“Research software is a fundamental and vital part of research worldwide, yet there remain significant challenges to software productivity, quality, reproducibility, and sustainability. Improving the practice of scholarship is a common goal of the open science, open source software and FAIR (Findable, Accessible, Interoperable and Reusable) communities, but improving the sharing of research software has not yet been a strong focus of the latter.
To improve the FAIRness of research software, the FAIR for Research Software (FAIR4RS) Working Group has sought to understand how to apply the FAIR Guiding Principles for scientific data management and stewardship to research software, bringing together existing and new community efforts. Many of the FAIR Guiding Principles can be directly applied to research software by treating software and data as similar digital research objects. However, specific characteristics of software — such as its executability, composite nature, and continuous evolution and versioning — make it necessary to revise and extend the principles.
This document presents the first version of the FAIR Principles for Research Software (FAIR4RS Principles). It is an outcome of the FAIR for Research Software Working Group (FAIR4RS WG).
The FAIR for Research Software Working Group is jointly convened as an RDA Working Group, FORCE11 Working Group, and Research Software Alliance (ReSA) Task Force.”
“GigaByte (ISSN:2709-4715) aims to promote the most rapid exchange of scientific information in a formal peer-reviewed publishing platform. Modern research is data-driven, iterative, and aims to be FAIR: Findable, Accessible, Interoperable and Reusable. It is also fast moving, with available data and computational tools changing constantly and swiftly evolving fields continuously being tested, updated and modified by the community. Given that, GigaByte is focused on publishing short, focused, data-driven articles using a publishing platform that will allow nearly immediate online publication on acceptance as well as an ability to update published articles. This drastically reduces writing and reviewing. With that, GigaByte provides scientists a venue to rapidly and easily share and build upon each other’s research outputs.
Currently we publish two types of articles: Data Release highlight and contextualizing exceptional and openly available datasets, while Technical Release articles are present an open-source software tool or an experimental or computational method for the analysis or handling of research data.
GigaByte is an open access and open science journal. As with our sister-journal GigaScience— we publish ALL reusable and shareable research objects, such as data, software tools and workflows, from data-driven research. …”
“The grant, which follows an 2018 award for $850,000, will help expand two existing open-source software projects, as well as support the launch of two new ones:
Unpaywall, launched in 2017, has become the world’s most-used index of Open Access (OA) scholarly papers. The free Unpaywall extension has 400,000 active users, and its underlying database powers OA-related features in dozens of other tools including Web of Science, Scopus, and the European Open Science Monitor. All Unpaywall data is free and open.
Unsub is an analytics dashboard that helps academic libraries cancel their large journal subscriptions, freeing up money for OA publishing. Launched in late 2019, Unsub is now used by over 500 major libraries in the US and worldwide, including the national library consortia of Canada, Australia, Greece, Hong Kong, and the UK.
JournalsDB will be a free and open database of scholarly journals. This resource will gather a wide range of data on tens of thousands of journals, emphasizing coverage of emerging open venues.
OpenAlex will be a free and open bibliographic database, cataloging papers, authors, affiliations, citations, and journals. Inspired by the ancient Library of Alexandria, OpenAlex will strive to create a comprehensive map of the global scholarly conversation. In a recent blog post, the team announced that OpenAlex will be released in time to serve as a replacement for Microsoft Academic Graph, whose discontinuation was also recently announced….”
Abstract: In many countries around the world that use authorship and academic papers for career advancement and recognition, the accurate identity of participating authors is vital. ORCID (Open Researcher and Contributor ID), an author disambiguation tool that was created in 2012, is being vociferously implemented across a wide swathe of journals, including by many leading publishers. In some countries, authors who publish in indexed journals, particularly in journals that carry a Clarivate Analytics’ Journal Impact Factor, are rewarded, sometimes even monetarily. A strong incentive to cheat and abuse the publication ethos thus exists. There has been a recent spike in the detection of papers apparently derived from paper mills that have multiple issues with figures. The use of such figures across many papers compromises the integrity of the content in all those papers, with widespread ramifications for the integrity of the biomedical literature and of journals that may be gamed by academics. The use of ORCID does not guarantee the authenticity of authors associated with a paper mill-derived paper, nor does it fortify the paper’s integrity. These weaknesses of ORCID may dampen trust in this tool, especially if the ORCID platform is being populated by “ghost” (empty) ORCID accounts of academics whose identities cannot be clearly verified, or disposable accounts (perhaps created by paper mill operators) that are used only once, exclusively to pass the paper submission step. Open-source forensic tools to assist academics, editors and publishers to detect problematic figures, and more stringent measures by ORCID to ensure robust author identity verification, are urgently required to protect themselves, and the wider biomedical literature.
“Open access is a major step towards achieving the SDGs by being able to monitor progress and build collective understanding. Because the SDG datasets and the cartographic guidance in this book are openly available, more people than ever before can make maps in support of an economically, environmentally, and socially sustainable future….
However, maps both historically and currently are part of the problem, contributing to the global inequities the SDGs seek to dissolve and thus reinforcing dominant power structures. Questions on who can make and access maps—as well as the knowledge to make and access these maps—persist. In this book, we attempt to open this knowledge on cartographic design too often paywalled behind expensive textbooks or university courses. While opening this knowledge is one step towards democratizing cartography, it is not enough to confront the SDGs. We call on the global community of cartographers to continue developing and sharing open data, maps, and mapping technologies to better the world….”
“These workshops offer a unique opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry. Attendees will be able to choose from sessions covering accessing online resources; data processing and visualisation; ligand and structure-based design, or computational chemistry. All software and training materials required for the workshop will be provided for attendees to install and run on their own computers….”
“All scientists working Chemistry need software tools for accessing, handling and storing chemical information, or performing molecular modelling and computational chemistry. There is now a wealth of open-source tools to help in these activities, however many are not as well-known as commercial offerings….”
Abstract: Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific software. The ready-to-use packaging of hundreds of tools and workflows, combined with the implementation of interoperability standards, enables users to launch analyses across multiple environments. Dockstore is widely used, more than twenty-five high-profile organizations share analysis collections through the platform in a variety of workflow languages, including the Broad Institute’s GATK best practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few. Here we describe the improvements made over the last four years, including the expansion of system integrations supporting authors, the addition of collaboration features and analysis platform integrations supporting users, and other enhancements that improve the overall scientific reproducibility of Dockstore content.
eLife is pleased to announce today its ongoing support for Coko to develop open-source software solutions for publishing, including Kotahi – a new journal platform that can also help facilitate the publication and review of preprints.