A few things to focus attention on (but please mention others as well):

PeerJ is interesting but obviously still a giant unknown, which we spent plenty of time speculating about.

figshare has a lot of what we talked about in spirit: a place to publish and cite all kinds of objects. Although textual objects can be put there, the emphasis there is on visual objects, so it doesn’t match quite as well with our conversational focus. But it seems to me whatever we build should include linking to figshare in a nice, integrated way.

PaperCritic by Mendeley is at the other end of the spectrum, totally focused on peer review of actual papers. It doesn’t serve as a place to actually post papers, however. Its usefulness seems intimately tied to how Mendeley-ized your life is, and I think there are both benefits and obvious drawbacks to this. And certainly it’s as unpervasive in the culture as anything else.

Also, Lonnie’s question of why exactly did Nature Precedings fail seems to me very important. Without actually knowing anything, I suspect it’s the lack of a focused community.

Utopia Docs is a desktop app (PDF reader) + web service that allows users to annotate PDFs in a localized (anchored), conversational format. Annotations are universally visible: if another user opens the same PDF, they’ll see other users’ annotations.

http://getutopia.com/

Stack Overflow

Upvoting/downvoting of questions/answers/comments, credit accumulation, new capabilities as credit is accumulated (e.g., can only upvote comments after some number of points have been gained).

Mismatch between length of questions & the long-form articles we want to be able to handle.

http://stackoverflow.com/

Commentpress

Fine-grained commenting theme for WordPress, so that conversations can happen on paragraphs. Big advantage over Utopia: in the browser; in WordPress and therefore more hackable.

http://www.futureofthebook.org/commentpress/

Annotum

WordPress theme for “journal” publication/review used for PLoS Currents

http://annotum.org/

http://currents.plos.org/

PLoS Hubs

“Portal” platform, currently only one example.

http://hubs.plos.org

Thoughts/mashups

• Pull Utopia Docs/other annotations could into a Stack Overflow or other-like service via an API?
• WordPress-based solution using Annotum/CommentPress/ratings plugin, etc., etc.
• Some other content management system/framework (Drupal etc.)

• continuous
• community rejection—the “quack” button
• “reputation” for reviewing quality, meta-reviews
• a review is a citable object (that therefore can be peer-reviewed)
• scoring:
• different levels of depth: review (continuum & content) vs. reader score
• commenting: no score assigned
• anchored reviewing (line #/annotation): can review pieces of an article
• notification after revision, old versions marked as deprecated
• versioning: what is the user interface to prevent confusion about the timeline?
• private review possible
>comment as real person or pseudonym?
• comments tied to a single account
• conflict of interest for scored reviews