now, we depart the full agreement category, with all due respect to the long history of using the killer app, email. When it comes to using email for topic-centric discourse, the term killer app might not be so appropriate in its original sense. I believe that there are existing and emerging technologies that allow for the integration of structured conversations (which, in the long run, could be conducted with email clients after suitable features are added); here, I am thinking about the various dialects of argument or dialogue mapping. These platforms started out life as desktop applications and are now migrating to the web. Debategraph is among the pioneers; see Mark Klien’s blog for more about Deliberatorium, see the bCisive online platform for a new product, and see the Global Sensemaking wiki for more on such tools.

The recap of my view is this:

  1. Wikis satisfy the need to capture and organize knowledge resources, provide a platform for linking, as if behaving as a topic map, though a more general purpose topic map, a federation platform that unites many such wikis and other platforms, should be a web-services portlet window on each page
  2. Blogs satisfy the need for storytelling
  3. The many tools of hypermedia discourse, including IBIS platform such as Compendium, bCisive, Cohere, Debategraph, Deliberatorium and others, satisfy the dialogue needs in ways that, I believe, constitute improvement over traditional email clients, online forum platforms, and so forth.

My present projects include the fabrication of a prototype federation server, fabrication (through crowd-sourced “hackathons”) of a variety of AJAX-like adapters to allow communication between three platforms: Semantic MediaWiki, Drupal, and Wordpress, to the federation server, and the construction of a MediaWiki instance that demonstrates these systems at work.

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