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\begin{document}

\title{Open Access + Preprints: Journals and scholars take action}


 \author{The Authorea Team & The Scholastica Team}


\date{}

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\subsection*{Intro}\label{intro}

As academics transition to digital journal publishing, the Open Access
(OA) movement, which aims to make research freely available at or soon
after publication, is picking up record speed. According to a recent
Simba report titled Open Access Journal Publishing 2016-2020, ``the
number of OA research articles published annually is growing at double
the rate of the complete spectrum of research articles.'' The report
also found that about a third of all research articles currently
published are OA, when factoring in those with complete embargo
periods.\\

The rise in OA publishing comes as a result of scholars banding together
to reveal the mounting cost of research access for institutions and
individuals, such as those behind the Cost of Knowledge Project who
started a boycott of Elsevier, which now has profit margins exceeding
30\%. At the same time governments and funding bodies have introduced
new OA mandates and calls for early sharing of research. Such as the
Wellcome Trust, Bill \& Melinda Gates Foundation, and others who this
February urged journals and research funding agencies to sign a pledge
to make all papers related to the Zika virus OA in the wake of the
public health crisis.\\

Yet, despite the scholarly community embracing OA publishing, the
Authorea team reveals that 65 of the most cited papers in the world are
still behind often hefty paywalls, inaccessible to those who can't
afford article fees or journal subscriptions. Today this pattern
continues with more groundbreaking articles being published in journals
with prohibitive paywalls. As the drumbeat for OA gets louder, it's
apparent that researchers and journal publishers must come together to
find sustainable ways to make such research freely accessible.\\

Among promising OA solutions is preprint servers, or online databases of
manuscripts posted by scholars prior to formal publication.\\

In this guide we'll look at the place of preprints in the digital
publishing landscape for journals and scholars, including:\\

\begin{itemize}
\tightlist
\item
  How preprints are helping scholars and journals make research more
  open\\
\item
  Challenges to be addressed when publishing via preprints\\
\item
  New publishing models journals are pioneering using preprint servers\\
\end{itemize}

Let's get started!\\

\subsection*{Preprints and the modern publishing
landscape}\label{preprints-and-the-modern-publishing-landscape}

Researchers utilize the most advanced tools in the world to perform
their experiments. From massively parallel computing clusters
approaching exoscale computation power to high-powered microscopes
redefining the limits of resolution, we're in age where the tools we use
to perform research are truly awesome. However, such innovations have
fallen short when it comes to how researchers write or ultimately
publish their work.~ In short, scientists are doing 21st century
research, writing it on 20th century tools, and packaging it in 17th
century formats.\\

\subsubsection*{The origin of scholarly journals: 300 years with little
change}\label{the-origin-of-scholarly-journals-300-years-with-little-change}

The first scholarly article, published in 1655 in Philosophical
Transactions, was an important step for researchers towards formalizing
and preserving the scholarly record.~ Recognizing the importance of
research communication, the opening editorial stated:\\

\begin{quote}
``Whereas there is nothing more necessary for promoting the improvement
of Philosophical Matters, than the communication of such.''\\
\end{quote}

Over the ensuing centuries new publications from The Lancet in 1823 to
Virchows Archiv in 1847 were launched (fun fact: Thomas Wakely launched
The Lancet at age 27 and Rudolf Virchow launched Virchow's Archiv at the
age of 26). Considered radical in their time, these journals and others
soon grew in prominence becoming the standard method for communicating
research. Many of which are now household names and contain some of the
world's most important findings.\\

The increasing volume of academic publications brought about a
formalized peer review system in the early 19th century and with it an
increase in technological capabilities over time, like structured
typesetting, which were largely born out of a desire to share research
better. In the 1960's the way scholars consumed and disseminated their
research began to change\ldots{} at least for some researchers.\\

In the 1960's, while the majority of researchers communicated via
journals exclusively, a subset of researchers began to utilize new forms
of communication. Physicists began to share their paper manuscripts
directly with each other prior to them being peer reviewed or published
in a journal. These shared manuscripts become known as ``preprints.''
Databases in the US and in Germany housed the bibliographic information
of preprints and facilitated their sharing, which eventually became so
widespread it became onerous and even unfeasible to manage for those
without adequate resources.~ Indeed, the library at the Stanford Linear
Accelerator Center (SLAC), which housed preprints, was receiving
thousands of preprints per year at one point, a large amount of
information at the time to be organized and collected.\\

\subsection*{Preprints and the web}\label{preprints-and-the-web}

To deal with the growing amount of bibliographic information
accumulating at SLAC a computer database was developed, termed the
Stanford Physics Information Retrieval System (SPIRES).~ SPIRES not only
organized bibliographic information, creating a standard used across
universities, but also allowed for researchers to email the database and
request that a list of preprints be sent to them. Since papers could not
be emailed at the time, the system relied on snail mail.\\

While SPIRES greatly improved the flow of information, it often still
took weeks for preprints to reach their requester's mailbox.~ A
typesetting system called .tex introduced in the late 70's early `80s
soon changed this by allowing researchers to write their documents in a
specified manner that could be emailed and downloaded and compiled
without the need for physical mail.\\

Soon researchers, primarily physicists, were emailing and downloading
.tex files at great rates hastening the process of research
communication, which again created the problem of information overload.~
To manage this process, in March 1989 Tim Berners-Lee wrote a paper
modestly entitled, ``Information Management: A Proposal.'' Soon after
the World Wide Web, Berners-Lee's own invention, and with it a central
preprint repository, later to be named arXiv, were born.\\

\subsection*{What researchers are saying about
preprints}\label{what-researchers-are-saying-about-preprints}

The rise of open research sharing, the web, and a central preprint
repository drastically changed how researchers communicate their
research. However, these advances did not penetrate all research
disciplines and to this day preprints have struggled to gain widespread
adoption.~ Nevertheless, in recent years preprint usage has been on the
rise and there are now preprint repositories for various disciplines
including arXiv, for math, physics and other sciences; BioArXiv, for
biology; SocArXiv, for social sciences; as well as discipline-agnostic
repositories like Authorea.\\

``New technology does a better job of finding me stuff to read than the
table of contents of any given journal (Pubchase, custom RSS
feeds,~Twitter recs from respected colleagues).~ Especially with the
option of versioning articles, I think this system would capture much of
the current value of peer review, be faster, and more sustainable.''-
Angela DePace, Assistant Professor, Department of Systems Biology,
Harvard Medical School\\

``Posting preprints offers people the chance to be more thoroughly
evaluated, which is especially beneficial for younger
scientists.''-James Fraser, Assistant Professor, UCSF\\

One limitation that has held back the widespread adoption of preprints
is the confusion over whether you can still publish in a traditional
journal after posting a preprint. This fear, despite the fact that most
preprints on arXiv are ultimately published in journals, arises from the
so-called Ingelfinger rule that limits duplicate publications as well as
communication by some publishers that has cast an artificial uncertainty
into the decision making process of researchers.\\

Nevertheless, there are clear rules for writing and posting of preprints
and journals are quickly embracing preprints in wider disciplines.~ In
fact, some journals have even instituted ``preprint editors'' to solicit
preprints for journal publication off of repositories\\

\subsection*{Preprints reshaping the author
experience}\label{preprints-reshaping-the-author-experience}

Preprint servers arose with the use of new technology, specifically
authors writing their documents in .tex files.~ Today, much of the world
is able to write online and even execute their own programs for data
analyses.~ Despite this widespread adoption of technology, scientific
papers remain primarily static objects (PDFs) and generally require
typesetting to be done by journal publishers.\\

New collaborative writing tools, such as Authorea, simplify this process
by allowing authors to produce manuscripts that are not limited to just
text and image but also allow rich media such as datasets, software,
source code, and videos. Tools like Authorea make it easy to write,
cite, collaborate, host, and to preprint. By putting the control of
typesetting in the hands of authors that write in markdown, latex or
rich text control of publishing is shifted towards the research
community, not just professional publishers.\\

\textbf{5 Ways you can start using preprints to publish}\\

\begin{enumerate}
\tightlist
\item
  Check preprint policies at journals to which you're considering
  submitting\\
\item
  Email the editors of the journal you plan to submit to if you're
  unsure about their preprint policies\\
\item
  Use collaborative writing tools to write and post preprints\\
\item
  Share your preprints with colleagues via social media and email to
  solicit feedback\\
\item
  Educate and encourage others to share their work openly\\
\end{enumerate}

\subsection*{The role of preprints in academic journal
publishing}\label{the-role-of-preprints-in-academic-journal-publishing}

In the digital scholarly communication landscape the primary value of
preprints for researchers is that preprints allow them to disseminate
their work faster and to a much wider audience than they could in
traditional paywalled journals. A recent Editage Insights article
titled, ``The role of preprints in research dissemination`` details why
many scholars are choosing to submit their work to preprints prior to
formal journals. Among primary benefits are that preprints:\\

Give scholars working on time-sensitive projects a way communicate their
research while undergoing peer review\\

Can serve as a way for scholars to establish priority over a particular
research discovery or method\\

Ensure that an OA version of scholars' work will be available regardless
of where they formally publish\\

The increase in preprint use, along with scholars publicly coming
together to endorse preprints, such as those at the 2016 ASAPbio
meeting, is forcing journal publishers to address the place of preprints
in the publishing landscape.\\

\subsection*{Preprints and Green OA}\label{preprints-and-green-oa}

Despite ``preprint'' sounding like something reserved for
pre-publication, ``preprint'' servers and published journals don't have
to be as separate as their names suggest. Preprints have actually been a
driving force behind Green OA, in which scholars deposit their articles
into an institutional repository or subject repository in order to make
a version of their work OA. Depending on the requirements of the
journal, Green OA preprints may be manuscripts or copies of final
articles.\\

Among leaders of the Green OA movement is Stevan Harnad, Professor in
the Department of Psychology at Universit\selectlanguage{ngerman}é du Québec à Montréal and
Affiliate Professor in Electronics and Computer Science at University of
Southampton, UK.\\

In 1994 Harnad published the Subversive Proposal stating that
researchers should self-archive their research articles to make them
free for all online. Self-archiving later went on to become ``Green OA''
(and OA journals became ``Gold OA''). Harnad also commissioned the first
OA repository software, EPrints, in 1999. Since then, Green OA via
repositories and preprint servers has become increasingly popular.\\

When asked how Green OA should work, Harnad says it's simple.\\

``All researchers should self-archive their articles immediately upon
acceptance for publication by depositing them in their institutional OA
repository. And all institutions and funders should mandate this.''\\

\subsection*{How journals can facilitate Green OA via
preprints}\label{how-journals-can-facilitate-green-oa-via-preprints}

In order to use preprint servers to make research Green OA,scholars need
journal support. ``Open Access compliance: How publishers can reach the
recommended standards,'' a 2016 report released by Jisc, outlines some
key ways publishers and journals can take action to help scholars make
their research OA. Among steps Jisc outlines are:\\

\begin{itemize}
\tightlist
\item
  Making clear OA policies easily accessible on journal websites\\
\item
  Ensuring embargo periods, if deemed necessary, meet funder
  requirements and are reasonable to the academic community\\
\item
  Applying Digital Object Identifiers (DOIs) to all articles, so
  scholars can link the different versions of their work\\
\item
  Adopting ORCID IDs, which can be used to populate institutional
  repositories and track OA compliance\\
\item
  Providing journal and article level OA licensing terms to clarify any
  differences at either level\\
\end{itemize}

As journal publishers continue to work out whether they're ready to
transition to an OA model, supporting Green OA by allowing authors to
submit manuscripts they've posted to preprints is a great place to
start. By considering manuscripts scholars have uploaded to preprint
servers publishers can better meet institutional and funder OA mandates
as well as scholar expectations. A key aim journal publishers must have
to facilitate Green OA is to provide clear policies for preprints, so
there is no confusion among scholars as to whether they can upload their
manuscript to a preprint server prior to formal publication.\\

Importance of clear preprint policies\\

A recent article in the Journal of Librarianship and Information Science
titled ``What does `green' open access mean? Tracking twelve years of
changes to journal publisher self-archiving policies,'' traces the
self-archiving policies over the last 12 years of the original 107
publishers listed on the SHERPA/RoMEO Publisher Policy Database. The
study found that while the volume of publishers allowing self-archiving
has increased by 12\%, the volume of restrictions around self-archiving
has increased by 119\%.\\

Many preprint limitations enacted by publishers are not immediately
apparent, making it vital for submitting authors and journal editors to
carefully review publishers' self-archiving policies to ensure they're
comfortable with the stances the journals they're working with are
taking. Confusing preprint policies can slow down Green OA and even
deter scholars from submitting to preprint servers, due to unfounded
fears of being penalized for publishing their paper in two places.\\

With OA publishing becoming an expectation among the academic community,
today some journal editors are speaking out in instances of publishers
increasing the cost of research access or enacting policies to limit OA
options. In some cases where editors and publishers haven't been able to
work out differences editors have actually left the publisher to start
OA friendly counterparts to old journals.\\

An early example is Michael Rosenzweig, Professor of Ecology and
Evolutionary Biology at the University of Arizona, who in 1998 became
one of the first editors-in-chief to leave his publisher when he led the
editorial board of Evolutionary Ecology in declaring independence from
the journal's then publisher, International Thomson. Evolutionary
Ecology's editorial board left in protest of high subscription costs
which, despite the editors' best efforts to combat them, were rising at
a rate of 19\% a year. The editors started a new Green OA journal titled
Evolutionary Ecology Research. Since then more journals have followed
suit, including the editorial board of~ Elsevier journal Lingua, who
also left in protest of prohibitive price hikes and started their own
journal Glossa.\\

Peter Suber, director of the Harvard Office for Scholarly Communication,
Senior Researcher at the Berkman Center, Senior Researcher at SPARC, and
Research Professor of Philosophy at Earlham College, has been following
the trajectory of editors leaving their publishers to start more OA
friendly journals. Since the late '80s he's maintained the ``Journal
declarations of independence'' list that he started on the Open Access
Directory (OAD) website with OAD co-founder Robin Peek.\\

Suber believes that if publishers do not address prohibitive paywalls
and OA policies it's only a matter of time before more editors take a
stand and launch solo journals on their own.\\

``Every time a journal declaration of independence takes place,
frustrated editors at other journals will think about whether they
should follow suit, because they will know it can be done,'' said
Suber.\\

\subsection*{Questions surrounding preprint
publications}\label{questions-surrounding-preprint-publications}

Preprints aren't without questions to be worked out. Some publishers
have been wary of fully endorsing preprints due to perceived challenges
in the preprint model. Among those who've voiced uncertainty about
preprints is Emilie Marcus, Editor-in-Chief of Cell and CEO of Cell
Press.\\

Questions and uncertainties about preprints raised by Marcus include:\\

\begin{itemize}
\tightlist
\item
  Are preprints by themselves valid publications and should preprints be
  citable?\\
\item
  If preprints are citable, do scholars have to read through all
  preprint literature in addition to published articles to account for
  preprints in their references?\\
\item
  Is there an optimal number of preprints per discipline and what should
  that be?\\
\end{itemize}

A concern among some scholars and publishers is that preprints don't go
through peer review, and post-publication vetting of preprints isn't
generally guaranteed or monitored. Though, pre-publication peer review
is also an imperfect process with room for error. Uncertain manuscript
vetting is a key concern among publishers when it comes to preprints,
making some including Marcus, regard preprints as ways of accelerating
the sharing of ideas but not a ``publishing'' solution. However, this
isn't the only way to view preprints. There are editors who are
establishing new methods to link preprints and formal journals making
research more open as a result.\\

\subsection*{Journals pioneering new preprint publishing
models}\label{journals-pioneering-new-preprint-publishing-models}

A primary contention some publishers and editors have with preprints is
that they lack the validation of formal journal articles. But what if
preprint manuscripts were actually vetted and peer reviewed? Enter the
vision of the overlay journal. Overlay journals are open access journals
that perform the peer review function of a traditional journal but,
rather than directly accepting manuscript submissions, pull in
manuscripts from a preprint server.\\

Overlay journals started appearing in the 1990s beginning with Physical
review D, the first partial overlay journal launched by Paul Ginsparg in
1996. From there more overlay journals followed. Generally, in the
overlay model journal editors vet submissions, coordinate peer review,
and then, rather than publishing accepted articles in an issue, they
republish final versions to a preprint server along with a DOI. Overlay
journals can be open access or use subscription models for final
versions.\\

Some editors have been able to make their journals both free to read and
free to publish in via the overlay model. Among examples are Peter
Coles, Professor of Theoretical Astrophysics at Cardiff University, who
founded the Open Journal of Astrophysics and Royal Society Research
Professor and Fields Medalist Timothy Gowers who founded the new math
journal Discrete Analysis. Both Coles' and Gowers' journals work in
tandem with arXiv. The journals are formal publications, which can be
abstracted, indexed, and accrue impact.\\

As a new overlay journal Discrete Analysis is taking steps to further
develop the publishing model. Discrete Analysis stands out from other
overlay journals because it has a formal publication website, which
includes article categories visitors can choose from to access complete
article listings and designated pages for each of its articles with an
image and description. In this way Discrete Analysis offers readers a
journal browsing experience on its website while still using arXiv to
handle the publishing process.\\

Discrete Analysis manages peer review and publishes its journal via
Scholastica. Using Scholastica's arXiv integration authors are able to
submit papers they already posted to the arXiv for consideration by
Discrete Analysis editors. The journal's editorial board then
coordinates peer review for all submissions and accepted manuscripts are
edited and re-uploaded to arXiv as final versions with DOIs. The journal
has already published top research including editor Terence Tao's
article on crowdsourcing the solution to the Erd\selectlanguage{polish}ő\selectlanguage{english}s discrepancy
problem.\\

For Timothy Gowers and other overlay journal founders and supporters,
the primary goal of the overlay model is to lower the barrier to
publishing OA and speed up research dissemination.\\

``I want to be aggressively modern. I want to use the internet properly
-- when you've got something, you post it,'' Gowers explained. ``We're
not pretending to be a traditional journal, we're something else.''\\

The overlay model presents a much leaner publishing approach that
eliminates the costs of time and budget journals must usually allocate
to ``printing services,'' such as typesetting, making the publishing
process quicker and more affordable. It's one of many new OA publishing
models out there for journals to explore.\\

\subsection*{Closing}\label{closing}

Research dissemination has not dramatically changed since the Royal
Society published the first scholarly journal, Philosophical
Transactions, in 1665. However, today's digital publishing age is
starting to transform the way scholars and journals approach research
publication, spurring important questions about the traditional
paywalled publishing model. With the shift towards digital publishing,
OA, and new impact indicators, it's becoming harder for publishers to
justify the need for ``printing'' costs. Additionally, factors like a
journal's Impact Factor and the clout of its publisher are becoming less
important to authors, making them more likely to consider alternatives
to ``band-name'' paywalled journals. Rather, scholars, as well as
universities, funding bodies, and government organizations, are
encouraging researchers and journals to take steps to make content
freely accessible. Preprint servers are one tool that is helping to
facilitate Green OA via the archiving of preprints and even Gold (free
to read) and Diamond (free to read and free to publish) OA via new
overlay journal models that virtually eliminate publisher costs. Now's
an exciting and significant time for the academic community to address
the place of preprints in the publishing landscape.~ Tools for
researchers and journal editors to do their work in a modern way are now
at hand; it's time to start utilizing them.

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