Étiquette : open access

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Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing

Authors : Kevin M. Mendez, Leighton Pritchard, Stacey N. Reinke, David I. Broadhurst

Background

A lack of transparency and reporting standards in the scientific community has led to increasing and widespread concerns relating to reproduction and integrity of results. As an omics science, which generates vast amounts of data and relies heavily on data science for deriving biological meaning, metabolomics is highly vulnerable to irreproducibility.

The metabolomics community has made substantial efforts to align with FAIR data standards by promoting open data formats, data repositories, online spectral libraries, and metabolite databases.

Open data analysis platforms also exist; however, they tend to be inflexible and rely on the user to adequately report their methods and results. To enable FAIR data science in metabolomics, methods and results need to be transparently disseminated in a manner that is rapid, reusable, and fully integrated with the published work.

To ensure broad use within the community such a framework also needs to be inclusive and intuitive for both computational novices and experts alike.

Aim of Review

To encourage metabolomics researchers from all backgrounds to take control of their own data science, mould it to their personal requirements, and enthusiastically share resources through open science.

Key Scientific Concepts of Review

This tutorial introduces the concept of interactive web-based computational laboratory notebooks. The reader is guided through a set of experiential tutorials specifically targeted at metabolomics researchers, based around the Jupyter Notebook web application, GitHub data repository, and Binder cloud computing platform.

URL : Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing

DOI : https://doi.org/10.1007/s11306-019-1588-0

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EN

Open Up – the Mission Statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab on Open Science

Authors : Christina B. Reimer, Zhang Chen, Carsten Bundt, Charlotte Eben, Raquel E. London, Sirarpi Vardanian

The present paper is the mission statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab regarding Open Science. As early-career researchers (ECRs) in the lab, we first state our personal motivation to conduct research based on the principles of Open Science.

We then describe how we incorporate four specific Open Science practices (i.e., Open Methodology, Open Data, Open Source, and Open Access) into our scientific workflow. In more detail, we explain how Open Science practices are embedded into the so-called ‘co-pilot’ system in our lab.

The ‘co-pilot’ researcher is involved in all tasks of the ‘pilot’ researcher, that is designing a study, double-checking experimental and data analysis scripts, as well as writing the manuscript.

The lab has set up this co-pilot system to increase transparency, reduce potential errors that could occur during the entire workflow, and to intensify collaborations between lab members.

Finally, we discuss potential solutions for general problems that could arise when practicing Open Science.

URL : Open Up – the Mission Statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab on Open Science

DOI : http://doi.org/10.5334/pb.494

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EN

Animal Research, Accountability, Openness and Public Engagement: Report from an International Expert Forum

Authors : Elisabeth H. Ormandy, Daniel M.Weary, Katarina Cvek, Mark Fisher, Kathrin Herrmann, Pru Hobson-West, Michael McDonald, William Milsom, Margaret Rose, Andrew Rowan, Joanne Zurlo, Marina A.G. von Keyserlingk

The issues of openness, transparency and public engagement about animal research have taken focus in several different countries in recent years. This paper gives an account of a two-day-long expert forum that brought together policy experts and academics from Australia, Canada, Germany, New Zealand, Sweden, the United Kingdom and the United States.

The aim was to share current governance practices regarding openness and transparency of animal research and to brainstorm ideas for better public engagement.

The facilitated conversations were transcribed and analysed to create this report and recommendations that encourage international policy-makers and other stakeholders to engage in genuine dialogue about the use of animals in research.

URL : Animal Research, Accountability, Openness and Public Engagement: Report from an International Expert Forum

DOI : https://doi.org/10.3390/ani9090622

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EN

How libraries can support society publishers to accelerate their transition to full and immediate OA and Plan S

Authors : Alicia Wise, Lorraine Estelle

The relationship between libraries and society publishers has not previously been a close one. While transactions have in the past been mediated by third parties, larger commercial publishers or agents, there is now an opportunity for strategic new collaborations as societies seek to transition to open access (OA) and deploy business models compliant with Plan S.

Wellcome, UK Research and Innovation (UKRI) and the Association of Learned and Professional Society Publishers (ALPSP) commissioned Information Power Ltd to undertake to support society publishers in accelerating their transition to OA in alignment with Plan S.

Outcomes demonstrate support in principle from library consortia and their members to repurpose existing expenditure to help society publishers to successfully make a full transition to OA.

Principles to inform the short- and medium-term development of OA transformative agreements have been co-developed by consortium representatives and publishers to inform development of an OA transformative agreement toolkit.

URL : How libraries can support society publishers to accelerate their transition to full and immediate OA and Plan S

DOI : http://doi.org/10.1629/uksg.477

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EN

A Crisis in “Open Access”: Should Communication Scholarly Outputs Take 77 Years to Become Open Access?

Authors : Abbas Ghanbari Baghestan, Hadi Khaniki, Abdolhosein Kalantari, Mehrnoosh Akhtari-Zavare, Elaheh Farahmand, Ezhar Tamam, Nader Ale Ebrahim, Havva Sabani, Mahmoud Danaee

This study diachronically investigates the trend of the “open access” in the Web of Science (WoS) category of “communication.” To evaluate the trend, data were collected from 184 categories of WoS from 1980 to 2017.

A total of 87,997,893 documents were obtained, of which 95,304 (0.10%) were in the category of “communication.” In average, 4.24% of the documents in all 184 categories were open access. While in communication, it was 3.29%, which ranked communication 116 out of 184.

An Open Access Index (OAI) was developed to predict the trend of open access in communication. Based on the OAI, communication needs 77 years to fully reach open access, which undeniably can be considered as “crisis in scientific publishing” in this field.

Given this stunning information, it is the time for a global call for “open access” by communication scholars across the world. Future research should investigate whether the current business models of publications in communication scholarships are encouraging open access or pose unnecessary restrictions on knowledge development.

URL : A Crisis in “Open Access”: Should Communication Scholarly Outputs Take 77 Years to Become Open Access?

DOI : https://doi.org/10.1177/2158244019871044

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EN

Evolution of an Institutional Repository: A Case History from Nebraska

Author : Paul Royster

The 13-year history of the institutional repository (IR) at the University of Nebraska–Lincoln is recounted with emphasis on local conditions, administrative support, recruitment practices, and management philosophy.

Practices included offering new services, hosting materials outside the conventional tenure stream, using student employees, and providing user analytics on global dissemination. Acquiring trust of faculty depositors enhanced recruitment and extra-library support.

Evolution of policies on open access, copyright, metadata, and third-party vendors are discussed, with statistics illustrating the growth, contents, and outreach of the repository over time.

A final section discusses future directions for scholarly communications and IRs in particular.

URL : https://digitalcommons.unl.edu/libraryscience/382/

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EN

The Transcript OPEN Library Political Science Model: A Sustainable Way into Open Access for E-Books in the Humanities and Social Science

Authors : Alexandra Jobmann, Nina Schönfelder

The strategic goal of the project “National Contact Point Open Access OA2020-DE” is to create the conditions for a large-scale open-access transformation in accordance with the Alliance of German Science Organizations.

In close collaboration with the publisher transcript, we developed a business model that strengthens the transformation process for e-books in the humanities and social sciences.

It largely addresses the drawbacks of existing models. Moreover, it is manageable, sustainable, transparent, and scalable for both publishers and libraries. This case report describes the setup of the model, its successful implementation for the branch “political science” of transcript in 2019, and provides a Strengths–Weaknesses–Opportunities–Threats (SWOT) analysis.

We believe that it has the potential to become one of the major open-access business models for research monographs and anthologies in the humanities and social sciences, especially for non-English e-books.

URL : The Transcript OPEN Library Political Science Model: A Sustainable Way into Open Access for E-Books in the Humanities and Social Science

DOI : https://doi.org/10.3390/publications7030055