Related papers: User-friendly Composition of FAIR Workflows in a N…
The Sixth Assessment Report (AR6) of the Intergovernmental Panel on Climate Change (IPCC) has adopted the FAIR Guiding Principles. The Atlas chapter of Working Group I (WGI) is presented as a test case. Here, we describe the application of…
Machine learning (ML) is an increasingly important scientific tool supporting decision making and knowledge generation in numerous fields. With this, it also becomes more and more important that the results of ML experiments are…
Numerical algorithms and computational tools are instrumental in navigating and addressing complex simulation and data processing tasks. The exponential growth of metadata and parameter-driven simulations has led to an increasing demand for…
Open-science collaboration using Jupyter Notebooks may expose expensively trained AI models, high-performance computing resources, and training data to security vulnerabilities, such as unauthorized access, accidental deletion, or misuse.…
The massive trend of integrating data-driven AI capabilities into traditional software systems is rising new intriguing challenges. One of such challenges is achieving a smooth transition from the explorative phase of Machine Learning…
In this paper we describe the development and evaluation of AITK, the Artificial Intelligence Toolkit. This open-source project contains both Python libraries and computational essays (Jupyter notebooks) that together are designed to allow…
The way science is currently practiced shows conclusions but hides how they were reached. Researchers work privately, polish their results, publish a finished paper, and defend it. Errors are punished by retraction rather than corrected by…
Data - arguably the most important product of worldwide materials research investment - are rarely shared. The small and biased proportion of results published are buried in plots and text licensed by journals. This situation wastes…
Scientists rely on simulations to study natural phenomena. Trusting the simulation results is vital to develop sciences in any field. One approach to build trust is to ensure the reproducibility and traceability of the simulations through…
In the rapidly evolving field of bioimaging, the integration and orchestration of Findable, Accessible, Interoperable, and Reusable (FAIR) image analysis workflows remains a challenge. We introduce BIOMERO, a bridge connecting OMERO, a…
Science reproducibility is a cornerstone feature in scientific workflows. In most cases, this has been implemented as a way to exactly reproduce the computational steps taken to reach the final results. While these steps are often…
Despite the widespread adoption of computational notebooks, little is known about best practices for their usage in collaborative contexts. In this paper, we fill this gap by eliciting a catalog of best practices for collaborative data…
With the adoption of Semantic Web technologies, an increasing number of vocabularies and ontologies have been developed in different domains, ranging from Biology to Agronomy or Geosciences. However, many of these ontologies are still…
Jupyter notebooks represent a unique format for programming - a combination of code and Markdown with rich formatting, separated into individual cells. We propose to perceive a Jupyter Notebook cell as a simplified and raw version of a…
In the Jupyter ecosystem, data visualization is usually done with "widgets" created as notebook cell outputs. While this mechanism works well in some circumstances, it is not well-suited to presenting interfaces that are long-lived,…
Democratic societies need accessible, reliable information. Videos and Podcasts have established themselves as the medium of choice for civic dissemination, but also as carriers of misinformation. The emerging Science Communication…
With the rapidly increasing amount of scientific literature,it is getting continuously more difficult for researchers in different disciplines to be updated with the recent findings in their field of study.Processing scientific articles in…
To satisfy the principles of FAIR software, software sustainability and software citation, research software must be formally published. Publication repositories make this possible and provide published software versions with unique and…
Researchers face a persistent barrier when applying computational algorithms with parameter configuration typically demanding programming skills, interfaces differing across environments, and settings rarely persisting between sessions.…
The availability of metadata for scientific documents is pivotal in propelling scientific knowledge forward and for adhering to the FAIR principles (i.e. Findability, Accessibility, Interoperability, and Reusability) of research findings.…