Patching Science – amending the literature through version control | bioRxiv

Abstract:  The ideal of self-correction in science is not well served by the current culture and system surrounding amendments to published literature. Here we report on a survey (N = 132) that highlights academics’ dissatisfaction with the status quo and their support for an alternative approach. We then describe our view of how amendments could and should work by drawing on the idea of an author-led version control system. Here authors would include a link in their published manuscripts to an updatable website (e.g. a GitHub repository or similar) that could be disseminated in the event of any amendment. Such a system is already in place for computer code and, as such, requires nothing but buy-in from the scientific community – a community that is already evolving towards various open science frameworks. This would remove a number of frictions that discourage amendments thus leading to an improved scientific literature and a healthier academic climate.

A comment on “The big idea: should we get rid of the scientific paper?” | SciELO in Perspective

“In The big idea: should we get rid of the scientific paper?, published by the Guardian newspaper, Stuart Ritchie argues for a radical action: scientists should abandon the current format of the scientific paper, which is static and not interactive. Despite being currently published in electronic medium, they are still very similar to the printed version that dominated the scientific publishing landscape for more three centuries. In fact, the current scientific article is only an electronic version of “the physical black and white printed paper” in PDF (portable document format). This format is not friendly for reading on the screen of computers, tablets and mobile phones, which are dynamic and offer countless alternatives to interact with information. Reading a scientific article nowadays should be more than getting passive information about a subject matter, rather it should be an opportunity to think, check, review and reproduce the data and analysis presented in the article.

However, the standards of scientific publishing industry, and the rules of academic establishment as well, oppose any change in this static, passive and mostly non-transparent system of science dissemination. The Guardian newspaper article points out some alternatives to the PDF packaging of scientific articles, e.g., interactive “notebooks” that combine images, data, code, methods, and analysis into a single interactive and dynamic “article” that might be read, reviewed, reproduced, edited, and shared at any time. This format is known as “living article”.

But the problem does not lay solely on the “static scientific article”. There are the journals and the rules dictated (mostly) by the financial interests of the major commercial publishers. The predominant system for the communication of scientific results has not been developed by scientists, and they cannot freely decide what is the best “vehicle” or format to disseminate their research work. Actually, the publishers of scientific journals decide and control which format is accepted or not. A scientist today must follow the rules determined by journal editors, who are also dependent on the consensus and standards defined by the entire publishing industry.

By this reasoning, the problem is not the article itself, rather it is the vehicle that widespread the scientist’s message: the scientific journal and its rules! It is not possible to “get rid of the scientific article” without reforming the concept and practice of the “scientific journal”! ”

To protect and to serve: developing a road map for research data management services

Abstract:  Research Data Management (RDM) has become a major issue for universities over the last decade. This case study outlines the review of RDM services carried out at the University of Oxford in partnership with external consultants between November 2019 and November 2020. It aims to describe and discuss the processes in undertaking a university-wide review of services supporting RDM and developing a future road map for them, with a strong emphasis on the design processes, methodological approaches and infographics used. The future road map developed is a live document, which the consulting team handed over to the University at the end of the consultation process. It provides a suggested RDM action plan for the University that will continue to evolve and be iterated in the light of additional internal costings, available resources and reprioritization in the budget cycle for each academic year. It is hoped that the contents of this case study will be useful to other research-intensive universities with an interest in developing and planning RDM services to support their researchers.


Glossary | FORRT – Framework for Open and Reproducible Research Training

“In order to reduce barriers to entry and understanding, we present a Glossary of terms relating to open scholarship. We aim that the glossary will help clarify terminologies, including where terms are used differently/interchangeably or where terms are less known in some fields or among students. We also hope that this glossary will be a welcome resource for those new to these concepts, and that it helps grow their confidence in navigating discussions of open scholarship. We also hope that this glossary aids in mentoring and teaching, and allows newcomers and experts to communicate efficiently….

Following the success of Phase 1, we invite you to help us continue to improve this resource. We are interested in a wide range of contributions to improve existing definitions, extend the scope of the terms, as well as translating terms to improve accessibility. We have opened four live working documents (see the landing page for instructions and links to working documents). Please read the instructions for contributors. We have prepared these to help guide constructive feedback and facilitate a smooth editorial process.

We aim to regularly implement suggested changes and improvements. If you believe an existing definition is incorrect please contact the project leads, we aim to correct any mistakes as quickly as possible. We see the glossary as a potential starting point for other projects and resources the community feels may be needed. Please contact us if you have suggestions for publications or have ideas for related projects that could use or adapt the glossary….”

Open Science Success Stories

“The Open Science Success Stories Database compiles research articles, perspectives, case studies, news stories, and other materials that demonstrate the myriad ways in which open science benefits researchers and society alike. 

Scientists, scholars, librarians, department chairs, university administrators, philanthropic program officers, government agency representatives, policymakers, publishers, journalists and other stakeholders can use the curated resources to understand how open science is positively impacting specific disciplines and communities, as well as how these lessons can be applied to the global scientific endeavor.

The Open Science Success Stories Database is a collaboration between Arizona State University and the Open Research Funders Group, in conjunction with the National Academies of Sciences, Engineering, and Medicine’s Roundtable on Aligning Incentives for Open Science. …”

An open repository of real-time COVID-19 indicators | PNAS

Abstract:  The COVID-19 pandemic presented enormous data challenges in the United States. Policy makers, epidemiological modelers, and health researchers all require up-to-date data on the pandemic and relevant public behavior, ideally at fine spatial and temporal resolution. The COVIDcast API is our attempt to fill this need: Operational since April 2020, it provides open access to both traditional public health surveillance signals (cases, deaths, and hospitalizations) and many auxiliary indicators of COVID-19 activity, such as signals extracted from deidentified medical claims data, massive online surveys, cell phone mobility data, and internet search trends. These are available at a fine geographic resolution (mostly at the county level) and are updated daily. The COVIDcast API also tracks all revisions to historical data, allowing modelers to account for the frequent revisions and backfill that are common for many public health data sources. All of the data are available in a common format through the API and accompanying R and Python software packages. This paper describes the data sources and signals, and provides examples demonstrating that the auxiliary signals in the COVIDcast API present information relevant to tracking COVID activity, augmenting traditional public health reporting and empowering research and decision-making.


EIFL Checklist for DSpace Repositories updated! | EIFL

“We have updated and revised How To Make Your OA Repository Work Really Well, the EIFL checklist that repository managers and administrators, librarians and others can use to improve institutional open access (OA) repositories that use DSpace free and open source software.

DSpace is the most commonly used repository software in EIFL partner countries.

This is the fifth revision of the Checklist. We have included the new DSpace 7.1 software release – the largest release in the history of DSpace software. We have updated information about repository interoperability, and added COAR controlled vocabularies, OpenAIRE and Wikipedia to the discoverability section. We have also updated the repository policy and licensing sections and added more tips on ORCID-DSpace integrations….”

‘New journals concept’ from CUP’s Research Directions | The Bookseller

“Cambridge University Press is launching an initiative it describes as a “new concept” for the journal, bringing researchers from different fields together to explore fundamental questions which cut across traditional disciplines.

Research Directions is the brainchild of Fiona Hutton, CUP executive publisher and its head of STM Open Access publishing. A former research scientist, Hutton wants to provide alternatives to traditional journal formats and bring communities together to frame research to problems that no one discipline would be able to tackle alone, said the publisher.

CUP said the approach would “speed discovery by fostering collaboration and knowledge sharing between subject communities” as well as provide “opportunities to publish research from areas not well served by traditional, discipline-specific journals”. 

The first titles under the Research Directions banner will be published in 2022, with an initial set of questions to answer, informed by feedback from hundreds of researchers. The publishing model will “mirror the research lifecycle”, with the results, analysis and impact reviews all published as separate, Open Access, peer-reviewed and citable outputs on CUP’s Cambridge Core platform….”

Getty Publications: how Quire is creating solutions to open access publishing – MuseumNext

“In anticipation of MuseumNext’s Digital Collections Summit next week (4-6 October) we caught up with Erine Cecele Dunigan, Community Manager for Quire, an open-source digital publishing tool developed by Getty.

Erin will be giving a talk on Wednesday 6 October entitled, Open Access: Getty’s Approach to Digital Collection Catalogues….

Quire is a modern digital publishing tool developed by Getty. It’s ideal for creating dynamic publications in a variety of formats, including web, print, and e-book. In addition to being optimised for scholarly and visually rich publishing, Quire books are designed for longevity, sustainability, and discoverability.

Getty originally conceived Quire as a solution to its open access publishing needs, but the tool quickly gained the attention of other organisations within the fields of digital humanities, arts, and academia. While access is currently available for free upon request, we will be launching as a fully open-source publishing tool by Spring 2022. Open-sourcing Quire will enable others to leverage the work Getty has done to create, customise, and distribute critical digital scholarship online, at a low cost, and with little ongoing maintenance….”

An Open-Publishing Response to the COVID-19 Infodemic

Abstract:  The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript’s figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis.


Advocating for Open Education – BCcampus OpenEd Resources

“Affordability is often the main driver for the use of OER, but it’s not the only reason. Using OER gives faculty the ability to customize their learning materials to support their curriculum and the learning outcomes for their course. The course materials can be dynamic, with a wide selection of OER available to create engagement, improve understanding, and break down barriers to accessibility….”

A Strengths-Based Approach to Evaluation and Transformational Change in Publishing | Educopia Institute

“When Katherine Skinner and I published the Values and Principles Framework and Checklist last year, we introduced them as mechanisms to hold actors in the scholarly communication system accountable to their stakeholders and demonstrate their commitment to openness in concrete and documentable ways. We conceived the framework and checklist as living, iterative, and adaptable documents. Our first major revision, to be released this fall, reflects a deliberate shift to a strengths-based model of evaluation and change….

The revised framework will include resources that help organizations demonstrate their signature contributions to a more open, equitable, and productive scholarly communication ecosystem and that help them build towards their ideals….”