Étiquette : open science

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Open laboratory notebooks: good for science, good for society, good for scientists

Authors : Matthieu Schapira, The Open Lab Notebook Consortium, Rachel J. Harding

The fundamental goal of the growing open science movement is to increase the efficiency of the global scientific community and accelerate progress and discoveries for the common good. Central to this principle is the rapid disclosure of research outputs in open-access peer-reviewed journals and on pre-print servers.

The next bold step in this direction is open laboratory notebooks, where research scientists share their research — including detailed protocols, negative and positive results — online and in near-real-time to synergize with their peers. Here, we highlight the benefits of open lab notebooks to science, society and scientists, and discuss the challenges that this nascent movement is facing.

We also present the implementation and progress of our own initiative at openlabnotebooks.org, with more than 20 active contributors after one year of operation.

URL : Open laboratory notebooks: good for science, good for society, good for scientists

DOI : https://doi.org/10.12688/f1000research.17710.1

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Open Science challenges, benefits and tips in early career and beyond

Authors : Christopher Allen, David Mehler

The movement towards open science is an unavoidable consequence of seemingly pervasive failures to replicate previous research. This transition comes with great benefits but also significant challenges that are likely to afflict those who carry out the research, usually Early Career Researchers (ECRs).

Here, we describe key benefits including reputational gains, increased chances of publication and a broader increase in the reliability of research. These are balanced by challenges that we have encountered, and which involve increased costs in terms of flexibility, time and issues with the current incentive structure, all of which seem to affect ECRs acutely.

Although there are major obstacles to the early adoption of open science, overall open science practices should benefit both the ECR and improve the quality and plausibility of research.

We review three benefits, three challenges and provide suggestions from the perspective of ECRs for moving towards open science practices.

URL : Open Science challenges, benefits and tips in early career and beyond

DOI : https://doi.org/10.31234/osf.io/3czyt

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Open science precision medicine in Canada: Points to consider

Authors : Palmira Granados Moreno, Sarah E. Ali-Khan, Benjamin Capps, Timothy Caulfield, Damien Chalaud, Aled Edwards, E. Richard Gold, Vasiliki Rahimzadeh, Adrian Thorogood, Daniel Auld, Gabrielle Bertier, Felix Breden, Roxanne Caron, Priscilla M.D.G. César, Robert Cook-Deegan, Megan Doerr, Ross Duncan, Amalia M. Issa, Jerome Reichman, Jacques Simard, Derek So, Sandeep Vanamala, Yann Joly

Open science can significantly influence the development and translational process of precision medicine in Canada. Precision medicine presents a unique opportunity to improve disease prevention and healthcare, as well as to reduce health-related expenditures.

However, the development of precision medicine also brings about economic challenges, such as costly development, high failure rates, and reduced market size in comparison with the traditional blockbuster drug development model.

Open science, characterized by principles of open data sharing, fast dissemination of knowledge, cumulative research, and cooperation, presents a unique opportunity to address these economic challenges while also promoting the public good.

The Centre of Genomics and Policy at McGill University organized a stakeholders’ workshop in Montreal in March 2018. The workshop entitled “Could Open be the Yellow Brick Road to Precision Medicine?” provided a forum for stakeholders to share experiences and identify common objectives, challenges, and needs to be addressed to promote open science initiatives in precision medicine.

The rich presentations and exchanges that took place during the meeting resulted in this consensus paper containing key considerations for open science precision medicine in Canada.

Stakeholders would benefit from addressing these considerations as to promote a more coherent and dynamic open science ecosystem for precision medicine.

URL : Open science precision medicine in Canada: Points to consider

DOI : https://doi.org/10.1139/facets-2018-0034

 

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Open science, reproducibility, and transparency in ecology

Authors : Stephen M. Powers, Stephanie E. Hampton

Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility and also transparency.

Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility can still be achieved.

Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study.

When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy.

Expectations for computational reproducibility and transparency are shifting rapidly in the sciences.

In this work, we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity.

URL : Open science, reproducibility, and transparency in ecology

DOI : https://doi.org/10.1002/eap.1822

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Someone has to pay: The global sustainability coalition for open science services (SCOSS)

Authors : Martin Borchert, Vanessa Proudman

The Open Access (OA) and Open Science (OS) movement is gaining momentum with an increasing number of scholarly outputs openly and freely available to researchers and the community. OA and OS cannot however, be free for everyone.

Someone has to pay for the infrastructure and there has to be a supporting economy. While many commercial publishers are charging for OA, there are many OA and OS infrastructure providers baring the cost of providing infrastructure. Without funding, essential services that many are dependent upon to implement government and funder OA policies worldwide, are at risk of service degradation, reduced availability and even survival. Something had to be done.

In response, the Global Sustainable Coalition for Open Science Services (SCOSS) was formed in 2017 as a result of collaborations between key global stakeholders, with SPARC Europe as the co-ordinator.

It aims to develop and apply a rigorous proposal and assessment process to provide guidance to the OA and OS community on what to fund.

It uses a new financial crowdfunding contribution model seeking a three-year commitment for funding for the services it recommends. This will help improve the financial position, resilience and sustainability of these OA / OS infrastructure services and will help them on their way to find a mid to long-term sustainable solution for years to come.

The first open science services to receive assistance were Sherpa RoMEO which is operated by the Joint Information Steering Committee (Jisc, UK) and provides summary information of journal and publisher OA polices; and the Directory of Open Access Journals (DOAJ) which provides a list of over 10,000 peer-reviewed open access journals.

Since launching in November 2017, a growing number of university libraries from across the globe are committing to fund Sherpa/Romeo and DOAJ for the next there years.

This paper will provide an introduction to SCOSS and its purpose, governance, processes, and challenges and will give an update on institutional financial commitments to date.

URL : https://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=2229&context=iatul

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Open science and codes of conduct on research integrity

Author : Heidi Laine

The purpose of this article is to examine the conceptual alignment between the ethical principles of research integrity and open science. Research integrity is represented in this study by four general codes of conduct on responsible conduct of research (RCR), three of them international in scope, and one national.

A representative list of ethical principles associated with open science is compiled in order to create categories for assessing the content of the codes. According to the analysis, the current understanding of RCR is too focused on traditional publications and the so called FFP definition of research misconduct to fully support open science.

The main gaps include recognising citizen science and societal outreach and supporting open collaboration both among the research community and beyond its traditional borders.

Updates for both the content of CoCs as well as the processes of creating such guidelines are suggested.

URL : Open science and codes of conduct on research integrity

DOI : https://doi.org/10.23978/inf.77414

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Text data mining and data quality management for research information systems in the context of open data and open science

Authors : Otmane Azeroual, Gunter Saake, Mohammad Abuosba, Joachim Schöpfel

In the implementation and use of research information systems (RIS) in scientific institutions, text data mining and semantic technologies are a key technology for the meaningful use of large amounts of data.

It is not the collection of data that is difficult, but the further processing and integration of the data in RIS. Data is usually not uniformly formatted and structured, such as texts and tables that cannot be linked.

These include various source systems with their different data formats such as project and publication databases, CERIF and RCD data model, etc. Internal and external data sources continue to develop.

On the one hand, they must be constantly synchronized and the results of the data links checked. On the other hand, the texts must be processed in natural language and certain information extracted.

Using text data mining, the quality of the metadata is analyzed and this identifies the entities and general keywords. So that the user is supported in the search for interesting research information.

The information age makes it easier to store huge amounts of data and increase the number of documents on the internet, in institutions’ intranets, in newswires and blogs is overwhelming.

Search engines should help to specifically open up these sources of information and make them usable for administrative and research purposes. Against this backdrop, the aim of this paper is to provide an overview of text data mining techniques and the management of successful data quality for RIS in the context of open data and open science in scientific institutions and libraries, as well as to provide ideas for their application. In particular, solutions for the RIS will be presented.

URL : https://arxiv.org/abs/1812.04298