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The vast majority of scientific contributions in the field of computational systems biology are based on mathematical models. These models can be broadly classified as either dynamic (kinetic) models or steady-state (constraint-based)…
Jupyter Notebooks have become a mainstream tool for interactive computing in every field of science. Jupyter Notebooks are suitable as companion applications for Science Gateways, providing more flexibility and post-processing capability to…
Reproducibility is a cornerstone of science, as the replication of findings is the process through which they become knowledge. It is widely considered that many fields of science are undergoing a reproducibility crisis. This has led to the…
Science has a data management problem, as well as a project management problem. While industrial-grade data science teams have embraced the agile mindset, and adopted or created all kind of tools to create reproducible workflows,…
Experimental studies are prevalent in Evolutionary Computation (EC), and concerns about the reproducibility and replicability of such studies have increased in recent times, reflecting similar concerns in other scientific fields. In this…
This article aims to provide the information retrieval community with some reflections on recent advances in retrieval learning by analyzing the reproducibility of image-text retrieval models. Due to the increase of multimodal data over the…
Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…
Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how…
Jupyter Scatter is a scalable, interactive, and interlinked scatterplot widget for exploring datasets in Jupyter Notebook/Lab, Colab, and VS Code. Its goal is to simplify the visual exploration, analysis, and comparison of large-scale…
Reproducibility is central to the credibility of scientific findings, yet complete replication studies are costly and infrequent. However, many biological experiments contain internal replication, which is defined as repetition across…
GitHub Copilot, an extension for the Visual Studio Code development environment powered by the large-scale language model Codex, makes automatic program synthesis available for software developers. This model has been extensively studied in…
In a new effort to make our research transparent and reproducible by others, we developed a workflow to run and share computational studies on the public cloud Microsoft Azure. It uses Docker containers to create an image of the application…
Computational micromagnetics has become an essential tool in academia and industry to support fundamental research and the design and development of devices. Consequently, computational micromagnetics is widely used in the community, and…
As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike. Though…
The information retrieval (IR) community has a strong tradition of making the computational artifacts and resources available for future reuse, allowing the validation of experimental results. Besides the actual test collections, the…
Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The relevance of machine learning research can only be improved if we also employ empirical rigor that incorporates…
Automatic evaluation of text generation tasks (e.g. machine translation, text summarization, image captioning and video description) usually relies heavily on task-specific metrics, such as BLEU and ROUGE. They, however, are abstract…
Research processes often rely on high-performance computing (HPC), but HPC is often seen as antithetical to "reproducibility": one would have to choose between software that achieves high performance, and software that can be deployed in a…
During the ESCAPE project, a pilot analysis facility was developed with a bottom-up approach, in collaboration with all the project partners. As a result, the CERN Virtual Research Environment (VRE) initiative proposes a workspace that…
It is recommended that teacher-scholars of data science adopt reproducible workflows in their research as scholars and teach reproducible workflows to their students. In this paper, we propose a third dimension to reproducibility practices…