The nano.org project is currently in early beta testing - during this phase the peer review process described below is not available. Read more about the beta test here.

Background
For readers who might be unfamiliar with the normal process of peer review, here is a brief summary.

• When scientists wish to add their latest research results to the body of publicly known science, they generally do so by writing a research article and seeking publication in a peer reviewed journal. This is a journal, such as the magazine Nature, where the editors solicit confidential reviews from other scientists in order to reach a opinion as to the scientific merit of a given article.

• Typically the editors send a newly received article out to two or three reviewers. Usually the reviewers are permitted to see the identity of the authors. When the editors receive back the reviews they make a decision regarding publication ("yes"/"no"/"maybe, after revisions") and write to the authors, attaching the reviews.

• The authors are not permitted to know the identity of the reviewers. Thus the reviewers can feel free to write honest appraisals even if those appraisals are so negative that they would damage professional relationships if the reviewer were known to the author.

The merit of this procedure is that is provides a filter which (usually) prevents poor quality science from reaching the mainstream. It also allows a hierarchy of journals to exist, with those at the top of the pile, such as Nature and Science, able to select only those submissions rated as extremely important and high quality reports. From the author's perspective, the process of review (and the existence of the hierarchy) can be helpful in improving the manuscript. However, there are some very significant drawbacks. Despite the best efforts of the editors, sometimes a referee will be chosen who has a poor grasp of some of the necessary background science, and who therefore reaches incorrect conclusions (either positive or negative) in his/her review. Equivalently, the reviewer may have some personal bias regarding the authors or the research topic, which is not reflected by the community at large and therefore should not be influencing the publication decision. These issues are not detected because there is no "review of the reviewers" - that is, the only parties involved in the review process are the editor (not a specialist in the topic of the paper), the authors (biased in their own favor of course) and the reviewer.
Other weaknesses of the system include the fact that it is rather slow, in part because all transactions regarding the paper must pass though the relevant editor: the authors and reviewers cannot directly interact to resolve confusions.

Open peer review at nano.org
In view of these drawbacks, several journals are exploring Open Peer Review (OPR) models. The nano.org project uses its own OPR system, offering authors a formal review of their work within an open environment. When an author uploads a manuscript, such as a preprint, to nano.org, they have the option of submitting that paper to OPR. This process occurs on top of (and integrated with) the discussion thread that is automatically associated with any submitted manuscript. On nano.org the purpose of OPR is not to reach any kind decision analagous to "publish"/"don't publish", but rather to provide authors with feedback and to simulate high quality discussion and analysis. Note that the open nature of the process means that opinions of the Reviewers may be challenged by other Scholars, resulting in a lively and engaging thread that brings exposure to the research. Threads into which OPR reviews have been posted are flagged as such, and many Scholars browsing nano.org many choose to focus their attention onto those papers. Here is an outline of the process:

Open Peer Review - During process of uploading a manuscript to nano.org, the author is presented with the option to submit the manuscript for OPR. The article will be immediately uploaded and made available, and a standard discussion thread will be created. However a subsequent process will now occur. The manuscript will be assigned to an OPR Moderator, who will inspect the manscript to ensure that it is, in principle, suitable for nano.org in terms of topic covered etc. Then the Moderator will contact the corresponding author by email and invite him/her to provide a list of suitable reviewers. The Moderator then selects two reviewers from the scientific community (not necessarily from the author's list) and writes to them, requesting that they post a review into the nano.org discussion thread. When they do so, their post is flagged as "REVIEWER". Others can see these reviews, and indeed comment on them if they feel that they are unfair for example. The intention is to elevate the level of the discussion in the thread though the input of the Reviewers, who have taken time to scrutinize the paper. As with any poster, the reviewer may choose to reveal his/her name or to be anonymous. The reviewers may also use the thread as a channel to directly interact with the authors, e.g. to clarify claims the authors are making, without requiring the Moderator to act as 'middle man'. If a reviewer requests changes to the paper, the authors may choose to make those changes and replace their paper, again without involvement from the Moderator. Crucially, the reviews are available to all readers of the thread, so that a poor review can be challenged by 3rd party scholars. The Moderator will periodically read the discussion thread and may, for example, politely 'chase' tardy reviewers or invite additional reviewer(s) when there is controversy. When the Moderator examines a thread, he/she will also seek to form an impression of how the manuscript is regarded by the nominated reviewers, by the wider nano.org community, and possibly by the entire scientific community (though citations). In the event that this impression is exceptionally positive, the Moderator may flag the manuscript and its discussion thread as "Outstanding". The purpose of this flag is to draw attention to papers that have been very well received and generally felt to be important research. Many readers may make it a point to check all recent "Outstanding" papers whenever they visit nano.org, for example.

We emphasise that only papers which garner a exceptionally strong positive response will be flagged as Outstanding, so that the lack of this flag does not imply that the paper is not worthy of publication at even the highest level. Moreover, a paper may naturally take some time to be fully appreciated - for example if it proposes an exotic explanation for some phenomenon which is later proven to be the correct explanation, or more simply if it eventually accrues a large number of strong citations.