Five reasons you should upload a preprint to a repository before submitting to a journal

Source: https://jcoynester.wordpress.com/2017/01/24/five-reasons-you-should-upload-a-preprint-to-a-repository-before-submitting-to-a-journal/ 

January 24, 2017James C Coyne authorship, copyright, open access, PeerJ, PLOS One, preprint, Scientific writing, Uncategorized Tags: bioRxiv, GRIM, PLOS Genetics, University of Groningen, Wellcome Trust, Winnower

Credit:Editage

A preprint is a completed draft of a scientific manuscript that is uploaded by the author on a public server; often it is the same version of the manuscript that is submitted to a journal. Once the manuscript is uploaded, it goes through a quick check to ascertain that it is scientific in nature. It is then posted online within a day or two without peer review and is made freely available for everyone to view.  Revised versions of the same manuscript can be uploaded later on, but the older versions also remain.

See What is a “Preprint” Anyways? at The Winnower for more discussion.
Uploading a preprint to a repository before submitting it as a manuscript to a journal is a well-established practice in some fields like mathematics, computer science, and physics. It’s getting growing acceptance in other fields, especially biology, even if there is still some ambivalence being expressed. See a balanced presentation of contrasting views at Biomedical Journals and Preprint Services: Friends or Foes?
Wikipedia has a list of journals and publishers with known preprint policies. I recommend checking it before committing yourself to a course of action. However, journal policies are changing quickly. Sometimes you will get a positive ad hoc decision to consider your preprint if you contact an editor who has not previously been faced with the question.
In a recent blog, I discussed a new requirement at  University of Groningen and University of Groningen Medical Centre that authors affiliated with these institutions upload final versions of their papers to a university maintained repository immediately upon acceptance by a journal. This is part of a commitment to a green road open access.
But this is something different from what we’re going to be discussing here. Even at Groningen, researchers can both upload a preprint to a repository somewhere else and then upload another one to the journal maintained repository upon acceptance of a paper.
I anticipate uploading preprints to repositories increasingly to become a routine practice because of the advantages that it offers over waiting for conventional peer review. I recommend that you become an early adopter, if the practice is not yet common in your field of study.
Here are five reasons why you should consider uploading your preprint before submitting a manuscript.

1. You can get a preliminary appraisal from peers as to whether your work is ready to be submitted to a journal.

 James Heathers and Nick Brown provide an excellent success story in this regard.
They posted a preprint at the repository PeerJ Preprints where, according the Nick Brown, it received 1000 downloads the first month.

The GRIM test: A simple technique detects numerous anomalies in the reporting of results in psychology 

They each blogged about the preprint, James Heathers The GRIM test — a method for evaluating published research. and Nick Brown Academic publishing death match: Double blind review vs. preprints.
The preprint attracted media attention, including from prestigious The Economist.
Only then, was the manuscript submitted to Social Psychological and Personality Science (SPPS).

2. You can cite the uploaded manuscript in letters of inquiry to editors as to possible interest in publishing the manuscript.

Preliminary letters of inquiry to editors are an underutilized strategy in getting consideration of your manuscript. If you send a brief email to the editor, you will generally get a quick response. If there is no interest in your manuscript,  the move saves the editor and you what could be a lot of time. It is better to get an immediate decision than to have to go through a prolonged review process that ends up in a rejection.
An encouraging response from an editor to a letter of inquiry is certainly not a contract to publish your manuscript, but if editors respond favorably, they usually are more likely to at least send a manuscript out for review, rather than desk reject it. That of course is barring something unexpected being revealed in the abstract or the manuscript itself that you submit.
You generally would not include your manuscript with a letter of inquiry, only perhaps your abstract. Otherwise, you are creating confusion with whether you actually submitting your manuscript, and risk annoying the editor.
Yet, a letter of inquiry linked to an uploaded preprint allows an editor to consider the amount of attention the preprint has been receiving and the kinds of feedback it is eliciting. No obligation on the editor of course, but you have made it easier for the editor to peek. In some fields, it’s already an accepted practice that manuscripts are submitted with the feedback  received on repositories. In some fields, reviews received of a preprint may prove sufficient for a first round decision. But in other fields, submitting a manuscript which has previously been available as a preprint is part of a less established and more informal process.

3. You can cite your uploaded manuscript and the feedback it has received in your cover letter when you actually submitted to the journal.

 Many journals increasingly rely on desk rejections as a way of dealing with an overwhelming number of manuscripts being submitted. Editors feel the need to protect their limited pool of reviewers from what would on the basis of a quick screening seemed like a inevitably be a negative decision. Many of these desk rejections occur without anyone actually reading carefully the manuscript. Some prestigious journals post their percent desk rejections on their website, apparently to warn authors, but maybe as some bragging as well.
Authors need to depend on their three assets to avoid a desk rejection and get a manuscript out for review: their title, their abstract, and the cover letter. Of the three, the cover letter is most informal and even conversational. Unlike the title and the abstract, the cover letter does not serve any further function, once the editor has decided to send the paper out for review. The cover letter typically will not become a matter of public record.
It is strategic to take advantage of the informal nature of a cover letter as a communication. Think of the metaphor of it being like an informal encounter with an editor at a conference. A preprint becomes like a paper that you presented at a conference in a session with the editor is in attendance.  [On the other hand, it takes a lot less chutzpah to mention a preprint in a cover letter, then to approach an editor at a conference and ask “Hey, did you see my presentation, how about if I submitted as a manuscript?”]
Citing a publicly available preprint in a cover letter gives the editor an opportunity to look at your work, without being committed to do so. Any reactions the preprint has received, including the number of views or downloads, become evidence that can be cited in in the cover letter in support of the recognition that you manuscript is likely to obtain if is published in the journal.

Dear Editor:
Enclosed please find a manuscript [title] which we wish to submit for review and possible publication in your journal. We do so noting the extensive attention the manuscript has received as a preprint… We believe the manuscript will attract similar attention from your readership, if it is accepted…

4. The option of uploading a manuscript to a repository rather than submitting to a journal and waiting for a decision increasingly allows researchers to concentrate on grant applications citing the work.

Particularly with early career researcher (ECR), there is often a dilemma between focusing on establishing a reputation with publications versus pursuing the funding that will allow more resourced research. It can be quite frustrating when an ECR decides to concentrate first on getting some research published, only to find that it languishes in long reviews, revise-and-resubmit decisions that have no guarantee of eventual acceptance, or an outright rejection that requires a fresh resubmission elsewhere.
Sure, if the ECR is confident that manuscript will be accepted in time for citation in a grant application, particularly because a journal has been chosen explicitly because of the short turnaround time of review, it might be best simply to send the manuscript off to the Journal. But the decision can be different if there is any ambiguity about this.
By uploading the manuscript to repository rather wait for an editorial decision, the ECR can concentrate on a grant application in which the uploaded manuscript is cited and even linked.
It is important to establish with funding opportunities whether free prints can be cited and linked. The Wellcome Trust recently announced it would allow researchers to submit preprints in both applications and progress reports.
A group of scientists has organized to urge NIH to accept preprints. Another group has expressed concern , while acknowledging it would benefit early career investigators. NIH also recently formally requested feedback on the advisability of their accepting preprints with applications . No decision has yet been reached has of January 2017.
Undoubtedly, the trend is towards increased acceptance of preprints, but best to check updated policies with granting agencies. If you don’t see a mention there, it might be worth directly contacting a program officer. Strategically, doing so also lets you talk about your work as it is reflected in your preprint. Furthermore, even when there is no formal encouragement, preprints can be cited as evidence of relevant previous work. That too should be discussed with a program officer, if you can.

5. You can attract the attention of an editor, even multiple editors, who are increasingly browsing preprint repositories looking for manuscripts to invite to submit.

Journals can be expected to increasingly have dedicated editorial staff whose responsibilities include periodically stopping by depositories or watching on social media for news of promising preprints, which they will then invite to be submitted to the Journal.
Genome Biology has been doing this for about a year. PLOS Genetics formally announced in December 2016 such a policy and had as hired three preprint editors.
bioRxiv (pronounced “bio-archive”)  is a free online repository for the life sciences operated by Cold Spring Harbor laboratory. It has the additional feature of allowing direct transfer of manuscripts to journals:

Direct transfer from bioRxiv  to journals or peer review services (B2J)
bioRxiv can save authors time in submitting papers to journals or peer review services by transmitting their manuscript files and metadata directly from bioRxiv. This means authors do not have to spend time re-loading manuscript files and re-entering author information at the journal or peer review service website.

Think of that: essentially by uploading an appropriate preprint at bioRxiv, an author is effectively soliciting consideration for multiple journals. Can’t beat that.  Unfortunately, bioRxiv is limited to life sciences and will only consider manuscripts from physical sciences, mathematics, or social sciences if they have direct relevance the life sciences.
Other journals can be expected to quickly follow suit. Informally, the procedure has probably existed for a while.
I am sure that other reasons for posting preprints at repositories will be discovered when the practice gets better established. I for one have recently published a number of papers with co-authors I had not met before submitting the paper. Such productive Internet-based collaborations are likely to much more be common in the future. They can be facilitated by preprints placed in repositories at whatever stages of development in order to gather collaborators. Think strategically about posting preprints in repositories as being the Internet version of giving a talk at a conference and welcoming collaborators.
So, you place a preprint in a repository and you announce on Twitter and Facebook:

I have uploaded a preprint at Repository X [PeerJ Preprints, for instance]. And while I’m pleased with it, I think I could use additional collaborators in turning it into an even better manuscript…