EN

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

Posted on by Hans Dillaerts

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.

DOI : https://doi.org/10.1002/psp4.12473

Non classé

bioRxiv: the preprint server for biology

Posted on by Hans Dillaerts

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

DOI : https://doi.org/10.1101/833400

EN

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

Posted on by Hans Dillaerts

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

Background

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.

Methods

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.

Results

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.

Conclusions

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

DOI : https://doi.org/10.7717/peerj.7850

EN

The History and Future of Data Citation in Practice

Posted on by Hans Dillaerts

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

DOI : http://doi.org/10.5334/dsj-2019-052

EN

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

Posted on by Hans Dillaerts

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

DOI : http://doi.org/10.18352/lq.10303

EN

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

Posted on by Hans Dillaerts

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

DOI : http://doi.org/10.18352/lq.10298

EN

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

Posted on by Hans Dillaerts

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.

URL : https://repository.jmls.edu/lawreview/vol52/iss2/2/