Scientific sinkhole: The pernicious price of formatting

Authors : Allana G. LeBlanc, Joel D. Barnes, Travis J. Saunders, Mark S. Tremblay, Jean-Philippe Chaput


To conduct a time-cost analysis of formatting in scientific publishing.


International, cross-sectional study (one-time survey).


Internet-based self-report survey, live between September 2018 and January 2019.


Anyone working in research, science, or academia and who submitted at least one peer-reviewed manuscript for consideration for publication in 2017. Completed surveys were available for 372 participants from 41 countries (60% of respondents were from Canada).

Main outcome measure

Time (hours) and cost (wage per hour x time) associated with formatting a research paper for publication in a peer-reviewed academic journal.


The median annual income category was US$61,000–80,999, and the median number of publications formatted per year was four. Manuscripts required a median of two attempts before they were accepted for publication.

The median formatting time was 14 hours per manuscript, or 52 hours per person, per year. This resulted in a median calculated cost of US$477 per manuscript or US$1,908 per person, per year.


To our knowledge, this is the first study to analyze the cost of manuscript formatting in scientific publishing. Our results suggest that scientific formatting represents a loss of 52 hours, costing the equivalent of US$1,908 per researcher per year.

These results identify the hidden and pernicious price associated with scientific publishing and provide evidence to advocate for the elimination of strict formatting guidelines, at least prior to acceptance.

URL : Scientific sinkhole: The pernicious price of formatting


Open Systems Pharmacology community – an open access, open source, open science approach to modeling and simulation in pharmaceutical sciences

Authors : Jörg Lippert, Rolf Burghaus, Andrea Edginton, Sebastian Frechen, Mats Karlsson, Andreas Kovar, Thorsten Lehr, Peter Milligan, Valerie Nock, Sergej Ramusovic, Matthew Riggs, Stephan Schaller, Jan Schlender, Stephan Schmidt, Michaël Sevestre, Erik Sjögren, Juri Solodenko, Alexander Staab, Donato Teutonico

Systems Pharmacology integrates structural biological and pharmacological knowledge and experimental data enabling dissection of organism and drug properties and providing excellent predictivity.

The development of systems pharmacology models is a significant task requiring massive amounts of background information beyond individual trial data. Qualification of models needs repetitive demonstration of successful predictions.

Open Systems Pharmacology is a community that develops, qualifies and shares professional open source software tools and models in a collaborative open science way.


bioRxiv: the preprint server for biology

Authors : Richard Sever, Ted Roeder, Samantha Hindle, Linda Sussman, Kevin-John Black, Janet Argentine, Wayne Manos, John R. Inglis

The traditional publication process delays dissemination of new research, often by months, sometimes by years. Preprint servers decouple dissemination of research papers from their evaluation and certification by journals, allowing researchers to share work immediately, receive feedback from a much larger audience, and provide evidence of productivity long before formal publication.

Launched in 2013 as a non-profit community service, the bioRxiv server has brought preprint practice to the life sciences and recently posted its 64,000th manuscript.

The server now receives more than four million views per month and hosts papers spanning all areas of biology. Initially dominated by evolutionary biology, genetics/genomics and computational biology, bioRxiv has been increasingly populated by papers in neuroscience, cell and developmental biology, and many other fields.

Changes in journal and funder policies that encourage preprint posting have helped drive adoption, as has the development of bioRxiv technologies that allow authors to transfer papers easily between the server and journals.

A bioRxiv user survey found that 42% of authors post their preprints prior to journal submission whereas 37% post concurrently with journal submission. Authors are motivated by a desire to share work early; they value the feedback they receive, and very rarely experience any negative consequences of preprint posting.

Rapid dissemination via bioRxiv is also encouraging new initiatives that experiment with the peer review process and the development of novel approaches to literature filtering and assessment.

URL : bioRxiv: the preprint server for biology


Worldwide inequality in access to full textscientific articles: the example ofophthalmology

Authors : Christophe Boudry, Patricio Alvarez-Muñoz, Ricardo Arencibia-Jorge, Didier Ayena, Niels J. Brouwer, Zia Chaudhuri, Brenda Chawner, Emilienne Epee, Khalil Erraïs, Akbar Fotouhi, Almutez M. Gharaibeh, Dina H. Hassanein, Martina C. Herwig-Carl, Katherine Howard, Dieudonne Kaimbo Wa Kaimbo, Patricia-Ann Laughrea, Fernando A. Lopez, Juan D. Machin-Mastromatteo, Fernando K. Malerbi, Papa Amadou Ndiaye, Nina A. Noor, Josmel Pacheco-Mendoza, Vasilios P. Papastefanou, Mufarriq Shah, Carol L. Shields, Ya Xing Wang, Vasily Yartsev, Frederic Mouriaux


The problem of access to medical information, particularly in low-income countries, has been under discussion for many years. Although a number of developments have occurred in the last decade (e.g., the open access (OA) movement and the website Sci-Hub), everyone agrees that these difficulties still persist very widely, mainly due to the fact that paywalls still limit access to approximately 75% of scholarly documents.

In this study, we compare the accessibility of recent full text articles in the field of ophthalmology in 27 established institutions located worldwide.


A total of 200 references from articles were retrieved using the PubMed database. Each article was individually checked for OA. Full texts of non-OA (i.e., “paywalled articles”) were examined to determine whether they were available using institutional and Hinari access in each institution studied, using “alternative ways” (i.e., PubMed Central, ResearchGate, Google Scholar, and Online Reprint Request), and using the website Sci-Hub.


The number of full texts of “paywalled articles” available using institutional and Hinari access showed strong heterogeneity, scattered between 0% full texts to 94.8% (mean = 46.8%; SD = 31.5; median = 51.3%).

We found that complementary use of “alternative ways” and Sci-Hub leads to 95.5% of full text “paywalled articles,” and also divides by 14 the average extra costs needed to obtain all full texts on publishers’ websites using pay-per-view.


The scant number of available full text “paywalled articles” in most institutions studied encourages researchers in the field of ophthalmology to use Sci-Hub to search for scientific information.

The scientific community and decision-makers must unite and strengthen their efforts to find solutions to improve access to scientific literature worldwide and avoid an implosion of the scientific publishing model.

This study is not an endorsement for using Sci-Hub. The authors, their institutions, and publishers accept no responsibility on behalf of readers.

URL : Worldwide inequality in access to full textscientific articles: the example ofophthalmology


The History and Future of Data Citation in Practice

Authors : Mark A. Parsons, Ruth E. Duerr, Matthew B. Jones

In this review, we adopt the definition that ‘Data citation is a reference to data for the purpose of credit attribution and facilitation of access to the data’ (TGDCSP 2013: CIDCR6). Furthermore, access should be enabled for both humans and machines (DCSG 2014).

We use this to discuss how data citation has evolved over the last couple of decades and to highlight issues that need more research and attention.

Data citation is not a new concept, but it has changed and evolved considerably since the beginning of the digital age. Basic practice is now established and slowly but increasingly being implemented.

Nonetheless, critical issues remain. These issues are primarily because we try to address multiple human and computational concerns with a system originally designed in a non-digital world for more limited use cases.

The community is beginning to challenge past assumptions, separate the multiple concerns (credit, access, reference, provenance, impact, etc.), and apply different approaches for different use cases.

URL : The History and Future of Data Citation in Practice


A Case Report: Building communities with training and resources for Open Science trainers

Authors: Helene Brinken, Iryna Kuchma, Vasso Kalaitzi, Joy Davidson, Nancy Pontika, Matteo Cancellieri, Antónia Correia, José Carvalho, Remedios Melero, Damjana Kastelic, Filomena Borba, Katerina Lenaki, Ulf Toelch, Katerina Zourou, Petr Knoth, Eloy Rodrigues

To foster responsible research and innovation, research communities, institutions, and funders are shifting their practices and requirements towards Open Science. Open Science skills are becoming increasingly essential for researchers. Indeed general awareness of Open Science has grown among EU researchers, but the practical adoption can be further improved.

Recognizing a gap between the needed and the provided training offer, the FOSTER project offers practical guidance and training to help researchers learn how to open up their research within a particular domain or research environment.

Aiming for a sustainable approach, FOSTER focused on strengthening the Open Science training capacity by establishing and supporting a community of trainers. The creation of an Open Science training handbook was a first step towards bringing together trainers to share their experiences and to create an open and living knowledge resource.

A subsequent series of train-the-trainer bootcamps helped trainers to find inspiration, improve their skills and to intensify exchange within a peer group. Four trainers, who attended one of the bootcamps, contributed a case study on their experiences and how they rolled out Open Science training within their own institutions.

On its platform the project provides a range of online courses and resources to learn about key Open Science topics. FOSTER awards users gamification badges when completing courses in order to provide incentives and rewards, and to spur them on to even greater achievements in learning.

The paper at hand describes FOSTER Plus’ training strategies, shares the lessons learnt and provides guidance on how to reuse the project’s materials and training approaches.

URL : A Case Report: Building communities with training and resources for Open Science trainers


‘Is the library open?’: Correlating unaffiliated access to academic libraries with open access support

Authors: Katie Wilson, Cameron Neylon, Chloe Brookes-Kenworthy, Richard Hosking, Chun-Kai (Karl) Huang, Lucy Montgomery, Alkim Ozaygen

In the context of a growing international focus on open access publishing options and mandates, this paper explores the extent to which the ideals of ‘openness’ are also being applied to physical knowledge resources and research spaces.

This study, which forms part of the larger Curtin Open Knowledge Initiative project, investigates the relationship between academic library access policies and institutional positions on open access or open science publishing.

Analysis of library access policies and related documents from twenty academic institutions in Asia, Australia, Europe, North America, Africa and the United Kingdom shows that physical access to libraries for members of the public who are not affiliated with a university is often the most restricted category of access. Many libraries impose financial and sometimes security barriers on entry to buildings, limiting access to collections in print and other non-digital formats.

The limits placed on physical access to libraries contrast strongly with the central role that these institutions play in facilitating open access in digital form for research outputs through institutional repositories and open access publishing policies.

We compared library access policies and practices with open access publishing and research sharing policies for the same institutions and found limited correlation between both sets of policies.

Comparing the two assessments using Spearman’s rank correlation coefficient confirmed open access policies have a direct association with the narrow aspects of public access provided through online availability of formal publications, but are not necessarily associated (in the universities in this study) with delivering on a broader commitment to public access to knowledge.

The results suggest that while institutional mission statements and academic library policies may refer to sharing of knowledge and research and community collaboration, multiple layers of library user categories, levels of privilege and fees charged can inhibit the realisation of these goals.

As open access publishing options and mandates expand, physical entry to academic libraries and access to print and electronic resources has contracted. This varies within and across countries, but it conflicts with global library and information commitments to open access to knowledge.

URL : ‘Is the library open?’: Correlating unaffiliated access to academic libraries with open access support