1 Do You Speak Open Science Resources and Tips to Lear

1
Do You Speak Open Science? Resources and Tips to Learn the
Language.
Paola Masuzzo1, 2 - ORCID: 0000-0003-3699-1195, Lennart
Martens1,2 - ORCID: 0000-
0003-4277-658X
Author Affiliation
1 Medical Biotechnology Center, VIB, Ghent, Belgium
2 Department of Biochemistry, Ghent University, Ghent,
Belgium
Abstract
The internet era, large-scale computing and storage resources,
mobile devices, social media,
and their high uptake among different groups of people, have all
deeply changed the way knowledge
is created, communicated, and further deployed. These advances
have enabled a radical
transformation of the practice of science, which is now more
open, more global and collaborative,
and closer to society than ever. Open science has therefore
become an increasingly important topic.
Moreover, as open science is actively pursued by several high-
profile funders and institutions, it
has fast become a crucial matter to all researchers. However,
because this widespread interest in

open science has emerged relatively recently, its definition and
implementation are constantly
shifting and evolving, sometimes leaving researchers in doubt
about how to adopt open science,
and which are the best practices to follow.
This article therefore aims to be a field guide for scientists who
want to perform science in the
open, offering resources and tips to make open science happen
in the four key areas of data, code,
publications and peer-review.
The Rationale for Open Science: Standing on the Shoulders of
Giants
One of the most widely used definitions of open science
originates from Michael Nielsen [1]:
“Open science is the idea that scientific knowledge of all
kinds should be openly shared as early as
is practical in the discovery process”. With this in mind, the
overall goal of open science is to
accelerate scientific progress and discoveries and to turn these
discoveries into benefits for all. An
essential part of this process is therefore to guarantee that all
sorts of scientific outputs are publicly
available, easily accessible, and discoverable for others to use,
re-use, and build upon.
As Mick Watson has recently wondered, “[...] isn’t that just
science?” [2]. One of the basic
premises of science is that it should be based on a global,
collaborative effort, building on open
communication of published methods, data, and results. In fact,
the concept of discovering truth by
building on previous findings can be traced back to at least the

12th century in the metaphor of
dwarfs standing on the shoulders of giants: “Nanos gigantum
humeris insidentes”1.
While creativity and intuition are contributed to science by
individuals, validation and
confirmation of scientific findings can only be reached through
collaborative efforts, notably peer-
driven quality control and cross-validation. Through open
inspection and critical, collective
analysis, models can be refined, improved, or rejected. As such,
conclusions formulated and
validated by the efforts of many take prominence over personal
opinions and statements, and this
1 Metaphor attributed to Bernard of Chartres, and better known
in its English form as found in a 1676 letter of
Isaac Newton: “If I have seen further, it is by standing
on the shoulders of giants”
PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.2689v1 |
CC BY 4.0 Open Access | rec: 3 Jan 2017, publ: 3 Jan 2017
2
is, in the end, what science is about. While science has been
based for centuries on an open process
of creating and sharing knowledge, the quantity, quality, and
speed of scientific output have
dramatically changed over time. The beginning of scholarly
publication as we intend it today can
be traced back to the 17th century with the foundation of the

‘Philosophical Transactions’. Before
that, it was not at all unusual for a new discovery to be
announced in an encrypted message (e.g.,
as an anagram) that was usually indecipherable for anyone but
the discoverer: both Isaac Newton
and Leibniz used this approach. However, since the 17th
century, the increasing complexity of
research efforts led to more (indirect) collaborations between
scientists. This in turn led to the
creation of scientific societies, and to the emergence of
scientific journals dedicated to the diffusion
of scientific research. Paradoxically however, knowledge
diffusion has dramatically slowed down
over the same time. In his review of Michael Neilsen’s
book “Reinventing Discovery” [3], Timo
Hannay describes science as “self-serving” and
“uncooperative”, “replete with examples of secrecy
and resistance to change”, and furthermore defines the
natural state of researchers as “one of
extreme possessiveness” [4]. Hannay might have a point: the
majority of research papers are behind
a paywall [5], researchers still fail at making data and metadata
available [6], reproducibility is
hampered by the lack of appropriate reporting of methodologies
[7], software is often not released
[8], and peer-review is anonymous and slow [9].
As a reaction, the open science movement was born, almost as a
counterculture to the too-
closed system that re-emerged over the past few decades. More
and more academic and research
institutions are currently opening up the science they produce,
making the scientific research,
produced data and associated papers accessible to all levels of
an ever more inquiring society,
amateur or professional. And increasingly, major funding

agencies are mandating the same. For
example, the European Commission requires participants of the
H2020 funding framework to
adhere to the Open Access mandate and the Open Research Data
Pilot. Furthermore, both the
National Institutes of Health (NIH) and the Wellcome Trust
have developed specific mandates to
enforce more open and reproducible research. As a result,
practicing open science is no longer only
a moral matter, but has become a crucial requirement for the
funding, publication, and evaluation
of research.
Because the many benefits of open science have already been
extensively studied and reported
[10–16], this article instead intends to be a user guide for open
science. The next sections of this
article therefore provide an overview of the key pillars of open
science, along with resources and
tips to make open science happen in everyday research
practices. This collection of resources can
then serve as an open science guidebook for early-career
researchers, research laboratories, and the
scientific community at large.
Four Pillars of Open Science
Almost all scientists today will have bumped into the expression
“open science”. As an
umbrella term used to cover any kind of change towards
availability and accessibility of scientific
knowledge, “open science” evokes many different concepts
and covers many different fronts, from
the right to have free access to scholarly publications (dubbed
“open access”), over the demand for

a wider public engagement (typically referred to as citizen
science), to the development of free tools
for collaboration and open peer-review (as implemented in
science-oriented social media
platforms).
This diversity and perhaps even ambiguity of open science can
be explained by the many
stakeholders that are directly affected by a changing scientific
environment: researchers,
3
administrators, funders, policy makers, libraries, publishing
companies, and even the general
public. Five different schools of thought on open science have
been identified2, each with their
stakeholder groups, their aims, and their tools and methods to
achieve and promote these aims [12].
While these schools depict the whole scope of open science,
their fundamental aim is to enhance
openness in the four widely recognized thematic pillars: open
research data, open software code,
open access to papers, and open peer-review (Figure 1). The
following sections will briefly
introduce the rationale for each of these pillars, and will then
provide resources for their adoption
in daily research practice.

Figure 1: The four pillars of open science discussed in this
article.
Image adapted from [17], distributed under a CC BY 4.0
International license
(http://creativecommons.org/licenses/by/4.0/).
Open Data: Sharing the Main Actor of a Scientific Story
By open data in science we mean data that are freely avail able
on the public internet permitting
any user to download, copy, analyze, re-process, or use these
for any other purpose without
financial, legal, or technical barriers other than those
inseparable from gaining access to the internet
itself3.
In the digital era, data are more and more considered to be the
main part of a scientific
publication, while the paper serves the secondary role of
describing and disseminating scientific
results. This because open data tend to outlive the associated
paper. In fact, others (professional
researchers as well as interested members from the general
public) can conduct re-analyses on these
data, and can do so within the context of new questions, leading
to new scientific discoveries. In
2015 Borgman identified four rationales for sharing research
data: to reproduce research, to make
those data that can be considered public assets, available to the
public4, to leverage investments in
research, and to advance research and innovation [18]. Several
studies have furthermore reported
that scientific papers accompanied by publicly available data
are on average cited more often

[19,20], and are moreover characterized by fewer statistical
errors and a greater degree of robustness
[21].
2 Democratic, Pragmatic, Infrastructure, Public and
Measurement
3 see the full Open Definition at:
http://opendefinition.org/od/2.0/en/ and the Panton Principles
for Open Data in
Science at http://pantonprinciples.org
4 Privacy sensitive data for instance, do not belong to this
category.
4
Releasing data, however, is not sufficient by itself. For re-use
to happen efficiently, which is
ultimately the goal of open data, data sharing needs to become a
custom routine, should encompass
the full research cycle, and needs to assure long-term
preservation. Furthermore, data sharing
requires some amount of manual work, and a specific shift in
research habits, for which the current
credit system in research should accommodate. A nice example
of this shift is provided by the
journal Psychological Science, which adopted such an incentive
for open research data in January
2014, by offering “badges” to acknowledge and signal open
practices in publications. To receive

an ‘open data’ badge, authors must make all digitally shareable
data relevant to the publication
available on an open access repository. Similarly, to earn an
‘open materials’ badge, authors must
make all digitally shareable materials available on an open
access repository. Those who apply for
a badge and meet open data or open materials specifications
receive the corresponding badge
symbol at the top of their paper and provide an explicit
statement in the paper including a URL to
the data or materials at an open repository. A recent study has
shown that these badges are effective
incentives to improve the openness, accessibility, and
persistence of data and materials that underlie
scientific research [22].
Finally, for data sharing to encourage re-use, data curation and
metadata annotations are key
factors, together with reliable basic infrastructure for data
sharing: the availability of data
infrastructures that are well curated and well maintained in the
long-term, and a rich catalogue of
standards and formats that are moreover continuously updated
to keep up with shifts in technology
and knowledge.
Where to Submit Research Data? General-Purpose and Domain-
Specific Repositories
As a general rule, data should be submitted to a repository prior
to submission of a relevant
manuscript that describes these data. Thus, the authors can point
the readers to the location of the
data in the manuscript itself, increasing transparency,
reproducibility and validation of the results,

and aiding efficient peer-review. Two types of such data
repositories exist: general-purpose and
domain-specific repositories. The former are inter-disciplinary
repositories meant to host data for
which domain-specific repositories do not exist, as well as
general research output (such as posters,
presentations, code). The latter on the other hand, are well -
established subject or data-type specific
repositories that typically serve specific fields. Table 1 lists the
most widely used repositories
across both types. Although not exhaustive, this list provides a
good cross-section of repositories
that should be considered both for publication of data, and for
the location and retrieval of relevant
data for (re)use in research.
A global registry of research data repositories for different
scientific disciplines can be found
at the Registry of Research Data Repositories
(http://www.re3data.org). Furthermore, NCBI and
EBI online databases can be found at http://goo.gl/0KwIq8 and
http://goo.gl/j3stqD, respectively.
Biomed Central suggests a list of possible repositories at
https://goo.gl/dBHeZf, while another
interesting list, maintained by Nature Scientific Data, can be
found at https://goo.gl/G7cLFp.
Finally, the Biosharing catalogue includes bioscience databases
described according to domain
guidelines and standards (https://biosharing.org/databases/, 798
databases listed at the time of
writing).

5
Table 1: A list of general-purpose and domain-specific data
repositories (in alphabetical order).
Name Description Domain Website
Cell Image
Library
public repository of reviewed and
annotated images, videos, and
animations of cells from a variety of
organisms
biological imaging
http://www.cellimagelib
rary.org
Coherent X-ray
Imaging Data
Bank
open repository for X-ray images
macromolecular
structures
http://www.cxidb.org/id
-2.html

Crystallograph
y Open
Database
open-access collection of crystal
structures of organic, inorganic,
metal-organic compounds and
minerals, excluding biopolymers
macromolecular
structures
http://www.crystallogra
phy.net
DataOne
a framework and infrastructure for
Earth observational data
environmental and
ecological data
https://www.dataone.or
g
Dryad
a resource that makes the data
underlying scientific publications
discoverable, freely reusable, and
citable

general-purpose http://datadryad.org
Figshare
a repository where users can make all
of their research outputs available in
a citable,
shareable and discoverable manner
general-purpose https://figshare.com
GenBank
the NIH genetic sequence database,
an annotated collection of all
publicly available DNA sequences
sequence and omics
data
http://www.ncbi.nlm.ni
h.gov/genbank/
GEOSS portal a portal for Earth science data
environmental and
ecological data
www.geoportal.org
Global
Biodiversity
Information
Facility

a repository containing data about all
types of life on Earth, published
according to common data standards
environmental and
ecological data
http://www.gbif.org
JCB Data
Viewer
a platform to view, analyze and share
image data associated with articles
published in The Journal of Cell
Biology
biological imaging
http://jcb-
dataviewer.rupress.org
Morphbank
an image database documenting a
range of specimen-based research,
including comparative anatomy and
taxonomy
biological imaging
http://www.morphbank.
net

Movebank
an online database of animal tracking
data
environmental and
ecological data
https://www.movebank.
org
NERC data
centers
seven centers for: marine,
atmospheric, Earth observation, solar
and space physics, terrestrial and
environmental and
ecological data
http://www.nerc.ac.uk/r
esearch/sites/data/
PeerJ Preprints | https://doi.org/ 10.7287/peerj.preprints.2689v1 |
6
freshwater, geoscience, and polar and
cryosphere data

NeuroVault
a repository for statistical maps,
parcellations, and atlases produced
by MRI and PET studies
neuroimaging data http://neurovault.org
NIH 3D Print
Exchange
a repository with models for 3D
printers and tools to create and share
3D-printable models related to
biomedical science
3D-printable models http://3dprint.nih.gov
Open Energy
Information
a crowdsourced collection of
information, data and discussions
around multiple aspects of energy
engineering http://en.openei.org
Open Science
Framework
a research and workflow
management tool and open
repository; allows for integration

with several external tools like
Dropbox, Github, and Zotero
general-purpose https://osf.io
OpenfMRI
a project dedicated to the free and
open sharing of functional magnetic
resonance imaging (fMRI) datasets
neuroimaging data https://openfmri.org
OpenTrials
a project to locate, match, and share
all publicly accessible data and
documents on all trials conducted on
all medicines and other treatments
health data http://opentrials.net
PANGAEA a repository for geospatial data
environmental and
ecological data
https://www.pangaea.de
PRIDE
an archive of protein expression data
as determined by mass spectrometry
sequence and omics
data

http://www.ebi.ac.uk/pri
de/archive/
Protein Data
Bank
a databank for 3D protein structures
macromolecular
structures
http://www.rcsb.org/pdb
/home/home.do
The Knowledge
Network for
Biocomplexity
an international repository intended
to facilitate ecological and
environmental research
environmental and
ecological data
https://knb.ecoinformati
cs.org
Uniprot
a comprehensive resource for protein
sequence and functional annotation
data

sequence and omics
data
http://www.uniprot.org
Worldwide
Protein Data
Bank
a publicly available repository of
macromolecular structural data
macromolecular
structures
http://www.wwpdb.org
Zenodo
a repository that supports a wide
variety of content including
publications, presentations, images,
software (integration with GitHub),
and data
general-purpose https://zenodo.org

7
Submitting data: points to consider
The following section highlights some key aspects to keep in
mind when submitting research
data.
x Research materials in a broad sense (essentially any research
output such as figures, posters,
code, presentations, and media) are best deposited in general -
purpose repositories. Domain-
specific data on the other hand, are best submitted to a domain-
specific repository (see Table
1). Recent surveys have shown that the majority of researchers
still prefer to share data as
supplementary material to an article, but this is certainly not an
optimal solution, because it is
essentially a very static representation of data (often also
formatted in document rather than
data mark-up formats, such as PDF) and therefore does not
allow for dynamic inspection and
re-use of the data. It may also not represent a long-term data
storage solution.
x If researchers wish to publish data sets through a data article,
they can target appropriate data
journals. Rather than presenting any analysis, results, or
conclusions on the data, such a data
article focuses on detailed descriptions of these data, and
presents arguments about the value of
the data for future (re-)analysis. Notable examples of data
journals are: GigaScience (BioMed
Central, http://gigascience.biomedcentral.com), Scientific Data
(Nature Publishing Group,

http://www.nature.com/sdata/) and Data in Brief (Elsevier,
http://www.journals.elsevier.com/data-in-brief/). A data journal
will not normally host data
itself but will instead recommend a suitable repository where
the data set should be deposited,
and then link to it.
x When targeting a particular journal to publish their research,
scientists should check for any
policies on data. In fact, journals are increasingly requiring
authors to deposit the data
underlying their articles in a recognized repository, to
complement or even replace any in-house
facility for supplementary materials. For example, Public
Library of Science (PLOS)
recommends repositories it recognizes as “trusted within their
respective communities” and
also points to re3data as a more general source.
x The following questions can assist a researcher in choosing
the right repository for their data:
o Is the repository well known?
Is it community-recognized (e.g., listed in the re3data registry)?
Some repositories are
certified, meaning that they have passed a check in terms of
reliable and long-term
access to the data collections they host, but one should keep in
mind that some good
repositories are not compliant yet, and this might remain the
case for some time.
o Will the repository accept my data?
With the obvious exception of general-purpose repositories,
most online databases
accept data sets that relate to a specific research topic or

domain, typically also
formatted in a specific way. Three key aspects therefore need to
be taken into account:
(1) the data must be of a specific data type (e.g., microarrays, or
biological imaging);
(2) the data must be submitted in a specific data format (most
likely an open, standard
format instead of proprietary ones); (3) specific legal terms and
conditions need to be
satisfied (e.g., informed consent forms must be collected for
health data).
x Use a recognized waiver or license that is appropriate for
data. The OpenDefinition project
lists conformant licenses (both for content and data):
http://opendefinition.org/licenses/.
Importantly, licenses non-conformant to the open definition are
also reported:
http://opendefinition.org/licenses/nonconformant/. As a general
rule, it is important to
remember that the use of licenses which limit commercial re-use
or limit the production of
derivative works by excluding use for specific purposes is
discouraged. This because these
8
licenses can make it quite a bit harder to effectively re-use
datasets, and could also prevent
(tangential) commercial activities that could be used to support

data preservation in the long-
term5.
x Share the metadata along with the data. As Gray has put it:
“Data is incomprehensible and
hence useless unless there is a detailed and clear description of
how and when it was gathered,
and how the derived data was produced” [23]. Clear metadata
make it easier to understand if
data are appropriate for a project; without clear metadata data
sets can be overlooked or even
go unused. Worse yet, such data sets may be misinterpreted.
The recently released FAIR
(Findability, Accessibility, Interoperability, and Reusability)
guidelines are a good starting
point to check for efficient metadata reporting [24].
x Whenever possible, use standard file formats.
This applies for both data and metadata file formats. The
Biosharing registry lists a
comprehensive collection of standards for the life sciences
(https://biosharing.org/standards/)
(663 standards at the time of writing). To ensure that both data
and metadata are reported
accurately and compliant with community-established standards,
use (semantic) validation
tools, whenever available.
Open Source: Sustainable Software for Sustainable Science
Open source refers to software that is made available under a
license that permits anyone to
use, change, improve, or derive from existing source code, and
sometimes even to distribute the
software6. The case for open source code is straightforward: the

code researchers write and use to
analyze data is a vital part of the scientific research cycle, and,
similar to data, is not only necessary
to reproduce and interpret the results and corresponding
conclusions, but can also be used to answer
novel research questions. Therefore, if researchers write code as
a means to obtain results from data,
then this code should be released as well [8]. Clear
arrangements for the storage and preservation
of the code should be made, instructions need to be provided
that will allow the code to be compiled
and run without issue, and the code should be accompanied by a
description of the core
functionalities and hard- and software requirements for its use.
This in turn means that source code
alone is not sufficient: the software environment needs to be
described too, including for instance,
any linked libraries, any runtime environments or virtual
machines, The open source container
engine Docker is intended to provide an efficient solution for
computational reproducibility (see
www.docker.com) [25,26].7
Researchers sometimes prefer not to share code because of a
lack of complete and clear
documentation. While documentation is undoubtedly essential
for code validation and re-use, as a
general rule, sharing undocumented code is preferable to not
sharing code at all [27]. Another
concern that might stop researchers from sharing their code is
the fear that they will have to provide
full user support afterwards. One solution to this problem is to
setup a simple online mailing list
(for example through Google), and point all users to ask
questions through it. In this way, answers
are searchable on the web and available to other users who

might have the same issue/question. In
fact, this system utilizes a core property of open source code, in
that a community can come into
being around useful code. This community can then maintain,
support, and update this code even
in the absence of the original author.
5 see also the Panton Principles for Open Data at:
http://pantonprinciples.org
6 see the full Open Source definition at the Open Source
Initiative webpage: https://opensource.org/docs/osd
7 see also: http://goo.gl/oba1qN
9
It should however, be noted that many of the issues with code
quality and sharing can actually
be addressed by following simple best practices in code
organization and planning. For instance, a
key tool that all research programmers should incorporate into
their workflow is the use of a Version
Control System (VCS) such as git [28] or subversion (SVN). A
VCS provides a way for taking
snapshots of evolving code that allow tracking of changes, and
for reverting these if necessary (e.g.,
after making a change that ends up breaking the functionality of
the code). A rapidly growing
community of scientists use the Github platform
(https://github.com), which is a freely available

implementation of the git system, to contribute to collaborative
projects, and to review and test code
in a transparent and efficient way [29]. Interestingly, GitHub
also promises to be a useful tool in
assessing part of a researcher’s impact. For example, a
repository can be forked (which means there
will be adaptations of the code), starred (showing appreciation
for the work), pull requests can
happen (which show public engagement with the work and the
degree of potential collaboration),
as well as downloads (which may signal software installations
or code use).
Another interesting way to make code available is by
integrating it with tools that enable data
interrogation and interactive visualization. This approach,
known as literate programming [30],
seamlessly integrates analysis code, visualization plots, and
explanations in the form of narrative
text. There are a number of tools available to support this style
of research, including Jupyter (for
R, Python and Julia, http://jupyter.org), R Markdown (for R,
http://rmarkdown.rstudio.com), and
matlabweb (for MATLAB,
https://www.ctan.org/pkg/matlabweb). With these tools,
researchers
can create code files (in the case of Jupyter these are called
Notebooks8) that can be then shared on
Github, in turn allowing other people to directly run these
integrated code files through their
browser, without having to install any additional software.
Resources for open source
x The Software Sustainability Institute provides further

guidance on the benefits and
methods of software preservation, including guidance on code
repositories
(http://goo.gl/CE1OLY).
x Another comparative list of source code hosting facilities is
maintained on Wikipedia
(https://goo.gl/KfMfPu).
x The Open Source Initiative (OSI, http://opensource.org/) is an
organization dedicated
to promoting open source software. Amongst the resources
made available by the
organization, a list of open source licenses is available at
https://opensource.org/licenses. For each license, a full
description is reported, together
with terms and conditions of use.
x The NumFOCUS is a nonprofit organization that supports and
promotes world-class,
innovative, open source scientific software
(http://www.numfocus.org). The mission
of NumFOCUS is to promote sustainable high-level
programming languages, open
code development, and reproducible scientific research. A list
of sponsored projects is
available at http://goo.gl/VQgw0M. Amongst these:
o The IPython (Interactive Python, http://ipython.org), with the
Jupyter
Notebook available at https://jupyter.org, and a gallery of
interactive
Notebooks available at https://goo.gl/z3HgwH.
o The rOpenSci (R Open Science, http://ropensci.org), which
promotes the open

source R statistical environment for transparent and
reproducible research. A
8 a gallery of Notebooks is available at http://nb.bianp.net
10
list of open source rOpenSci packages is available at
http://ropensci.org/packages/. Some of these packages enable
communication
with widely used repositories, such as Figshare and Dyrad.
o The Software Carpentry (http://software-carpentry.org) is a
training
organization that runs workshops and lessons to teach scientists
basic
computing skills. All educational materials are developed
collaboratively
online on GitHub (https://github.com/swcarpentry), and are
distributed under
the open CC-BY license.
o The Data Carpentry (http://www.datacarpentry.org) is a sister
organization
to Software Carpentry, and aims to teach basic concepts, skills
and tools for
working more effectively with data. Again, lessons and
workshop materials are
available online and distributed under the open CC-BY license.

Open Access: The Right to Knowledge
Open access is a term coined for the first time at the Open
Access Budapest Initiative, and it
refers to an unrestricted online access to scholarly research,
primarily intended for scholarly journal
articles9. The case for open access has been extensi vely
reported in the literature [14,16,31–33]10.
Essentially, advocates of open access want full access to, and
use of, published scientific articles,
moved by the core argument that publicly funded universities
and granting bodies have a moral
duty to make academic research output available on the web at
no charge. Usage data from
PubMedCentral (the online repository of the US National
Institutes of Health) show that 25% of
the daily unique users are from universities, 17% from
companies, 40% of users are individual
citizens, and the remaining 18% are from government or other
categories (UNESCO, 2012).
To answer this call for open access to scientific publications, a
variety of full open access
journals have been launched in recent years, BioMed Central
and PLOS are just two examples of
publishers whose journals are all open access (see resources
below for a comprehensive list).
However, researchers may actively opt against open access
journals as a possible venue for their
research output. This reluctance is often related to the fact that
the highest impact factors remain
associated with subscription-based journals, and these are
therefore more prestigious dissemination
devices. However, as Sydney Brenner wrote twenty years

ago, “Before we develop a pseudoscience
of citation analysis, we should remind ourselves that what
matters absolutely is the scientific content
of a paper and that nothing will substitute for either
knowing it or reading it” [34]. In the long term,
it should be irrelevant where researchers publish their findings.
What is important is that to speed
up scientific progress, discovery and impact, research should be
shared and made available without
delay for others to use and to build upon.
Because citation rates and journal impact factors have become
key evaluation criteria in funding
decisions and research staff appointments and promotions, and
because scientists are inherently
rather conservative in their adoption of new approaches and
tools, researchers should keep in mind
that there still remain ways to make their work open, while still
publishing in traditional
subscription-based journals. Authors can make their work
available on the web by posting preprints
prior to formal peer-review and journal publication. This
methodology is very well established in
domains with lengthy peer-review cycles such as physics,
astronomy, computer science, and
9 see the full definition of open access at the Budapest Open
Access Initiative:
http://www.budapestopenaccessinitiative.org/read
10 see also: http://www.nature.com/openresearch/about-open-
access/benefits-for-authors/

11
mathematics [35,36], with a very large amount of articles posted
on the special-purpose arXiv
repository every day. The overall use of preprints in the life
sciences however, is still not significant,
although a modest increase has been observed with the launch
of PeerJ PrePrints and BioRxiv [37].
A list of all available preprint servers is given in Table 2.
Submitting unpublished work to a preprint server at (or even
before) the time of submission
brings two broad scientific benefits. First, it achieves free and
immediate dissemination of the
scientific results, and can solicit a wider input from the
community that constitutes prompt feedback
for possible improvement to the authors. Second, because
preprints have DOIs assigned, these can
be referenced even before the work is published in a journal. An
interesting side-effect is that the
DOI comes with a timestamp in the preprint archive, which can
be important for priority claims.
Table 2: List of preprint servers.
Preprint server Discipline Webpage
arXiv
physics, mathematics,
computer science, statistics,
quantitative biology and

finance
http://au.arXiv.org
bioRxiv
biology, genomics,
biochemistry, bioinformatics,
biophysics, life sciences at
large
http://biorxiv.org
CERN Document Server high-energy physics
https://cds.cern.ch/collection/Preprints
PeerJ Preprints
biology, medicine, computer
science
https://peerj.com/archives-preprints/
Resources for open access
x The Budapest Open Access Initiative -
http://www.budapestopenaccessinitiative.org
The BOAI has taken place in 2001 in response to the growing
demand to make research free
and available to anyone. BOAI is an active and diverse coalition
that has issued guidelines on
open access policies, licensing, infrastructures, and advocacy
(http://goo.gl/d2lVx0).
x Open Access Button - https://www.openaccessbutton.org/
The goal of the OA Button project is to find the number of

research outputs that are behind a
subscription paywall. When looking for a research article, and
not being able to access it, users
can mark the article using the OA Button browser bookmarklet.
When users bookmark those
restricted items, the system automatically connects to CORE
and Google Scholar and searches
for an available open access version of the same research
output, and links it back to the user.
x Open Knowledge Maps - http://openknowledgemaps.org
Launched very recently, Open Knowledge Maps is a large-scale
system of open, interactive and
interlinked knowledge maps spanning all fields of research
(currently based on the PLOS
library). Figure 2 shows an example of a knowledge map for
the query “cell migration”.
12
Figure 2: The Open Knowledge Map for the query “cell
migration”.
x Open Access Week - http://www.openaccessweek.org/
Every year in October, the scholarly community celebrates the
International Open Access Week

with events around the world. These events can be registered on
the Open Access Week
website, which also contains plenty of open access advocacy
material.
x Open Access Tracking Project - http://bit.ly/o-a-t-p
The OATP uses social tagging to capture new developments on
open access to research. The
OATP offers an updated catalogue of OA-related news and
comments, and furthermore
organizes knowledge of the open access field by tag or subtopic .
The project also lists resources
for open data, open educational resources, and anything related
to open science. Researchers
interested in the latest open access developments can also
subscribe to the daily news feed.
x SPARC Europe Open Access Diary -
http://sparceurope.org/oadiaryeurope/
To capture open access developments in Europe, the SPARC
Europe Open Access Diary
collects data from Europe from the OATP and then highlights
the most important news in an
interactive map, such as open access funders’ policies,
presentations, and other news related to
the movement.
x SHERPA/RoMEO - http://www.sherpa.ac.uk/romeo/index.php
13

RoMEO is part of SHERPA Services based at the University of
Nottingham, and it allows
authors to check policies from over 2,100 journals, i.e., if
public archiving of papers published
in these journals is permitted, and to which level (pre-print
and/or post-print and/or publisher's
version/PDF).
Another list of academic journals by preprint policy is
maintained on Wikipedia
(https://goo.gl/RFmlBw).
x Directory of Open Access Journals (DOAJ) - https://doaj.org
The DOAJ is an online directory that indexes and provides
access to high quality, open access,
peer-reviewed journals. At the time of writing, the directory
contains more than 10 000 open
access journals covering all areas of science, technology,
medicine, social science and
humanities, and therefore constitutes a useful resource to guide
researchers in their choice of
open access journal.
x Cofactor Journal Selector -
http://cofactorscience.com/journal-selector
The Cofactor UK company has developed an online tool, the
journal selector, which allows
researchers to look for journals that meet certain criteria,
including the option for open peer-
review and open access.
x Eigenfactor Project - http://www.eigenfactor.org
This project maintains a full list of no-fee open access journals
for all research fields, which is
accessible at:
http://www.eigenfactor.org/openaccess/fullfree.php.

x Open Access Overview - http://bit.ly/oa-overview
This is an introduction to open access (OA) for those who are
new to the concept, created and
maintained by Peter Suber. Amongst useful resources, the Open
Access Book is available at
http://bit.ly/oa-book.
Open Peer-Review: Transparent Research Evaluation
An often heard complaint among researchers is that the peer -
review system is ‘broken’. A
considerable number of articles have appeared in various
journals that question the process, and
how it is employed [38–41]. Most of these articles have raised
issues with the consistency of review,
its definition, ethics, cost, and the speed of the process [9].
Perhaps the first problem lies in the recognition of who peer -
review is for. Peer-review is
perhaps the best example of a community-wide way to practice
science, and should provide authors
with feedback on their work, preferably also with input for
improving it. However, in most cases,
peer-review also helps journal editors decide which submitted
manuscripts not to publish.
Furthermore, in most cases, the authors do not know the identity
of their reviewers, and, with very
few exceptions, these pre-publication reviews are discarded as
soon as articles are published. This
is unfortunate, as a lot of valuable context and insight goes to
waste through this discarding. Another
important aspect to consider is that traditional peer-review
gives very few incentives (or none at
all) to the reviewers, who are not credited for the considerable

amount of time and energy they
spend in performing manuscript reviews.
Another flaw of the current peer-review system seems to be
associated with the number of
retractions of articles that journals announce every year. In
2014 and 2015, Springer and IEEE
retracted over 100 published fraudulent articles from several
journals [42,43]. Similarly, the
Retraction Watch (http://retractionwatch.com) reports on these
issues in other journals. Although it
is not easy to evaluate the amount of published scientific papers
containing incorrect conclusions,
the number of retractions may provide information on the
problems associated with traditional peer-
14
review. In 2012, Grieneisen and Zhang surveyed 42 of the
largest bibliographic databases for major
scholarly fields and publisher websites [44]. They found that
the number of retractions has increased
considerably after 2001. Retractions happen more often in fields
such as medicine, life sciences and
chemistry than in fields such as mathematics, physics,
engineering and the social sciences.
According to the study, the main cause of retraction is
publishing misconduct (such as plagiarism
and authorship or copyright issues), followed by incorrect use
of data or incorrect data

interpretation, and research misconduct (e.g., the use of
fraudulent or fabricated data).
To address the abovementioned issues, open peer-review models
are emerging, in many cases
to complement traditional models. For example, BioMed
Central’s GigaScience, all the journals in
BioMed Central’s medical series, and the journal
F1000Research all publish reviewer reports, either
as part of the pre-publication review process, or subsequent to
publication. This last case is referred
to as open post-publication peer-review: after a first editorial
quality check, submitted manuscripts
are published online, peer-review is then carried out openly
(reports and names are published
alongside the article), and the authors are the invited to publish
a revised version of the article,
together with their response to the reviewers (see Figure 3).
Another form of open review comes from comments on blogs or
third party sites, independent
of any formal peer-review that may have already occurred on
the article. Amongst other platforms,
PubMed Commons was launched in 2013 as an initiative to
enable signed post-publication
commenting on articles indexed by PubMed. It is worth noting
that this platform is not related to
any specific journal or publisher, and as such constitutes a
forum for public scientific discourse.
Figure 3: A schematic overview of a post-publication open-
review model.
Importantly, studies have shown that open peer-review can

produce reviews of higher quality,
with better verified claims, and more construc tive criticisms,
when compared to closed review
[21,45]. Of course, one should keep in mind that open and
transparent peer-review does not come
without risks: especially young, early-career researchers might
fear that by signing critical and
thorough reviews they could become a target for retaliation at a
sensitive point in their career. In
this sense, the traditional closed process provides, in theory, a
sort of protection for the reviewer.
Table 3 lists publishing platforms and journals with an open
peer-review policy, either as part
of a pre- or a post-publication process.
Table 3: A list of platforms and journals (in alphabetical order)
that support an open peer-review policy.
Platform/Journal
Open peer-
review type
Website Comments
Copernicus post-publication
http://publications.cop
ernicus.org
manuscripts are first published as
discussion papers, then undergo an
interactive public discussion, and
are wherefore revised and published

15
F1000Research post-publication
http://f1000research.c
om
referees are selected and invited,
and their reports and names are
published alongside the article,
together with the authors' responses
and comments from registered users
GigaScience,
BioMed Central11
pre-publication
http://gigascience.bio
medcentral.com
anonymous peer review is not an
option; final reviewer reports are
online, distributed under a CC-BY
license
Nature
Communications,
NPG
pre-publication
www.nature.com/nco
mms/

as of January 2016 [46], an opt-out
open review is available: authors
can have the review history
published along with their
manuscript, unless they ask not to
PeerJ pre-publication https://peerj.com
optional open peer-review: referees
are encouraged, but not required, to
disclose their names; an all-or-
nothing option then publishes the
complete review history of the
paper
Publons
pre- and post-
publication
https://publons.com
reviewers can sign up and record
their history of peer reviews, both
before and after publication
PubMed
Commons
post-publication
https://www.ncbi.nlm.
nih.gov/pubmedcomm
ons /
authors of publications in PubMed
can post public comments on
published papers

PubPeer post-publication https://pubpeer.com
a non-profit organization that
allows authors to openly comment
on published research papers
Royal Society
Open Access
pre-publication
http://rsos.royalsociety
publishing.org
if both authors and referees agree
on an open peer-review model, then
signed referee reports are made
public online; in-between scenarios
are also possible
Miscellaneous Resources for Open Science
This section provides a list of general resources for open
science, from e-learning platforms,
over conferences and events, to open science coalitions and
opportunities for early-career
researchers’ fellowships.
1. COnnecting REpositories (CORE) - https://core.ac.uk
11 many more BioMed Central journals implement an open
peer-review model, for a full list see:
https://www.biomedcentral.com/journals

PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.2689 v1 |
16
CORE is the largest search engine of open access research
outputs. At the time of writing,
CORE indexes 861 repositories and contains more than 26
million records.
2. Open Knowledge Foundation - https://okfn.org
Open Knowledge International is a worldwide, non-profit
network of people passionate about
openness. This network uses advocacy, technology, and training
to unlock information, and
enables people to work with the network to create and share
knowledge. Researchers can get
involved through chapters and local groups:
https://okfn.org/network/.
3. Right to Research Coalition (R2RC) -
http://www.righttoresearch.org
The R2RC is a student and early career researcher organization
that aims to promote open
access, based on the belief that no student should be denied
access to the articles they need
because their institution cannot afford the often (too) high cost
of subscription.
Amongst other resources, a database of speakers on open
access, open data, and open education
is maintained by 2RC (see
http://www.righttoresearch.org/resources/Speakersdatabase/inde

x.shtml), which constitutes a
useful resource in case researchers would like to invite speakers
at their institutions to hear
more about specific aspects of open science.
4. OpenCon - http://www.opencon2016.org
OpenCon is an annual conference for students and early career
researchers who are interested
in the promotion of open access, open data, and open
educational resources. The conference
offers scholarship opportunities for applicants, and a live
stream for people not attending.
Students can join the coalition to be educated about open access
and to promote open access in
their institution or research field.
5. Facilitate Open Science Training for European Research
(FOSTER) -
https://www.fosteropenscience.eu
The FOSTER project maintains an e-learning platform that
brings together a variety of training
resources for those who need to know more about open science,
or who need to develop
strategies and skills for implementing open science practices in
their daily workflows. A nice
overview of available resources is given through the open
science taxonomy, as shown in
Figure 4.
6. The Future of Research Communication and e-Scholarship
(FORCE11) -
https://www.force11.org
FORCE11 is a community of scholars, librarians, archivists,
publishers, and research funders
that has grown to bring a change in modern scholarly
communications through the effective

use of information technology.
7. Research Data Alliance (RDA) - https://rd-alliance.org
The RDA promotes the development and adoption of
infrastructure for data sharing and data-
driven research, in order to accelerate the growth of a cohesive
data community that integrates
contributors across domain, research, national, geographic, and
generational boundaries. RDA
Plenaries are held every six months in different places around
the world. Interested early career
researchers can apply for a scholarship to support their
participation (both for USA and Europe:
https://rd-alliance.org/get-involved/studentearly-career-
programms).
8. Mozilla Science Lab - https://www.mozillascience.org
The Mozilla Science Lab facilitates learning about open source
and open data, and furthermore
offers fellowships for early-career researchers.
In particular, the Mozilla Fellowship for Science enables early-
career researchers to spend ten
months to work on open, web-enabled research and to further
open science as mentors within
the community (see https://www.mozillascience.org/fellows).
9. Center for Open Science - https://cos.io
17

The COS is a non-profit technology company that provides free
and open services to increase
inclusivity and transparency of research. Amongst the
interesting resources are the
“Transparency and Openness Promotion” (TOP) Guidelines
[13] (https://cos.io/top/), and a
curated list of public open science projects
(https://osf.io/explore/activity/#newPublicProjects).
10. Opening Science - http://www.openingscience.org
A project for the free sharing of open science resources,
Opening Science has published the
Open Book: “Opening Science – The Evolving Guide on
How the Internet is Changing
Research, Collaboration and Scholarly Publishing”
(http://www.openingscience.org/get-the-
book/).
Figure 4: The FOSTER Open Science taxonomy.
Image credit: Knoth, Petr; Pontika, Nancy (2015): Open Science
Taxonomy. figshare. -
https://dx.doi.org/10.6084/m9.figshare.1508606.v3 - Retrieved:
12 11, May 19, 2016 (GMT)
18
What Can You Do?

If you are willing to engage in open science, there are a number
of practices and resolutions
that can be adopted without too much effort; Box 1 lists the key
ones.
Box 1: Practices and resolutions to adopt in order to engage in
open science.
Conclusions
The next scientific revolution is underway. Modern science is
undergoing profound structural
changes enabled by the advent of digital technology and
communications, and these shifts are
occurring on multiple levels of the scientific process at once. If
we want to speed up scientific
progress, we must engage in open science practices, and make
our research output freely available
to the scientific community, and to the public at large.
However, scientists are inherently quite conservative in their
adoption of new approaches.
Novel methods often struggle to be accepted until their
superiority is confirmed, and found
overwhelming. As a result, a wide community of researchers is
currently awaiting evidence-based
benefits of open science practices before adopting them. From
an optimistic viewpoint, this
situation provides a perfect occasion for individuals to show
initiative and take immediate action,
potentially yielding a first-mover advantage. At the same time,
adherence to open science often

relies on the complete support of colleagues, supervisors,
research leaders, and host institutions,
especially for early-career researchers. In this respect, training
academics early in their career is
crucial: graduate programs should incorporate open science into
their existing curricula. A key topic
to be included in such curricula is training on publishing
practices, such as author rights, appropriate
citation practices, and open access publishing. Institutions and
funding agencies could together
1. When possible, use and cite existing public data.
2. Whenever feasible, share your research data through trusted
repositories.
General-purpose repositories and domain-specific ones are
available on the
web. Make sure you share relevant metadata as well, as these
are essential
for data interpretation and reproduction.
3. If you use software code as part of your research cycle,
release the code and
the environment needed to run it. Specify the open source
license you intend
to use, and link the readers to a stable repository that hosts the
code.
4. Post free copies of your research articles online. The majority
of journals
allow researchers to do so, sometimes after an embargo period
of 6-12
months.
5. Post preprints of your research manuscripts online, ideally at

the same time
of official submission to a journal.
6. When possible, choose an open access journal as venue for
your scientific
articles. Keep in mind that subscription journals also offer an
open access
solution, upon payment of extra fees.
19
provide skills training on data and code deposition, self-
archiving of articles, and modern scientific
computing, and could moreover consider mandates and policy
requirements for open science
practices. With appropriate training and support, early-career
researchers will thus be able to pursue
open science to the point that it becomes the default modus
operandi for all academic research.
This paper has presented an inventory of resources and practical
tips to conduct science in the
open. Of course, the availability of resources in the scientific
community is essential, but not
sufficient: scientists’ commitment is crucial, both at the
individual and at the collective level. Only
with commitment and wide participation will we be able to
unleash the potential of open research
practices, and reap the profound benefits of the increased

scientific progress that can be brought
about by open collaboration and ready exchange of ideas and
data between and beyond disciplines
and sectors.
Competing interests
PM is a Research Data Alliance early career fellow, an
OpenCon alumna, and is funded through an
EC H2020 project that aims to create an open data exchange
ecosystem.
Acknowledgments
The authors acknowledge funding from the European Union's
Horizon 2020 Programme under
Grant Agreement 634107 (PHC32-2014).
20
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