This guide will help you to learn how to make your code citable. It will take you step by step to archive your code using data and code archiving platform Zenodo and get a DOI for your code.
From Google’s English: “The National Open Science Plan announced in 2018 by the Minister of Higher Education, Research and Innovation, Frédérique Vidal, has enabled France to adopt a coherent and dynamic policy in the field of open science, coordinated by the Committee for Open Science, which brings together the ministry, research and higher education institutions and the scientific community. After three years of implementation, the progress made is notable. The rate of French scientific publications in open access rose from 41% to 56%. The National Open Science Fund was created, it launched two calls for projects in favor of open scientific publication and it supported structuring international initiatives. The National Research Agency and other funding agencies now require open access to publications and the drafting of data management plans for the projects they fund. The function of ministerial research data administrator has been created and a network is being deployed in the establishments. About twenty universities and research organizations have adopted an open science policy. Several guides and recommendations for putting open science into practice have been published. About twenty universities and research organizations have adopted an open science policy. Several guides and recommendations for putting open science into practice have been published. About twenty universities and research organizations have adopted an open science policy. Several guides and recommendations for putting open science into practice have been published.
The steps already taken and the evolution of the international context invite us to extend, renew and strengthen our commitments by adopting a second National Plan for Open Science, the effects of which will be deployed until 2024. With this new plan, France is continuing the ambitious trajectory initiated by the law for a digital republic of 2016 and confirmed by the research programming law of 2020, which includes open science in the missions of researchers and teacher-researchers.
This second National Plan extends its scope to source codes resulting from research, it structures actions in favor of the opening or sharing of data through the creation of the Research Data Gouv platform, it multiplies the levers of transformation in order to generalize open science practices and it presents disciplinary and thematic variations. It is firmly in line with a European ambition and proposes, within the framework of the French Presidency of the European Union, to act to take effective account of open science practices in individual and collective research evaluations. It is about initiating a process of sustainable transformation in order to make open science a common and shared practice…”
“We are grateful to these authors for taking their time to share their feedback with us, and for helping us showcase how Executable Research Articles can help improve the transparency, reproducibility and discoverability of research content across a variety of research subjects. Executable Research Articles are an open-source technology available to all, and we encourage any authors or publishers interested in the format to [get in touch] for more information….”
“On behalf of the leaders of 125 major research libraries, the Association of Research Libraries (ARL) is pleased to see that the US House of Representatives included the following policies in the National Science Foundation (NSF) for the Future Act (H.R. 2225), which center researchers and create public value by promoting the availability of publicly funded research:
Criteria for trusted open repositories to be used by federally funded researchers sharing data, software, and code. According to the House bill, the criteria would be developed with input from the scientific community. Research libraries look forward to partnering with NSF and the scientific community to develop these criteria.
Data management plans to facilitate public access to NSF-funded research products, including data, software, and code….
We strongly support public access to publications resulting from NSF-funded research with zero embargo, and we are heartened to see language in the Senate-passed US Innovation and Competition Act (S. 1260) requiring the publication of federally funded research data within 12 months, “preferably sooner.” Making research outputs publicly available to the widest possible audience in the timeliest manner possible, and machine-accessible for computation, is critical for developing scientific insights and solutions for public health, climate, technological advancement, and more….”
“This module can be used to explain how you have contributed to the generation of new ideas and hypotheses and which key skills you have used to develop ideas and test hypotheses. It can be used to highlight how you have communicated on your ideas and research results, both written and verbally, the funding you have won and any awards that you have received. It can include a small selection of outputs, with a description of why they are of particular relevance and why they are considered in the context of knowledge generation. Outputs can include open data sets, software, publications, commercial, entrepreneurial or industrial products, clinical practice developments, educational products, policy publications, evidence synthesis pieces and conference publications that you have generated….”
As Open Societies with democratic values we believe in academic freedom. The freedom to pursue intellectual enquiry and to innovate allows us to make progress on shared issues and drive forward the frontiers of knowledge and discovery for the benefit of the entire world. We recognise that research and innovation are fundamentally global endeavours. Nations, citizens, institutions, and businesses have made huge strides forward, not otherwise possible, through open research collaboration across borders. Working together we will use our position as leading science nations to collaborate on global challenges, increase the transparency and integrity of research, and facilitate data free flow with trust to drive innovation and advance knowledge.
Abstract: During last years “irreproducibility” became a general problem in omics data analysis due to the use of sophisticated and poorly described computational procedures. For avoiding misleading results, it is necessary to inspect and reproduce the entire data analysis as a unified product. Reproducible Research (RR) provides general guidelines for public access to the analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce the findings. We developed easyreporting, a novel R/Bioconductor package, to facilitate the implementation of an RR layer inside reports/tools. We describe the main functionalities and illustrate the organization of an analysis report using a typical case study concerning the analysis of RNA-seq data. Then, we show how to use easyreporting in other projects to trace R functions automatically. This latter feature helps developers to implement procedures that automatically keep track of the analysis steps. Easyreporting can be useful in supporting the reproducibility of any data analysis project and shows great advantages for the implementation of R packages and GUIs. It turns out to be very helpful in bioinformatics, where the complexity of the analyses makes it extremely difficult to trace all the steps and parameters used in the study.
“CIVIS universities promote the development of new research indicators to complement the conventional indicators for research quality and impact, so as to do justice to open science practices and, going beyond pure bibliometric indicators, to promote also non-bibliometric research products. In particular, the metrics should extend the conventional bibliometric indicators in order to cover new forms of research outputs, such as research data and research software….
Incentives and Rewards for researchers to engage in Open Science activities
Research career evaluation systems should fully acknowledge open science activities. CIVIS members encourage the inclusion of Open Science practices in their assessment mechanisms for rewards, promotion, and/or tenure, along with the Open Science Career Assessment Matrix….”
“We’re excited to announce our partnership with arXiv to support links to datasets on arXiv!
Machine learning articles on arXiv now have a Code & Data tab to link to datasets that are used or introduced in a paper….
This makes it much easier to track dataset usage across the community and quickly find other papers using the same dataset. From Papers with Code you can discover other papers using the same dataset, track usage over time, compare models and find similar datasets….”
“We make interactive computing more accessible and powerful for research and education. We strive to accelerate research and discovery, and to empower education to be more accessible, intuitive, and enjoyable. We do this through these primary actions: …”
“To ensure the Right to Replicate to our customers, 2i2c makes the following commitments to infrastructure we build and operate:
We MUST use only open source software to run our infrastructure. By only using software that is available to everyone on the same terms, we can ensure that customers can replicate the infrastructure without having to negotiate licensing terms with proprietary software vendors. In addition, any changes we make to open source software will be made in public and/or contributed upstream, so customers continue to have access to them regardless of where their infrastructure is.
We MUST NOT directly depend on proprietary cloud vendor specific products or APIs. Instead, we use cloud-managed open source software, or hide the dependency behind a layer of abstraction. This ensures that customers can port their infrastructure to any cloud provider of their choice, or run it on their own hardware with purely open source software.
This set of commitments acts as a business continuity plan for our customers, ensuring 2i2c will follow best practices within the open source, open education and open research ecosystems….”
“Springer Nature and the University of California (UC) today launched a new initiative to gain greater understanding of researcher attitudes to and motivations towards open research practices (including open access articles, data, and code; transparent peer review; and preprints). As part of the partnership, participating UC authors will also have the option to trial Guided Open Access (GOA) for some flagship Nature titles….”
“In an attempt to capture that information, Pacher and his colleagues created Open Editors, a database containing information such as names, affiliations and editorial roles of just under half a million editors working for more than 6,000 journals run by 17 scholarly publishers.
They outline their initiative in a SocArXiv preprint paper published on 11 March.
Although Open Editors already includes editor data from publishing heavyweights such as Elsevier and Cambridge University Press, Pacher says, other major players such as Springer Nature, John Wiley & Sons, and Taylor and Francis are so far missing.
Pacher has made the data and code freely available to encourage other academics to help build the database….”
Abstract: Background: “Open science” is an umbrella term describing various aspects of transparent and open science practices. The adoption of practices at different levels of the scientific process (e.g., individual researchers, laboratories, institutions) has been rapidly changing the scientific research landscape in the past years, but their uptake differs from discipline to discipline. Here, we asked to what extent journals in the field of sleep research and chronobiology encourage or even require following transparent and open science principles in their author guidelines.
Methods: We scored the author guidelines of a comprehensive set of 27 sleep and chronobiology journals, including the major outlets in the field, using the standardised Transparency and Openness (TOP) Factor. The TOP Factor is a quantitative summary of the extent to which journals encourage or require following various aspects of open science, including data citation, data transparency, analysis code transparency, materials transparency, design and analysis guidelines, study pre-registration, analysis plan pre-registration, replication, registered reports, and the use of open science badges.
Results: Across the 27 journals, we find low values on the TOP Factor (median [25 th, 75 th percentile] 3 [1, 3], min. 0, max. 9, out of a total possible score of 29) in sleep research and chronobiology journals.
Conclusions: Our findings suggest an opportunity for sleep research and chronobiology journals to further support recent developments in transparent and open science by implementing transparency and openness principles in their author guidelines.
“Given how essential newly developed code can be to computational biology research we have been collaborating with the Editorial Board of PLOS Computational Biology and consulting with computational biology researchers to develop a new more-rigorous code policy that is intended to increase code sharing on publication of articles….”