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<img
src="manuscript-biorxiv0x.png" alt="PICT" >
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
<html >
<head><title></title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="generator" content="TeX4ht (http://www.cse.ohio-state.edu/~gurari/TeX4ht/)">
<meta name="originator" content="TeX4ht (http://www.cse.ohio-state.edu/~gurari/TeX4ht/)">
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<meta name="src" content="manuscript-biorxiv.tex">
<meta name="date" content="2020-07-12 15:58:00">
<link rel="stylesheet" type="text/css" href="manuscript-biorxiv.css">
</head><body
>
<div class="flushleft"
>
<!--l. 76--><p class="noindent" >
<br
class="newline" /><span
class="cmr-12x-x-120">Towards Open and Reproducible Genomic Research: Lessons</span>
<span
class="cmr-12x-x-120">from OpenScienceKE </span><br
class="newline" /><br />
Caleb Kibet <sup class="textsuperscript"><span
class="cmr-9">1,3,*</span></sup>, Author 2<sup class="textsuperscript"><span
class="cmr-9">2</span></sup>, Author 3<sup class="textsuperscript"><span
class="cmr-9">1</span></sup>, Author 4<sup class="textsuperscript"><span
class="cmr-9">1</span></sup>, Author 5<sup class="textsuperscript"><span
class="cmr-9">2</span></sup>, Author 6<sup class="textsuperscript"><span
class="cmr-9">2</span></sup>,
OpenScienceKE<sup class="textsuperscript"><span
class="cmr-9">3</span></sup><br />
<span
class="cmbx-10">1 International Center of Insect Physiology and Ecology</span><br />
<span
class="cmbx-10">2 Affiliation B</span><br />
<span
class="cmbx-10">3 Members of the OpenScienceKE community.</span><br />
<span
class="cmbx-10">* ckibet@icipe.org</span>
</div>
<h3 class="likesectionHead"><a
id="x1-1000"></a>Abstract</h3>
<!--l. 105--><p class="noindent" >Open, collaborative and reproducible research – Open Science – has a great potential for
advancing science. However, the training in our local universities does not equip students with
the tools to practice open science. However, to work in the open and collaborate,
your collaborators should be equipped to use the tools that you use. The main
barrier to working open, therefore, is the lack of awareness of the collaboration tools
and the skills required to utilize these tools. Therefore, to fill the gap through an
open science community, funded by a Mozilla Mini-grant – OpenScienceKE, we
are promoting open science among bioinformatics students and researchers in the
Nairobi area by training using this model: sensitize, train, hack and collaborate. This
model first sensitizes on open science practices through seminars, trains on open
science tools through workshops, facilitates hands-on application of the tools through
hackathons, and finally fosters a community of open science enthusiasts through
meetups.
<!--l. 107--><p class="indent" > OpenScienceKE sought to address the following problems: the lack of awareness of open
science practices and tools within the Bioinformatics community in Kenya; the poor adoption
of open science practices in Bioinformatics; and the absence of research to establish the state
of affairs in adopting open science in Kenya. From the OpenScienceKE hackathon, we
managed to create an open resource that the students could use to figure out where they can
cost-effectively publish open access. In addition, through literature search and data mining,
we observed a growing interest in open science practices in Kenya but the lack of
awareness and skills hinder the adoption. The use of preprints for research dissemination
haven’t caught up in Kenya; out of the 20,069 papers downloaded from bioRXiv, only
18 have Kenyan authors, a majority of which are as a result of international (16)
collaborations. We also observed a lack of incentives and policy in academic and research
institutions to support open science. The fear of being scooped and the competitive
spirit within the scientific community are also major barriers to working in the
open.
<!--l. 109--><p class="indent" > The first iteration of the model which focused on academic institutions set the foundation
for next phase: promote the open and reproducible science in research institutions. This
model provides the framework for the adoption of open science practices within the
<img
src="manuscript-biorxiv1x.png" alt="PICT" >
<img
src="manuscript-biorxiv2x.png" alt="PICT" >
institution and others in the future. As genomic research data generated in Africa grows,
there is a need for the adoption of open science practices in data storage, reproducible
pipelines and collaborative research. We propose this approach, which develops the necessary
infrastructure within research institutions, and builds human capacity through the model:
sensitize, train, hack and collaborate. Promotion of open science in Africa recognizes the
future direction of research and OpenScienceKE is growing the culture and practice in the
research active region.
<!--l. 1--><p class="noindent" >
<h3 class="likesectionHead"><a
id="x1-2000"></a>Introduction</h3>
<a
id="x1-2000doc"></a>
<a
id="Q1-1-3"></a>
<!--l. 4--><p class="noindent" >Our Core message is to present a clear outlook on the adoption of Open Science practice by
African-based scientists, starting with Kenya.
<!--l. 7--><p class="indent" > Add an introduction of the Open Science. To cite an article, use <span class="cite"> [<a
href="#XSchlegel2016">3</a>]</span>. All the
bibliographies should be added to <span
class="cmtt-10">library.bib </span>in the BibTeX format. See the example in
<span
class="cmtt-10">library.bib</span>.
<!--l. 12--><p class="indent" > Since this will more or less be like a review article, we will need to identify the various
subsections based on the topics we need to cover in the review. See <a
href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619" >this article</a> for some tips
<span class="cite"> [<a
href="#XMensh2017">2</a>]</span>.
<!--l. 18--><p class="indent" > <span
class="cmbx-10">Placeholder Text for the Background </span>WILL UPDATE TO INTRODUCTION
<!--l. 20--><p class="indent" > Open, collaborative and reproducible research – Open Science – has a great potential for
advancing science. However, the training in our local universities does not equip students with
the tools to practice open science. However, to work in the open and collaborate,
your collaborators should be equipped to use the tools that you use. The main
barrier to working open, therefore, is the lack of awareness of the collaboration tools
and the skills required to utilize these tools. Therefore, to fill the gap through an
open science community, funded by a Mozilla Mini-grant – OpenScienceKE, we
are promoting open science among bioinformatics students and researchers in the
Nairobi area by training using this model: sensitize, train, hack and collaborate. This
model first sensitizes on open science practices through seminars, trains on open
science tools through workshops, facilitates hands-on application of the tools through
hackathons, and finally fosters a community of open science enthusiasts through
meetups.
<!--l. 36--><p class="indent" > OpenScienceKE sought to address the following problems: the lack of awareness of open
science practices and tools within the Bioinformatics community in Kenya; the poor adoption
of open science practices in Bioinformatics; and the absence of research to establish the state
of affairs in adopting open science in Kenya. From the OpenScienceKE hackathon, we
managed to create an open resource that the students could use to figure out where they can
cost-effectively publish open access. In addition, through literature search and data mining,
we observed a growing interest in open science practices in Kenya but the lack of
awareness and skills hinder the adoption. The use of preprints for research dissemination
haven’t caught up in Kenya; out of the 20,069 papers downloaded from bioRXiv, only
18 have Kenyan authors, a majority of which are as a result of international (16)
collaborations. We also observed a lack of incentives and policy in academic and research
institutions to support open science. The fear of being scooped and the competitive
spirit within the scientific community are also major barriers to working in the
open.
<!--l. 54--><p class="indent" > The first iteration of the model which focused on academic institutions set the foundation
for next phase: promote the open and reproducible science in research institutions. This
model provides the framework for the adoption of open science practices within the
<img
src="manuscript-biorxiv3x.png" alt="PICT" >
<img
src="manuscript-biorxiv4x.png" alt="PICT" >
institution and others in the future. As genomic research data generated in Africa grows,
there is a need for the adoption of open science practices in data storage, reproducible
pipelines and collaborative research. We propose this approach, which develops the necessary
infrastructure within research institutions, and builds human capacity through the model:
sensitize, train, hack and collaborate. Promotion of open science in Africa recognizes the
future direction of research and OpenScienceKE is growing the culture and practice in the
research acti
<!--l. 68--><p class="noindent" >
<h4 class="likesubsectionHead"><a
id="x1-3000"></a>Status of Open Science in Kenya: Literature search</h4>
<a
id="x1-3000doc"></a>
<a
id="Q1-1-5"></a>
<!--l. 72--><p class="noindent" >The report from the above team will be useful for writing the introduction, as well as
providing materials to be used in the discussion. In fact, we can use their resource to weave
the whole paper together.
<!--l. 77--><p class="indent" > In this section, and the introduction, we will conduct a review of the status of open science
in the country. - What kind of resources are available to support open science - Are there
policies or incentives for open science practices? - What kind of training activities have been
conducted to promote and train students and researchers on open science tools and practices?
- etc
<!--l. 85--><p class="noindent" >
<h5 class="subsubsectionHead"><span class="titlemark">0.0.1 </span> <a
id="x1-40000.0.1"></a>Proposed subsections and content</h5>
<!--l. 87--><p class="noindent" >The subsections will be based on the findings about the status of open science in
Kenya.
<!--l. 90--><p class="indent" >
<ol class="enumerate1" >
<li
class="enumerate" id="x1-4002x1">
Resources
to
support
open
science
are
insufficient.
The
resources
include:</li></ol>
<ul class="itemize1">
<li class="itemize">
ICT
infrastructure.
KENET
provides
infrastructure
<img
src="manuscript-biorxiv5x.png" alt="PICT" >
<img
src="manuscript-biorxiv6x.png" alt="PICT" >
for
open
science
training.
</li>
<li class="itemize">
Institutional
repositories.
Universities
and
Research
institutes
have
repositories
to
store
publications.
Also
repositories
to
store
research
data.
Do
all
institutions
have
these
repositories?</li></ul>
<!--l. 109--><p class="indent" >
<ol class="enumerate1" >
<li
class="enumerate" id="x1-4004x2">
Lacking
policies
and
incentives
from
the
government,
local
funders
and
institutions.
These
policies
and
incentives
lack
in
<img
src="manuscript-biorxiv7x.png" alt="PICT" >
<img
src="manuscript-biorxiv8x.png" alt="PICT" >
open
science
practices
such
as:</li></ol>
<ul class="itemize1">
<li class="itemize">
Research
data
management.
Apart
from
<a
href="https://cgspace.cgiar.org/handle/10568/63496" >ILRI’s
data
management
policy</a>,
do
other
institutions
have
these
policies?
</li>
<li class="itemize">
Open
access
publishing</li></ul>
<!--l. 129--><p class="indent" >
<ol class="enumerate1" >
<li
class="enumerate" id="x1-4006x3">
Limited
training
on
Open
Science.
Awareness
on
Open
Science
has
previously
been
through:</li></ol>
<img
src="manuscript-biorxiv9x.png" alt="PICT" >
<img
src="manuscript-biorxiv10x.png" alt="PICT" >
<ul class="itemize1">
<li class="itemize">
Open
access
week
in
universities.
(Do
research
institutions
participate
in
Open
Access
week?)
</li>
<li class="itemize">
Workshops
such
as
OpenScienceKE
Workshop
in
2018
</li>
<li class="itemize">
Others?</li></ul>
<!--l. 149--><p class="noindent" >
<h3 class="likesectionHead"><a
id="x1-50000.0.1"></a>Data Mining Section</h3>
<a
id="Q1-1-8"></a>
<!--l. 152--><p class="noindent" >This will be a data analysis section. The title of this section will depend on the results of your
analysis. For example, if Kenyan researchers are not publishing open access, we
will need to understand why that is the case. The solution may lie in the cost of
publishing, and that is how the resource created by Open Access options team is
useful.
<!--l. 159--><p class="indent" > We address questions like: - What is the publishing trend by Kenyan researchers - Are
they publishing open access, and how has this changed over the years? - Are Kenyan
researchers embracing pre-prints (BioRXiv, AriRXiv, ResearchGate, F1000Research). Who is
driving the adoption of pre-prints? Local researchers or foreign collaborators? -
What are the collaboration trends? Are Kenyan researcher collaborating locally or
internationally?
<!--l. 168--><p class="noindent" >
<h5 class="subsubsectionHead"><span class="titlemark">0.0.2 </span> <a
id="x1-60000.0.2"></a>Proposed title and content</h5>
<img
src="manuscript-biorxiv11x.png" alt="PICT" >
<img
src="manuscript-biorxiv12x.png" alt="PICT" >
<!--l. 170--><p class="noindent" >The title here should indicate whether <span
class="cmti-10">Kenyan researchers are embracing open science</span>
<span
class="cmti-10">practices </span>as per the findings of the Data Mining team. This section’s discussion may therefore
focus on supporting this claim based on:
<!--l. 175--><p class="indent" >
<ol class="enumerate1" >
<li
class="enumerate" id="x1-6002x1">
The
publishing
trend
of
Kenyan
researchers.
The
trend
indicates
that
open
access
publishing
is
popular.
The
popular
journals
where
Kenyan
researcher
publish
are
open
access.
</li>
<li
class="enumerate" id="x1-6004x2">
Pre-prints.
Pre-prints
are
yet
to
be
widely
adopted
by
Kenyan
scientists
and
foreign
collaborators
drive
the
<img
src="manuscript-biorxiv13x.png" alt="PICT" >
<img
src="manuscript-biorxiv14x.png" alt="PICT" >
adoption
of
pre-prints
among
Kenyan
authors
</li>
<li
class="enumerate" id="x1-6006x3">
Open
data
and
Code.
<a
href="https://github.com/BioinfoNet/Data-mining/issues/11" ><span
class="cmbxti-10">This</span>
<span
class="cmbxti-10">is</span>
<span
class="cmbxti-10">yet</span>
<span
class="cmbxti-10">to</span>
<span
class="cmbxti-10">be</span>
<span
class="cmbxti-10">completed</span></a><span
class="cmbxti-10">.</span>
<span
class="cmbxti-10">We</span>
<span
class="cmbxti-10">need</span>
<span
class="cmbxti-10">to</span>
<span
class="cmbxti-10">find</span>
<span
class="cmbxti-10">out</span>
<span
class="cmbxti-10">whether</span>
<span
class="cmbxti-10">Kenyan</span>
<span
class="cmbxti-10">authors</span>
<span
class="cmbxti-10">are</span>
<span
class="cmbxti-10">making</span>
<span
class="cmbxti-10">the</span>
<span
class="cmbxti-10">data</span>
<span
class="cmbxti-10">and</span>
<span
class="cmbxti-10">code</span>
<span
class="cmbxti-10">available</span>
<span
class="cmbxti-10">and</span>
<span
class="cmbxti-10">accessible,</span>
<span
class="cmbxti-10">and</span>
<span
class="cmbxti-10">whether</span>
<span
class="cmbxti-10">they</span>
<span
class="cmbxti-10">are</span>
<span
class="cmbxti-10">adhering</span>
<span
class="cmbxti-10">to</span>
<span
class="cmbxti-10">the</span>
<span
class="cmbxti-10">FAIR</span>
<span
class="cmbxti-10">principles</span>
</li>
<li
class="enumerate" id="x1-6008x4">
Collaboration
trends.
Are
<img
src="manuscript-biorxiv15x.png" alt="PICT" >
<img
src="manuscript-biorxiv16x.png" alt="PICT" >
Kenyan
authors
collaborating
from
within
or
without?
(based
on
pre-prints
from
bioRXiv,
we
see
that
Kenyan
authors
are
mostly
collaborating
internationally.
Is
this
the
case
from
the
rest
of
literature
obtained
during
data
mining?)
5
What
else?</li></ol>
<!--l. 200--><p class="noindent" >
<h3 class="likesectionHead"><a
id="x1-70000.0.2"></a>But Publishing Open Access is Expensive</h3>
<a
id="Q1-1-11"></a>
<!--l. 203--><p class="noindent" >The article processing charge is the main barrier to publishing open access, in addition to the
obsession with impact factors. However, for early career scientists and students, especially in
developing countries, most publishers offer waivers and subsidies but few are aware.
In this section, we explore some of the avenues to publishing open access at low
cost.
<!--l. 210--><p class="indent" > To address this problem, we created a resource that can guide ECR and students on where
they publish open access, and at low cost. We also provide information on how
they can still be open when they publish in paywalled journals, eg via the green
route.
<img
src="manuscript-biorxiv17x.png" alt="PICT" >
<img
src="manuscript-biorxiv18x.png" alt="PICT" >
<!--l. 216--><p class="noindent" >
<h5 class="subsubsectionHead"><span class="titlemark">0.0.3 </span> <a
id="x1-80000.0.3"></a>Proposed content of Section</h5>
<ul class="itemize1">
<li class="itemize">
Low
cost
open
access
publishing
is
available.</li></ul>
<!--l. 224--><p class="noindent" >Here our discussion will indicate that there are publishers offering waivers and subsidies for
developing countries (low income and lower middle income countries). Waiver is either Full or
50% of the APCs. Sometimes, waivers are offered on a case-by-case basis. The resource
created will create awareness on where to publish at low cost in an open access
way.
<!--l. 232--><p class="noindent" >
<h5 class="subsubsectionHead"><span class="titlemark">0.0.4 </span> <a
id="x1-90000.0.4"></a>Draft text for the section</h5>
<!--l. 234--><p class="noindent" >Access to literature is of paramount importance in the process of scientific inquiry. The free
flow of ideas and information are crucial to addressing economic, environmental and social
issues facing developing countries especially in Africa. However, contrary to concerted
research efforts to foster development, an assessment of Africa’s research output between 1999
- 2008 indicated that Africa lagged behind in it’s research output when compared to the rest
of the world <span class="cite"> [<span
class="cmbx-10">?</span>]</span>. Poor accessibility of scientific publications has been suggested as
one of the reasons for the low research output from Africa <span class="cite"> [<span
class="cmbx-10">?</span>]</span>. Accessibility of
scientific literature by African researchers is mostly hindered by the lack of access to
subscription-based journal articles due to their unaffordable cost. However, the
main barrier to equitable access and sharing of knowledge in Africa is the cost
publishing, which is unaffordable for most researchers in Low- and Middle-income
countries.
<!--l. 250--><p class="indent" > The concept of openness in scientific research has long been proposed as a means toward
equitable sharing of knowledge <span class="cite"> [<span
class="cmbx-10">?</span>]</span>. Consequently, most journals have shifted from
subscription-based access to research articles and embraced open access publishing. In this
case, however, the authors have to pay article publication fees which often run into thousands
of dollars - another barrier to publishing especially from authors in Low- and Middle-income
countries. In most Kenyan institutions, for example, students have to publish at least one
paper at MSc level. With limited funds and the need to publish in a reputable journal, most
students usually don’t know which journals to publish in due to the high cost of article
processing charges (APCs).
<!--l. 263--><p class="indent" > In this study, we observed that Kenyan authors are increasingly adopting open access
publishing, a trend that has been observed in Low Income countries <span class="cite"> [<a
href="#Xiyandemye_low_2019">1</a>]</span>. To help
students and early career scientists adopt this open access publishing trend, we
looked into publishers that publish open access and created a resource that acts as a
guideline for them to publish open access, and at low cost. We found that most Open
Access publishers offer waivers or subsidies to authors from developing countries. The
<img
src="manuscript-biorxiv19x.png" alt="PICT" >
<img
src="manuscript-biorxiv20x.png" alt="PICT" >
publishers had different criteria for offering waivers. Some publishers, such as Nature
Publishing Group, offered a full waiver to authors in low-income countries and 50%
discount for authors in low-middle-income countries. Some of the publishers’ waiver
policies are linked to the corresponding author, source of funds for research or the
financial need of the author. For example, PLOS offers waivers of about 50% or more
if the research was carried out in low or LMIC countries therefore linking their
waiver policy to source of research funds. Publishers such as Oxford University
Press and eLIFE offer waivers to authors in low- and middle-income countries who
experience financial hardships or have insufficient funds. Waivers are also available on a
case-by-case basis for authors in low- and middle-income countries by publishers such as
MDPI.
<!--l. 284--><p class="indent" > As a low-middle-income country, Kenyan authors are eligible for waivers and
subsidies. Although we found no special waiver to students identified so far, students
may apply for waivers as authors in financial need in developing countries whom
publishers offer waivers on a case-by-case basis. Additionally, students may also place
their manuscript on preprint servers, the green route of publishing, where they can
receive feedback on their work before publication in an open access journal. Both
the use of preprint servers and open access publishing by taking advantage of the
waivers offered by publishers will increase the accessibility of research literature in
Africa.
<!--l. 295--><p class="noindent" >
<h3 class="likesectionHead"><a
id="x1-100000.0.4"></a>Figures</h3>
<a
id="Q1-1-15"></a>
<!--l. 298--><p class="noindent" >You can add the figures as follows:
<!--l. 300--><p class="indent" > <hr class="figure"><div class="figure"
><a
id="x1-100011"></a>
<br /> <div class="caption"
><span class="id">Figure 1: </span><span
class="content">Figure 1</span></div><!--tex4ht:label?: x1-100011 -->
<!--l. 304--><p class="indent" > </div><hr class="endfigure">
<!--l. 306--><p class="indent" > And you can have it referenced as a figure
<!--l. 308--><p class="indent" >
<div class="quote">
<!--l. 309--><p class="noindent" ><span
class="cmbx-10">Box</span>
<span
class="cmbx-10">1</span>
To
highlight
of
defining
some
key
concepts
in
Open
science
without
disrupting
the
flow
<img
src="manuscript-biorxiv21x.png" alt="PICT" >
<img
src="manuscript-biorxiv22x.png" alt="PICT" >
of
the
articles,
you
can
use
a
quote
format.</div>
<!--l. 314--><p class="noindent" >
<h3 class="likesectionHead"><a
id="x1-110000.0.4"></a>Discussion</h3>
<a
id="Q1-1-18"></a>
<!--l. 317--><p class="noindent" >What do the results mean? How does your results fit to the current literature? How do they
compare to other similar studies?
<!--l. 320--><p class="noindent" >
<h3 class="likesectionHead"><a
id="x1-120000.0.4"></a>Conclusions</h3>
<a
id="Q1-1-20"></a>
<!--l. 323--><p class="noindent" >What is the take-home message from this article? What are the recommendations? - The need
for a framework to guide the adoption of open science practices. Take note of the barriers and
provide recommendations. - The need for low-cost publishing - The need for policies on open
science that can be implemented by various institutions. For example, we can provide a
template that can be adopted by most institutions
<!--l. 331--><p class="noindent" >
<h3 class="sectionHead"><span class="titlemark">1 </span> <a
id="x1-130001"></a>Acknowledgement</h3>
<!--l. 333--><p class="noindent" >We acknowledge the support from … and the contribution from Mozilla Science Lab and
KENET, and ICIPE.
<!--l. 336--><p class="indent" > Use this section to acknowledge funding and resource contributions to the project.
<!--l. 118--><p class="noindent" >
<h3 class="likesectionHead"><a
id="x1-140001"></a>Acknowledgments</h3>
<!--l. 119--><p class="noindent" >We thank KENET for providing us with an ample environment for our hackathon.
<!--l. 1--><p class="noindent" >
<h3 class="likesectionHead"><a
id="x1-150001"></a>References</h3>
<!--l. 1--><p class="noindent" >
<div class="thebibliography">
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1.<span class="bibsp">   </span></span>
<img
src="manuscript-biorxiv23x.png" alt="PICT" >
<img
src="manuscript-biorxiv24x.png" alt="PICT" >
<a
id="Xiyandemye_low_2019"></a>J. Iyandemye
and
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<img
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<img
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<a
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</p>
</div>
<img
src="manuscript-biorxiv27x.png" alt="PICT" >
<img
src="manuscript-biorxiv28x.png" alt="PICT" >
</body></html>
<img
src="manuscript-biorxiv29x.png" alt="PICT" >