Extension of partnership with Code Ocean will help Springer Nature authors to better share their code and data | Corporate Affairs Homepage | Springer Nature

“Following a successful trial, Springer Nature is extending its partnership with Code Ocean to better integrate code deposition and peer review with the manuscript submission process. Authors from select Nature portfolio titles will now have the option to share their code and data using the code ocean platform when they submit to one of the participating journals, and receive expert support to do so.

Speaking on the partnership, Erika Pastrana, Editorial Director, Health and Applied Sciences, Springer Nature said: “Code is a key component of research and increasingly computational approaches are utilised or developed as part of a research project. At SN, we want to support authors openly sharing and publishing the key research objects that support the manuscript, such as code, data and protocols. The sharing of code and data improves reproducibility , reduces duplication of effort, supports better transparency and enables faster advancement of research . Moreover, we believe that the code (and other key research objects) should be peer reviewed alongside the manuscript. For this reason, we have looked to deploy suitable technological capabilities to support authors and reviewers to comply with our open science policies. …”

Ley 14/2011, de 1 de junio, de la Ciencia, la Tecnología y la Innovación.

See Article 37 on open science. From Google’s English:  

“1. The public agents of the Spanish Science, Technology and Innovation System will promote the dissemination of the results of scientific, technological and innovation activity, and that the results of research, including scientific publications, data, codes and methodologies , are available in open access. Free and open access to the results will be promoted through the development of institutional or thematic open access repositories, own or shared.

2. Research personnel from the public sector or whose research activity is financed mainly with public funds and who choose to disseminate their research results in scientific publications, must deposit a copy of the final version accepted for publication and the data associated with them. in institutional or thematic open access repositories, simultaneously with the date of publication.

3. Beneficiaries of research, development or innovation projects financed mainly with public funds must comply at all times with the open access obligations set forth in the bases or subsidy agreements of the corresponding calls. Recipients of public aid and subsidies will ensure that they retain the necessary intellectual property rights to comply with open access requirements.

4. The results of the research available in open access may be used by the Public Administrations in their evaluation processes, including the evaluation of research merit.

5. The Ministry of Science and Innovation will facilitate access to open access repositories and their interconnection with similar national and international initiatives, promoting the development of systems that facilitate it, and will promote open science in the Spanish Strategy for Science, Technology and Innovation, recognizing the value of science as a common good and following the European recommendations on open science.

In addition to open access, and always with the aim of making science more open, accessible, efficient, transparent and beneficial for society, the Ministries of Science and Innovation and of Universities, each in their field of action, as well as the Communities Autonomous within the framework of their powers, they will also promote other initiatives aimed at facilitating free access and management of the data generated by research (open data), in accordance with the international FAIR principles (easy to find, accessible, interoperable and reusable). , to develop infrastructures and open platforms, to promote the publication of scientific results in open access, and the open participation of civil society in scientific processes, as developed in article 38.

6. The foregoing will be compatible with the possibility of taking the appropriate measures to protect, prior to scientific publication, the rights over the results of the research, development and innovation activity, in accordance with national and European regulations on the subject. of intellectual and industrial property, plant varieties or business secret.”

Full article: Establishing open science research priorities in health psychology: a research prioritisation Delphi exercise

Abstract:  Objective

Research on Open Science practices in Health Psychology is lacking. This meta-research study aimed to identify research question priorities and obtain consensus on the Top 5 prioritised research questions for Open Science in Health Psychology.

Methods and measures

An international Delphi consensus study was conducted. Twenty-three experts in Open Science and Health Psychology within the European Health Psychology Society (EHPS) suggested research question priorities to create a ‘long-list’ of items (Phase 1). Forty-three EHPS members rated the importance of these items, ranked their top five and suggested their own additional items (Phase 2). Twenty-four EHPS members received feedback on Phase 2 responses and then re-rated and re-ranked their top five research questions (Phase 3).

Results

The top five ranked research question priorities were: 1. ‘To what extent are Open Science behaviours currently practised in Health Psychology?’, 2. ‘How can we maximise the usefulness of Open Data and Open Code resources?’, 3. ‘How can Open Data be increased within Health Psychology?’, 4. ‘What interventions are effective for increasing the adoption of Open Science in Health Psychology?’ and 5. ‘How can we increase free Open Access publishing in Health Psychology?’.

Conclusion

Funding and resources should prioritise the research questions identified here.

1Future Leadership Fellows discuss open research with UKRI and UKRN

“On 12 October, UKRI convened several hundred Future Leaders Fellows in Birmingham. The UKRI open research team and the UK Reproducibility Network brought together some of those Fellows in two special interest session s to discuss open and transparent research . H ere we summarise the perspectives a nd ideas that we heard from the Fellows, who work in a range of disciplines and have engaged with open research in a variety of ways . Where we are aware of related work, we note this [in square brackets]….”

Open Access Week Workshop: Open Science and Open for Climate Justice – EELISA

“In the context of the Open Science Week UPB has prepared a Workshop to share Open Science Practices in the framework for Climate Justice. During this event participants will recive an overview of what is Open Science, best pracices, its reproducibility and successful case studies of the use of Open Science research methodologies at UPB. The lecturers will also talk about open sources, Open Science Software and Open Science code….”

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.

 

Toward practical transparent verifiable and long-term reproducible research using Guix | Scientific Data

Abstract:  Reproducibility crisis urge scientists to promote transparency which allows peers to draw same conclusions after performing identical steps from hypothesis to results. Growing resources are developed to open the access to methods, data and source codes. Still, the computational environment, an interface between data and source code running analyses, is not addressed. Environments are usually described with software and library names associated with version labels or provided as an opaque container image. This is not enough to describe the complexity of the dependencies on which they rely to operate on. We describe this issue and illustrate how open tools like Guix can be used by any scientist to share their environment and allow peers to reproduce it. Some steps of research might not be fully reproducible, but at least, transparency for computation is technically addressable. These tools should be considered by scientists willing to promote transparency and open science.

 

Scholarship in interaction | Scholarly Publications

Abstract:  Increasingly code and algorithms are techniques also applied in textual scholarship, giving rise to new interactions between software engineers and textual scholars. This book argues that much of that process and its effects on textual scholarship are still poorly understood and go unchecked by otherwise normal processes of quality control in scholarship such as peer review. The text provides case studies in which some of these interactions become more apparent, as well as the academic challenges and problems that they introduce. The book demonstrates that the space between code creation and conventional scholarship is one that offers many affordances to textual scholarship that until now remain unexplored. The author argues that it is an intellectual obligation of programmers and textual scholars to examine the properties of digital text and how its existence changes and challenges textual scholarship.

 

PLOS partners with DataSeer to develop Open Science Indicators – The Official PLOS Blog

“To provide richer and more transparent information on how PLOS journals support best practice in Open Science, we’re going to begin publishing data on ‘Open Science Indicators’ observed in PLOS articles. These Open Science Indicators will initially include (i) sharing of research data in repositories, (ii) public sharing of code and, (iii) preprint posting, for all PLOS articles from 2019 to present. These indicators – conceptualized by PLOS and developed with DataSeer, using an artificial intelligence-driven approach – are increasingly important to PLOS achieving its mission. We plan to share the results openly to support Open Science initiatives by the wider community.”

Easing Into Open Science: A Guide for Graduate Students and Their Advisors | Collabra: Psychology | University of California Press

Abstract:  This article provides a roadmap to assist graduate students and their advisors to engage in open science practices. We suggest eight open science practices that novice graduate students could begin adopting today. The topics we cover include journal clubs, project workflow, preprints, reproducible code, data sharing, transparent writing, preregistration, and registered reports. To address concerns about not knowing how to engage in open science practices, we provide a difficulty rating of each behavior (easy, medium, difficult), present them in order of suggested adoption, and follow the format of what, why, how, and worries. We give graduate students ideas on how to approach conversations with their advisors/collaborators, ideas on how to integrate open science practices within the graduate school framework, and specific resources on how to engage with each behavior. We emphasize that engaging in open science behaviors need not be an all or nothing approach, but rather graduate students can engage with any number of the behaviors outlined.

 

A survey of researchers’ code sharing and code reuse practices, and assessment of interactive notebook prototypes [PeerJ]

Abstract:  This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing–linking articles to a code repository–was also the most useful method of accessing code from the reader’s perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools.

 

Towards Robust, Reproducible, and Clinically Actionable EEG Biomarkers: Large Open Access EEG Database for Discovery and Out-of-sample Validation – Hanneke van Dijk, Mark Koppenberg, Martijn Arns, 2022

“To aid researchers in development and validation of EEG biomarkers, and development of new (AI) methodologies, we hereby also announce our open access EEG dataset: the Two Decades Brainclinics Research Archive for Insights in Neuroscience (TDBRAIN)….

The whole raw EEG dataset as well as python code to preprocess the raw data is available at www.brainclinics.com/resources and can freely be downloaded using ORCID credentials….”

Pro-Con Debate: Should Code Sharing Be Mandatory for Publication?

Abstract:  In this Pro-Con commentary article, we discuss whether or not code sharing should be mandatory for scientific publications. Scientific programming is an increasingly prevalent tool in research. However, there are not unified guidelines for code availability requirements. Some journals require code sharing. Others require code descriptions. Yet others have no policies around code sharing. The Pro side presented here argues that code sharing should be mandatory for all scientific publications involving code. This Pro argument comes in 2 parts. First, any defensible reason for not sharing code is an equally valid a reason for the manuscript itself not being published. Second, lack of code sharing requirements creates 2 tiers of science: one where reproducibility is required and one where it is not. Additionally, the Pro authors suggest that a debate over code sharing is itself a decade out-of-date due to the emerging availability of containerization and virtual environment sharing software. The Pro argument concludes with an appeal that authors release code to make their work more understandable by other researchers. The Con side presented here argues that computer source codes of medical technology equipment should not be subject to mandatory public disclosure. The source code is a crucial part of what makes a particular device unique and allows that device to outperform its competition. The Con authors believe that public disclosure of this proprietary information would destroy all incentives for businesses to develop new and improved technologies. Competition in the free marketplace is what drives companies to constantly improve their products, to develop new and better medical devices. The open disclosure of these “trade secret” details would effectively end that competitive drive. Why invest time, money, and energy developing a “better mousetrap” if your competitors can copy it and produce it the next day?

 

ETD 2022 – 25th International Symposium on Electronic Theses and Dissertations – ETD 2022, Novi Sad, Serbia

“The Networked Digital Library of Theses and Dissertations (NDLTD), an international organization dedicated to promoting the adoption, creation, use, dissemination, and preservation of electronic theses and dissertations (ETDs), invites you to attend the 25th International Symposium of Theses and Dissertations, ETD 2022.

ETD 2022 held in Novi Sad, Serbia, from 07 to 09 September, is hosted by University of Novi Sad (http://www.uns.ac.rs/), and co-organized by non-profit organizations Science 2.0 Alliance (http://sci2zero.org/) and NTLTD (http://www.ndltd.org/). It will be an excellent opportunity to exchange ETD experiences with professionals from different countries, to discuss innovative projects and initiatives and to share successful experiences and up-to-date practices, and to network with colleagues and friends from all over the world. Safety of the participants is the top priority for the organizers and we keep one eye on the COVID pandemic and war in Ukraine. 

The conference theme is “FAIRness of ETDs and its implications”. We hope the conference will raise a fruitful discussion on importance of application of FAIR principles at ETDs and supplement materials. We aim to address topics such as:

FAIRness of ETDs and supplement materials;
ETD and OpenScience;
ETDs and research data;
ETDs and source code; …”

Reproducibility of COVID-19 pre-prints | SpringerLink

Abstract:  To examine the reproducibility of COVID-19 research, we create a dataset of pre-prints posted to arXiv, bioRxiv, and medRxiv between 28 January 2020 and 30 June 2021 that are related to COVID-19. We extract the text from these pre-prints and parse them looking for keyword markers signaling the availability of the data and code underpinning the pre-print. For the pre-prints that are in our sample, we are unable to find markers of either open data or open code for 75% of those on arXiv, 67% of those on bioRxiv, and 79% of those on medRxiv.