Open science and data sharing in cognitive neuroscience with MouseBytes and MouseBytes+ | Scientific Data

Abstract:  Open access to rodent cognitive data has lagged behind the rapid generation of large open-access datasets in other areas of neuroscience, such as neuroimaging and genomics. One contributing factor has been the absence of uniform standardization in experiments and data output, an issue that has particularly plagued studies in animal models. Touchscreen-automated cognitive testing of animal models allows standardized outputs that are compatible with open-access sharing. Touchscreen datasets can be combined with different neuro-technologies such as fiber photometry, miniscopes, optogenetics, and MRI to evaluate the relationship between neural activity and behavior. Here we describe a platform that allows deposition of these data into an open-access repository. This platform, called MouseBytes, is a web-based repository that enables researchers to store, share, visualize, and analyze cognitive data. Here we present the architecture, structure, and the essential infrastructure behind MouseBytes. In addition, we describe MouseBytes+, a database that allows data from complementary neuro-technologies such as imaging and photometry to be easily integrated with behavioral data in MouseBytes to support multi-modal behavioral analysis.


ResearchGate and Royal Society extend scope of partnership after successful trial phase


ResearchGate and The Royal Society have today expanded the partnership that sees all articles from the Royal Society’s ten-journal portfolio syndicated directly to ResearchGate.

The Transformation of the Green Road to Open Access[v1] | Preprints

Abstract:  (1) Background: The 2002 Budapest Open Access Initiative recommended on self-archiving of scientific articles in open repositories as the “green road” to open access. Twenty years later, only one part of the researchers deposits their publications in open repositories; moreover, one part of the repositories’ content is not based on self-archived deposits but on mediated nonfaculty contributions. The purpose of the paper is to provide more empirical evidence on this situation and to assess the impact on the future of the green road. (2) Methods: We analyzed the contributions on the French national HAL repository from more than 1,000 laboratories affiliated to the ten most important French research universities, with a focus on 2020, representing 14,023 contributor accounts and 166,939 deposits. (3) Results: We identified seven different types of contributor accounts, including deposits from nonfaculty staff and import flows from other platforms. Mediated nonfaculty contribution accounts for at least 48% of the deposits. We also identified difference between institutions and disciplines. (4) Conclusions: Our empirical results reveal a transformation of open repositories from self-archiving and direct scientific communication towards research information management. Repositories like HAL are somewhere in the middle of the process. The paper describes data quality as the main issue and major challenge of this transformation.


How the Public Access Submission System is Ideally Suited to Address the New Office of Science and Technology Policy (OSTP) Memorandum | December 2022

“In August of this year, the White House Office of Science and Technology Policy announced new guidance that requires all federal agencies to define, by 2025, policies that ensure immediate public access to federally funded research publications in agency-designated repositories. These policy changes have the potential to dramatically increase access to public research, but they also come with implementation challenges. These agency-designated repositories can have highly variable submission requirements and capabilities, and research institutions often have their own open access policies and guidelines, which introduce additional expectations. Taken together, all of these requirements place a considerable burden on researchers who wish to comply with all applicable public access policies with minimal effort. The Public Access Submission System (PASS) was designed specifically to address these challenges. PASS was created to take into account the requirements of multiple federal agency and institutional repository systems and to guide researchers through the deposit process, ensuring that all of the necessary information is collected at one time and then submitted to all of the required deposit endpoints….”


Bill Branan, Senior Manager, Open Source Programs Office and Digital Research & Curation Center, Johns Hopkins University
John Kellerman, Eclipse Public Access Submission System (PASS) Program Manager, Eclipse Foundation
Sayeed Choudhury, Director of Open Source Programs Office, Carnegie Mellon University

ResearchGate and De Gruyter announce content partnership

“ResearchGate, the professional network for researchers, and De Gruyter, an independent academic publisher disseminating excellent scholarship since 1749, have today announced a content syndication partnership that will see content from 437 of De Gruyter’s journals added to ResearchGate.”

Integration with DSpace and authentication (#797) · Issues · dissemin / dissemin · GitLab

“The presentation about EasyDeposit2 by the University of Oregon at the green OA session of OR2019 showed how is used to allow researchers to upload a PDF to a repository record in reaction to an email without needing to login manually.

Some of the logic might turn out to be useful if we want to deposit on the authors’ behalf on DSpace and/or generate email notifications with access tokens….”

University of Leeds Publications Policy – Research and Innovation Service

“Author requirements

Authors must comply with their funders’ policies relating to open access and research data management. 
Authors must register for an individual ORCiD identifier and should link it to their University Publications Database profile [2], include it on any personal webpage, when submitting publications, when applying for grants, and in any research workflow to ensure that the individual is credited for their work and that the correct institutional affiliation is achieved.  
Authors must use a standardised institutional affiliation “University of Leeds” in all research outputs to ensure clear affiliation with the University of Leeds. 
Authors must specify authors’ contributions in all research outputs to ensure individuals’ roles are identifiable and duly recognised. 
Authors must include a Data Access Statement in all research outputs even where there are no data associated with the publication or the data are inaccessible. The statement informs readers where the associated underlying research materials are available and how they can be accessed.  
Authors must acknowledge the source of grant funding associated with a research output in all research outputs. Information about the grant should also be linked, by the author, to the record of the publication in the University Publications Database. Grant information in the University Publications Database is fed automatically from the University’s Grant Information System [3].  
Authors must retain the necessary rights to make the accepted manuscripts of research articles, including reviews and conference papers, publicly available under the terms of a Creative Commons Attribution (CC BY) licence. Recommended wording to include in manuscript submissions is in Appendix 1. This requirement does not apply but is strongly recommended for outputs solely or jointly authored by PGRs (only).  
Authors must record bibliographic details of all research outputs in the University’s publications database. For peer-reviewed research articles, including reviews and conference papers, this must be done as soon as possible after acceptance for publication. When creating the record in the University’s publications database, complete the appropriate fields to confirm that a data access and a rights retention statement have been added to the output itself. 
Authors must deposit full text copies of final accepted peer-reviewed research articles, including reviews and conference papers into the institutional repository, via the University’s publications database as soon as possible after acceptance for publication. Where the output is already available open access via the publisher website a link may be provided instead. The deposit of other outputs e.g. monographs is also encouraged where copyright permits. 
Where copyright allows and there are no confidentiality or commercial constraints, the research outputs in the institutional repository must be made ‘open access’, i.e. freely accessible over the internet. 
Outputs must be made open access as soon as possible after acceptance [4]….”

Public Access to Scientific Research Findings and Principles of Biomedical Research—A New Policy for the JAMA Network | Medical Journals and Publishing | JAMA Internal Medicine | JAMA Network

“Beginning in 2023, JAMA and all of the journals in the JAMA Network will adopt a new policy that permits authors of original research investigations to deposit their accepted manuscript in a public repository of their choosing immediately on the day that the manuscript is published by the JAMA Network….

With these and future policies, JAMA and the JAMA Network look forward to working collaboratively with scientists, research institutions, policy makers, funders, and other journals to lean in on first principles that support a thriving, robust scientific enterprise. Stakeholders have a shared responsibility to craft solutions that balance equity, accessibility, and sustainability. Together, we will continue to collegially debate and advance the steps to safeguard and evolve the growth and health of our ecosystem, which manifestly includes timely public access to biomedical research.”

Publications router – populating repositories automatically – Jisc

“Find out how you can capture your researchers’ articles automatically onto your institution’s repository or CRIS, including the correct version of the full-text article and its licence, without having to find and upload them manually.”

Celebrating an open access knowledge and information repository for CGIAR research | International Livestock Research Institute

“In late 2009, the International Livestock Research Institute (ILRI) established a digital repository to act as a complete open archive of the information and publications generated through its research. This was driven by ILRI’s aim to have its knowledge travel by making it open access, by publishing it in full, by giving it permanent identifiers, and by providing reliable access through robust open repositories and other communication channels. The goal was to have the information taken off unreliable websites, given permanent identifiers , and made easier to find and share through new digital and web services.

Over time, the repository has evolved from its initial ILRI focus into a collaboration involving seven CGIAR research centers, several CGIAR research programs and platforms and other initiatives and projects. The CGSpace repository is now the largest single collection of CGIAR-associated research outputs (read about CGSpace origins and early developments)….

Last month, the repository added its 100,000th unique item, reaching an important milestone on the route towards making CGIAR knowledge widely accessible….”

Rights retention policy: an update after 9 months | Open Scholarship

“2022 has been a big year for open access at the University of Edinburgh. We started the year off with a bang by introducing a revised Research Publications & Copyright policy in January. This mandatory open access policy applies to all University staff members with a responsibility for research. Going forwards all authors automatically grant the University a non?exclusive, irrevocable, worldwide licence to make manuscripts of their scholarly articles publicly available under the terms of a Creative Commons Attribution (CC BY) licence.

We are proud that the University of Edinburgh was the first institution in the UK to adopt this type of progressive rights retention open access policy, and we are hugely encouraged to see that many other universities are adopting similar policies. In many ways the policy is just the starting point and most of the hard work actually happens afterwards when supporting members of staff with new publishing processes.  This post is intended to give an update of progress so far and to give an account of how the University of Edinburgh policy is having a positive effect on the number of open access publications being immediately available….”

Experimenting with repository workflows for archiving: Automated ingest | Community-led Open Publication Infrastructures for Monographs (COPIM)

by Ross Higman

In a recent post, my colleague Miranda Barnes outlined the challenges of archiving and preservation for small and scholar-led open access publishers, and described the process of manually uploading books to the Loughborough University institutional repository. The conclusion of this manual ingest experiment was that while university repositories offer a potential route for open access archiving of publisher output, the manual workflow is prohibitively time- and resource-intensive, particularly for small and scholar-led presses who are often stretched in these respects.

Fortunately, many institutional repositories provide routes for uploading files and metadata which allow for the process to be automated, as an alternative to the standard web browser user interface. Different repositories offer different routes, but a large proportion of them are based on the same technologies. By experimenting with a handful of repositories, we were therefore able to investigate workflows which should also be applicable to a much broader spread of institutions.




“• Is it legal to post “postprints” online? • Depends on each publisher’s policies • We compiled a list of 60 Applied Linguistics journals (from Web of Science) • Examined their copyright policies from Sherpa Romeo ( • Publishers that permit postprints: • Cambridge, Elsevier, John Benjamins, SAGE, Emerald, De Gruyter, Akadémiai Kiadó • Publisher that permit postprints on personal websites only (embargo on repositories): • Springer, Oxford University Press, Taylor & Francis • Publishers that do NOT permit on postprints before an embargo period: • Wiley (usually 24-month embargo)…

What this Pledge is NOT asking you to do: • Does not ask you to break any laws. Sharing postprints is within your rights (see table next slide). • Does not ask you to share “preprints” but to share “postprints”. • Does not limit you to publishing in these journals. • Does not require you do anything else (like boycotting certain publishers or not reviewing for them)….” 

The Company of Biologists supplies articles to Publications Router – Research

“The Company of Biologists, a leading not-for-profit publisher, is now providing full-text articles for distribution to UK institutional repositories using Jisc’s Publications Router service….

The articles are provided daily, upon first publication of the version of record. This is nearly always within seven weeks of acceptance.


Publications Router matches the articles to the authors’ institutions and delivers them into their repositories automatically, together with rich, authoritative metadata….”