Amending the literature through version control | Biology Letters

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 describe our view of how amendments could and should work by drawing on the idea of an author-led version control system. We report a survey (n = 132) that highlights academics’ dissatisfaction with the status quo and their support for such an alternative approach. Authors would include a link in their published manuscripts to an updatable website (e.g. a GitHub repository) that could be disseminated in the event of any amendment. Such a system is already in place for computer code and requires nothing but buy-in from the scientific community—a community that is already evolving towards open science frameworks. This would remove a number of frictions that discourage amendments leading to an improved scientific literature and a healthier academic climate.


About Meta-Psychology

“Meta-Psychology publishes theoretical and empirical contributions that advance psychology as a science through critical discourse related to individual articles, research lines, research areas, or psychological science as a field. Important contributions include systematic reviews, meta-analyses, replicability reports, and replication studies. We encourage pre-registered studies and registered reports (i.e., peer-review on the basis of theory, methods, and planned data-analysis, before data has been collected). Manuscripts introducing novel methods are welcome, but also tutorials on established methods that are still poorly understood by psychology researchers. We further welcome papers introducing statistical packages or other software useful for psychology researchers….”



“Quarto® is an open-source scientific and technical publishing system built on Pandoc

Create dynamic content with Python, R, Julia, and Observable.
Author documents as plain text markdown or Jupyter notebooks.
Publish high-quality articles, reports, presentations, websites, blogs, and books in HTML, PDF, MS Word, ePub, and more.
Author with scientific markdown, including equations, citations, crossrefs, figure panels, callouts, advanced layout, and more….”

AWOL – The Ancient World Online: Active Open Access Journals

“This is a developing list of open access journals currently reviewing papers for publication. It is intended to offer opportunities for scholars interested in publishing openly. It is compiled in advance of my presentation at the ASOR Annual Meeting 2019: Best Practices for Digital Scholarship: “Sharing Your Work: Library Ethics, Privacy, and Commercial Repositories”. Journals included here cover a wide range of disciplines within the study of antiquity. It is not yet comprehensive. If you wish to add a title simply let me know (comments – below)….”

Enriching preprints to attain reproducible open science | Septentrio Conference Series

Abstract:  In order for science to be truly open, readers and reviewers must be able to understand how authors produced the computational results, which parameters were used for the analysis, and how manipulations to these parameters affect the results. Increasingly, journals and funding agencies are mandating that researchers share their code and data when reporting on computational results. However, even when data and code are provided by authors, and published, they are oftentimes just posted as links and relegated to platforms entirely separated from publishing workflows, disconnected from the published “full text”. We believe that preprints are better suited than external repositories in enabling open, reproducible science because they are connected to the published full text via scholarly infrastructure, they are author-centric, and allow versioning. In particular, we propose a simple (yet innovative and experimental) workflow whereby authors deposit a preprint version of their articles in an html-first preprint server. In it, authors can then enhance the preprint, through edits and revisions, with data, code, computational notebooks, interactive visualizations, and dashboards. As such, preprints can be used as an experimental vehicle for directly disseminating the interactive, data-driven, and multi-media nature of Open Science outputs, in parallel and connected with more traditional published outputs.


Directory of Open Access Preprint Repositories: Home

“It is becoming an increasingly common practice for researchers to share their preprints because it allows them to disseminate their research results quickly and openly with the rest of the world. As a result, there is a growing number of preprint-specific and generalist repositories that support the sharing of preprints.

This directory provides a list of preprint repositories that are available to the research community. It helps researchers find the most appropriate platform for them, enabling them to browse through existing repositories by discipline, location, language, functionalities, and other facets.

The directory is jointly managed by Centre pour la Communication Scientifique Directe (CCSD) and Confederation of Open Access Repositories (COAR). The data in this directory was originally compiled through the GPPdP (Groupe Projet Plateformes de Prepublications) project, with financial support from the French Ministry of Research’s Open Science Committee (CoSO)….”

A Synthesis of the Formats for Correcting Erroneous and Fraudulent Academic Literature, and Associated Challenges | SpringerLink

Abstract:  Academic publishing is undergoing a highly transformative process, and many established rules and value systems that are in place, such as traditional peer review (TPR) and preprints, are facing unprecedented challenges, including as a result of post-publication peer review. The integrity and validity of the academic literature continue to rely naively on blind trust, while TPR and preprints continue to fail to effectively screen out errors, fraud, and misconduct. Imperfect TPR invariably results in imperfect papers that have passed through varying levels of rigor of screening and validation. If errors or misconduct were not detected during TPR’s editorial screening, but are detected at the post-publication stage, an opportunity is created to correct the academic record. Currently, the most common forms of correcting the academic literature are errata, corrigenda, expressions of concern, and retractions or withdrawals. Some additional measures to correct the literature have emerged, including manuscript versioning, amendments, partial retractions and retract and replace. Preprints can also be corrected if their version is updated. This paper discusses the risks, benefits and limitations of these forms of correcting the academic literature.


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….”