Biomedical supervisors’ role modeling of open science practices | eLife

Abstract:  Supervision is one important way to socialize Ph.D. candidates into open and responsible research. We hypothesized that one should be more likely to identify open science practices (here publishing open access and sharing data) in empirical publications that were part of a Ph.D. thesis when the Ph.D. candidates’ supervisors engaged in these practices compared to those whose supervisors did not or less often did. Departing from thesis repositories at four Dutch University Medical centers, we included 211 pairs of supervisors and Ph.D. candidates, resulting in a sample of 2062 publications. We determined open access status using UnpaywallR and Open Data using Oddpub, where we also manually screened publications with potential open data statements. Eighty-three percent of our sample was published openly, and 9% had open data statements. Having a supervisor who published open access more often than the national average was associated with an odds of 1.99 to publish open access. However, this effect became nonsignificant when correcting for institutions. Having a supervisor who shared data was associated with 2.22 (CI:1.19–4.12) times the odds to share data compared to having a supervisor that did not. This odds ratio increased to 4.6 (CI:1.86–11.35) after removing false positives. The prevalence of open data in our sample was comparable to international studies; open access rates were higher. Whilst Ph.D. candidates spearhead initiatives to promote open science, this study adds value by investigating the role of supervisors in promoting open science.


(Why) Are Open Research Practices the Future for the Study of Language Learning? – Marsden – Language Learning – Wiley Online Library

Abstract:  Open research practices are relevant to all stages of research, from conceptualization through dissemination. Here, we discuss key facets of open research, highlighting its rationales, infrastructures, behaviors, and challenges. Part I conceptualizes open research and its rationales. Part II identifies challenges such as the speed and cost of open research, the usability of open data and materials, the difficulties of conducting replication research, and the economics and sustainability of open access and open research generally. In discussing these challenges, we have sought to provide examples of good practice, describe and evaluate emerging innovations, and envision change. Part III considers ongoing coevolutions of culture, infrastructure, and behaviors and acknowledges the limitations of our review and of open research practices. We argue that open research is indeed a large part of our future, and most—if not all—challenges are surmountable, but doing so requires significant changes for many aspects of the research process.

Alignment of Top?Down Policies With Emerging Bottom?Up Practices: A Commentary on “(Why) Are Open Research Practices the Future for the Study of Language Learning?” – Laakso – Language Learning – Wiley Online Library

“In their article, Marsden and Morgan-Short comprehensively review the current state and development trajectories for key areas within open research practices, both in general as well as more particularly in the context of language sciences. As the article reveals, the scope of open research practices is enormous and essentially touches upon every aspect of performing and interacting with research. The authors touch upon the lack of an established metascience within language sciences that would help inform and guide development of research practices, but, as I see it, the problem is universal, and there would be benefit in creating a stronger and more cohesive metascience discipline in general. While researchers have established practices of research, education, and dedicated scholarly communication outlets within the philosophy of science, history of science, information science, and higher education policy, metascience has remained an area where the discussion is highly distributed and appears sporadically across diverse research disciplines. As Marsden and Morgan-Short’s review demonstrates, there are a lot of open questions relating to how to move forward on a global scale in the best interest of research and researchers. A more cohesive core of metascience would aid in the creation of immediately useful knowledge….”

Open science practices in research published in surgical journals: A cross-sectional study | medRxiv

Open science practices are research tools used to improve research quality and transparency. These practices have been used by researchers in various medical fields, though the usage of these practices in the surgical research ecosystem has not been quantified. In this work, we studied the use of open science practices in general surgery journals. Eight of the highest-ranked general surgery journals by SJR2 were chosen and their author guidelines were reviewed. From each journal, 30 articles published between January 1, 2019 and August 11, 2021 were randomly chosen and analyzed. Five open science practices were measured (preprint publication prior to peer-reviewed publication, use of Equator guidelines, study protocol preregistration prior to peer-reviewed publication, published peer review, and public accessibility of data, methods, and/or code). Across all 240 articles, 82 (34%) used one or more open science practices. Articles in the International Journal of Surgery showed greatest use of open science practices, with a mean of 1.6 open science practices compared to 0.36 across the other journals (p<.001). Adoption of open science practices in surgical research remains low, and further work is needed to increase utilization of these tools.

Performing Patents Otherwise: Archival conversations with 320,000 clothing inventions

Performing Patents Otherwise is one of several experimental book pilot projects conducted by the experimental publishing group at the Community-led Open Publication Infrastructures for Monographs project. In the spirit of open infrastructures, we documented the publication process for each pilot book. Towards this end, the experimental publishing group curated the Experimental Publishing Compendium, which collates experimental book publishing tools and practices and examples of experimental scholarly publications. While we share some insights on the making of experimental scholarly books in the compendium, we will zoom in here on what it takes to make database books and Performing Patents Otherwise in particular.
In the Compendium, we categorised Performing Patents Otherwise as a database book. We define database books as books containing a dynamically searchable database within their pages; or books generated from a database. In ‘making of,’ we reflect on the making Performing Patents Otherwise in the hope that it will be helpful to other authors and publishers who are experimenting with database books.



© 2023 Julien McHardy & Kat Jungnickel, chapters by respective authors. Licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license. Data from the Politics of Patents research project hosted at Goldsmiths, University of London, and funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (#819458).


Experimental Publishing Compendium | Community-Led Open Publication Infrastructures for Monographs (COPIM)

The Experimental Publishing Compendium is a guide and reference for scholars, publishers, developers, librarians, and designers who want to challenge, push and redefine the shape, form and rationale of scholarly books. The compendium brings together tools, practices, and books to promote the publication of experimental scholarly works. Read more

Beta 1.0 (2023)

Version 1.0 has been curated by Janneke Adema, Julien McHardy, and Simon Bowie. Future versions will be overseen, curated, and maintained by an Editorial Board (members TBC).

Back-end coding by Simon Bowie, front-end coding by Joel Galvez, design by Joel Galvez & Martina Vanini.

Special thanks to Gary Hall, Rebekka Kiesewetter, Marcell Mars, Toby Steiner, and Samuel Moore, and everyone who has provided feedback on our research or shared suggestions of examples to feature, including the participants of COPIM’s experimental publishing workshop, and Nicolás Arata, Dominique Babini, Maria Fernanda Pampin, Sebastian Nordhoff, Abel Packer, and Armanda Ramalho, and Agatha Morka.

Our appreciation also goes out to the Next Generation Library Publishing Project for sharing an early catalogue-in-progress version of SComCat with us, which formed one of the inspirations behind the Compendium.

The compendium grew out of the following two reports:

Adema, J., Bowie, S., Mars, M., and T. Steiner (2022) Books Contain Multitudes: Exploring Experimental Publishing (2022 update). Community-Led Open Publication Infrastructures for Monographs (COPIM). doi: 10.21428/785a6451.1792b84f & 10.5281/zenodo.6545475.

Adema, J., Moore, S., and T. Steiner (2021) Promoting and Nurturing Interactions with Open Access Books: Strategies for Publishers and Authors. Community-Led Open Publication Infrastructures for Monographs (COPIM). doi: 10.21428/785a6451.2d6f4263 and 10.5281/zenodo.5572413

COPIM and the Experimental Publishing Compendium are supported by the Research England Development (RED) Fund and by Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin.

How to cultivate good closures: ‘scaling small’ and the limits of openness | Samuel Moore

Text of a talk given to the COPIM end-of-project conference: “Scaling Small: Community-Owned Futures for Open Access Books”, April 20th 2023.

Open access publishing has always had a difficult relationship with smoothness and scale. Openness implies seamlessness, limitlessness or structureless-ness – or the idea that the removal of price and permission barriers is what’s needed to allow research to reach its full potential. The drive for seamlessness is on display in much of the push for interoperability of standards and persistent identifiers that shape the infrastructures of openness. Throughout the evolution of open access, many ideas have been propagated around, for example, the necessity of CC BY as the one and only licence that facilitates this interoperability and smoothness of access and possible reuse. Similarly, failed projects such as One Repo sought to create a single open access repository to rule them all, in response to the perceived messy and stratified institutional and subject repository landscape.

Yet this relationship between openness and scale also leads to new kinds of closure, particularly the commercial closures of walled gardens that stretch across proprietary services and make researcher data available for increasing user surveillance. The economies of scale of commercial publishers require cookie-cutter production processes that remove all traces of care from publishing, in exchange for APCs and BPCs, thus ensuring that more publications can be processed cheaply with as little recourse to paid human labour as possible. Smoothness and scale are simply market enclosures by another name.



Open Sourcing Reuse | Community-led Open Publication Infrastructures for Monographs (COPIM)

Adema, J., Bowie, S., & Kiesewetter, R. (2023). Open Sourcing Reuse. Community-Led Open Publication Infrastructures for Monographs (COPIM). As part of the documentation for the first book coming out of the Combinatorial Books Pilot Project, we are introducing and discussing the set of modular, open source writing, editing, annotating, and publishing software, tools, and platforms we have used. This is the fifth blogpost in a series documenting the COPIM/OHP Pilot Project Combinatorial Books: Gathering Flowers. You can find the previous blogposts here, here, here, and here. In the context of the Combinatorial Books: Gathering Flowers Pilot Project one of our aims has been to use, wherever possible, modular and open source writing, editing, annotating, and publishing software, tools, and platforms. We wanted to show how these can be used in the context of reusing and rewriting existing open access books or collections of books. Instead of creating our own custom solutions we have tried to create (technical) workflows that consist of existing open source applications, to enable other authors and publishers to apply or adapt these to their own writing and publishing workflows. At this stage of the Pilot Project we want to share some preliminary insights and reflections in combination with a closer description of the tools and platforms we have used. We will do so in textual form and as part of an audio interview with Simon Bowie, who is working as an open source software developer on the COPIM project. Specifically, we want to share our rationale for using open source applications, and reflect upon how these tools can either be integrated into or require adaptations to classical editorial and publishing workflows, timelines, tasks, and relationalities between those involved in publishing a book (for example those between tool and platform providers, publishers, developers, and editors).    

PhD candidate Monitoring Open Science Policies and Practices – Leiden University

“The Centre for Science and Technology Studies (CWTS) of the Faculty of Social and Behavioural Sciences is looking for a

PhD candidate Monitoring Open Science Policies and Practices (1,0FTE)
Vacancy number 13576

Leiden University takes the transition towards Open Science seriously. In the first stages, this transition will aim at further opening of the scholarly communication and publication processes, further improvement of FAIR data management and open data and software practices, and further strengthening of the relationship between the university and society at large through citizen science.

Are you interested in studying this transition and its impact? And do you want to contribute to this important cultural and behavioural change by informing daily research practices with robust scientific evidence? Then we are looking forward to meeting you! We have a job opening for a PhD candidate with good qualitative and/or quantitative research skills to work in the research program Monitoring Open Science Policies and Practices….”

Final WP4 Report: Governing Scholar-Led OA Book Publishers | Community-led Open Publication Infrastructures for Monographs (COPIM)

We are pleased to announce the release of the final report from COPIM’s Governance Work Package (WP4), titled Governing Scholar-Led OA Book Publishers: Values, Practices, Barriers. This report develops some of the issues we have previously explored within COPIM with regard to community governance, such as the challenges of governing a collective and the relationship of governance to common resources, to explore how these apply in practice to the publication of books by small-to-medium Open Access publishers, as well as what barriers they have faced in implementing their governance models. It presents and discusses the results of six interviews with small and medium Open Access publishers from the ScholarLed consortium. It then offers some recommendations and insights into how other small and medium Open Access publishers might set up and/or improve their governance practices, including how the Open Book Collective and Open Book Futures project might support them in doing so.

Governing Scholar-Led OA Book Publishers was written by Dr. Judith Fathallah, with the kind assistance of the following interviewees:

François van Schalkwyk, Director of African Minds

Joe Deville, Co-Founder of Mattering Press

Jeff Pooley, Director of

Mercedes Bunz, Co-Founder of meson press

Alessandra Tosi, Co-Director of Open Book Publishers

Eileen Joy, Co-Director of punctum books.

After a contextual discussion on the need for scholar-led OA publishers and governance issues related to the concept of the knowledge commons, the report presents the interview data. The publishers discuss the impetuses to startup their presses; incorporation and its forms; the elements, resources and actors in their governance structures; the evolution of governance structures and processes; their current mechanisms and procedures;t ransparency and self assessment; their relationships with institutions and organizations; and their perspectives on current governance.

Some reccomendations are then made to assist new publishers in considering their governance, and links to tools and resources provided.

The report has been published as a living document on COPIM’s Open Documentation Site (PubPub), and is also availabe as a time-stamped PDF version on Zenodo at


Q2O: Closing the gap between questionable and open research practices using a metacognitive tool | NWO

“Unfortunately, however, so far there’s still limited evidence on the efficacy of open research practices to minimize questionable research practices. These two related practices might involve different cognitive processes. Can we close the gap between QRP [questionable research practices] and ORP [open research practices] using metacognitive interventions, which have been shown to improve behaviour calibration in educational settings?  The main goal of our Q2O Project is to gain insights into why researchers may commit questionable research practices, and how we can decrease these practices through metacognitive reasoning, and to what extent Open Science can help reduce those questionable research practices.’ …”

Open science, closed doors: The perils and potential of open science for research in practice | Industrial and Organizational Psychology | Cambridge Core

This paper advocates for the value of open science in many areas of research. However, after briefly reviewing the fundamental principles underlying open science practices and their use and justification, the paper identifies four incompatibilities between those principles and scientific progress through applied research. The incompatibilities concern barriers to sharing and disclosure, limitations and deficiencies of overidentifying with hypothetico-deductive methods of inference, the paradox of replication efforts resulting in less robust findings, and changes to the professional research and publication culture such that it will narrow in favor of a specific style of research. Seven recommendations are presented to maximize the value of open science while minimizing its adverse effects on the advancement of science in practice.

Community consensus on core open science practices to monitor in biomedicine | PLOS Biology

Abstract:  The state of open science needs to be monitored to track changes over time and identify areas to create interventions to drive improvements. In order to monitor open science practices, they first need to be well defined and operationalized. To reach consensus on what open science practices to monitor at biomedical research institutions, we conducted a modified 3-round Delphi study. Participants were research administrators, researchers, specialists in dedicated open science roles, and librarians. In rounds 1 and 2, participants completed an online survey evaluating a set of potential open science practices, and for round 3, we hosted two half-day virtual meetings to discuss and vote on items that had not reached consensus. Ultimately, participants reached consensus on 19 open science practices. This core set of open science practices will form the foundation for institutional dashboards and may also be of value for the development of policy, education, and interventions.


Toward open and reproducible epidemiology | American Journal of Epidemiology | Oxford Academic

Abstract:  Starting in the 2010s, researchers in the experimental social sciences rapidly began to adopt increasingly open and reproducible scientific practices. These practices include publicly sharing deidentified data when possible, sharing analysis code, and preregistering study protocols. Empirical evidence from the social sciences suggests such practices are feasible, can improve analytic reproducibility, and can reduce selective reporting. In academic epidemiology, adoption of open-science practices has been slower than in the social sciences (with some notable exceptions, such as registering clinical trials). Epidemiologic studies are often large, complex, conceived after data have already been collected, and difficult to directly replicate by collecting new data. These characteristics makes it especially important to ensure their integrity and analytic reproducibility. Open-science practices can also pay immediate dividends to researchers’ own work by clarifying scientific reasoning and encouraging well-documented, organized workflows. We consider how established epidemiologists and early-career researchers alike can help midwife a culture of open science in epidemiology through their research practices, mentorship, and editorial activities.