PubPeer 2.0

We are proud to announce the new version of PubPeer, developed with the generous financial support of the Laura and John Arnold Foundation.

The original site, developed by George Smith, one of the PubPeer founders, has proved remarkably effective and durable, especially considering that it was constructed and maintained as a spare-time project. However, as the function and aims of PubPeer have crystallised, as traffic increased and as George progressively moved on to other things, the site became more and more difficult to maintain and extend. It was time for a rewrite.

Many big changes are under the hood and will hopefully remain invisible to users: a new framework, a new database schema, better administration, simpler moderation, better backups… However, there are of course many user-visible changes, beyond the redesigned graphics.

The most significant is identity management. Like death and taxes, we consider it only a matter of time before user information would leak in some way: a bug, a site administration screw-up, a court case, a hack. The only certain protection is never to know information we don’t wish to see exposed. So henceforth we shall only hold account information for signed comments. Anonymous users can obtain an account with a pseudonym (assigned from the tree of life), which can be accessed with a code. The pseudonym accounts will make it easier to follow anonymous discussions and allow us to fast-track comments from trusted pseudonyms. Identifying a pseudonymous commenter would require obtaining their code from them and therefore knowing who they are in the first place. Keeping that code safe is the user’s responsibility. Although we don’t purposely keep IP logs, anonymous users wishing to prevent identification by traffic analysis or undetected site penetration should continue to use Tor. A downside of not storing this information is that we cannot automatically send alerts to users that have commented on publications; users will have to sign-up for alerts for each publication using the button on the right.

As before, comment content must be factual and verifiable. In addition, all pseudonym accounts can be switched between a whitelist (comments appear immediately) and a greylist (comments must be moderated) at will. All new pseudonym accounts are initially greylisted and must prove themselves worthy before they will be whitelisted. So please continue to report all comments that do not respect our guidelines.

The site comes with much more capable commenting features, including rich text, embedded images and tables, all based upon the simple markdown syntax. We are especially proud that it is now possible to include LaTeX equations and hope that this will encourage increased involvement of physicists and mathematicians. Comments can now be previewed, which will help catch typos and other easily-corrected mistakes, thereby improving comment quality.

We have also changed the threading model. All comments are displayed in flat chronological order of posting. If comments reply to others, back-links are inserted. References to other articles and threads will also be indicated by links inserted into the target threads; these are similar in function to the poorly visible “internal links” of the old site.

We request your help and patience during the transition to the new site. Please report any bugs you find. The plugins will not receive information about new comments for a short period.

Go forth and comment!