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


Can Accessibility Liberate The “Lost Ark” of Scholarly Work?: University Library Institutional Repositories Are “Places of Public Accommodation”

Authors : Raizel Liebler, Gregory Cunningham

For any body of knowledge – an ark of power or a corpus of scholarship – to be studied and used by people, it needs to be accessible to those seeking information. Universities, through their libraries, now aim to make more of the scholarship produced available for free to all through institutional repositories.

However, the goal of being truly open for an institutional repository is more than the traditional definition of open access. It also means openness in a more general sense. Creating a scholarship-based online space also needs to take into consideration potential barriers for people with disabilities.

This article addresses the interaction between the Americans with Disabilities Act (ADA) and university academic library based institutional repositories. This article concludes that institutional repositories have an obligation to comply with the ADA to make scholarly works available to potential users with disabilities.

For managers of institutional repositories, following the law is an opportunity to make scholarship even more widely available. University open access institutional repositories need to be accessible to existing and potential disabled users. However, there are no specific rules that university institutional repositories must follow to be compliant with the ADA’s “public accommodation” standard.

Accessibility is a changeable, moveable wall, consistently and constantly needing to be additionally inclusive of more – more technology and more users, regardless of disability or limitations.

Institutional repositories should not become the crated Ark of the Covenant with their secrets locked inside; instead, they should be as open as possible to all, sharing the scholarship inside.


Open Access — Towards a non-normative and systematic understanding

Authors : Niels Taubert, Anne Hobert, Nicolas Fraser, Najko Jahn, Elham Iravani

The term Open Access not only describes a certain model of scholarly publishing — namely in digital format freely accessible to readers — but often also implies that free availability of research results is desirable, and hence has a normative character.

Together with the large variety of presently used definitions of different Open Access types, this normativity hinders a systematic investigation of the development of open availability of scholarly literature.

In this paper, we propose a non-normative definition of Open Access and its usage as a neutral, descriptive term in bibliometric studies and research on science.

To this end, we first specify what normative figures are commonly associated with the term Open Access and then develop a neutral definition. We further identify distinguishing characteristics of openly accessible literature, called dimensions, and derive a classification scheme into Open Access categories based on these dimensions.

Additionally, we present an operationalisation method to assign scientific publications to the respective categories in practice. Here, we describe useful data sources, which can be employed to gather the information needed for the classification of scholarly works according to the presented classification scheme.


The diverse niches of megajournals: Specialism within generalism

Authors: Kyle Siler, Vincent Larivière, Cassidy R. Sugimoto

Over the past decade, megajournals have expanded in popularity and established a legitimate niche in academic publishing. Leveraging advantages of digital publishing, megajournals are characterized by large publication volume, broad interdisciplinary scope, and peer‐review filters that select primarily for scientific soundness as opposed to novelty or originality.

These publishing innovations are complementary and competitive vis‐à‐vis traditional journals. We analyze how megajournals (PLOS One, Scientific Reports) are represented in different fields relative to prominent generalist journals (Nature, PNAS, Science) and “quasi‐megajournals” (Nature Communications, PeerJ).

Our results show that both megajournals and prominent traditional journals have distinctive niches, despite the similar interdisciplinary scopes of such journals.

These niches—defined by publishing volume and disciplinary diversity—are dynamic and varied over the relatively brief histories of the analyzed megajournals. Although the life sciences are the predominant contributor to megajournals, there is variation in the disciplinary composition of different megajournals.

The growth trajectories and disciplinary composition of generalist journals—including megajournals—reflect changing knowledge dissemination and reward structures in science.

URL : The diverse niches of megajournals: Specialism within generalism


Revisiting “the 1990s debutante”: Scholar‐led publishing and the prehistory of the open access movement

Author : Samuel A. Moore

The movement for open access publishing (OA) is often said to have its roots in the scientific disciplines, having been popularized by scientific publishers and formalized through a range of top‐down policy interventions. But there is an often‐neglected prehistory of OA that can be found in the early DIY publishers of the late 1980s and early 1990s.

Managed entirely by working academics, these journals published research in the humanities and social sciences and stand out for their unique set of motivations and practices.

This article explores this separate lineage in the history of the OA movement through a critical‐theoretical analysis of the motivations and practices of the early scholar‐led publishers.

Alongside showing the involvement of the humanities and social sciences in the formation of OA, the analysis reveals the importance that these journals placed on experimental practices, critique of commercial publishing, and the desire to reach new audiences.

Understood in today’s context, this research is significant for adding complexity to the history of OA, which policymakers, advocates, and publishing scholars should keep in mind as OA goes mainstream.