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Whole Tale http://wholetale.org is a web-based, open-source platform for reproducible research supporting the creation, sharing, execution, and verification of "Tales" for the scientific research community. Tales are executable research…
We present an overview of the recently funded "Merging Science and Cyberinfrastructure Pathways: The Whole Tale" project (NSF award #1541450). Our approach has two nested goals: 1) deliver an environment that enables researchers to create a…
The reproduction and replication of reported scientific results is a hot topic within the academic community. The retraction of numerous studies from a wide range of disciplines, from climate science to bioscience, has drawn the focus of…
Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
The general purpose of a scientific publication is the exchange and spread of knowledge. A publication usually reports a scientific result and tries to convince the reader that it is valid. With an ever-growing number of papers relying on…
With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data…
Ensuring the reproducibility of scientific work is crucial as it allows the consistent verification of scientific claims and facilitates the advancement of knowledge by providing a reliable foundation for future research. However,…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
In recent years, the research community has raised serious questions about the reproducibility of scientific work. In particular, since many studies include some kind of computing work, reproducibility is also a technological challenge, not…
Computer science is also an experimental science. This is particularly the case for parallel computing, which is in a total state of flux, and where experiments are necessary to substantiate, complement, and challenge theoretical modeling…
The emergence of "big data" offers unprecedented opportunities for not only accelerating scientific advances but also enabling new modes of discovery. Scientific progress in many disciplines is increasingly enabled by our ability to examine…
Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…
Data tables play a central role in scientific papers. However, their meaning is often co-constructed with surrounding text through narrative interplay, making comprehension cognitively demanding for readers. In this work, we explore how…
Data makes science possible. Sharing data improves visibility, and makes the research process transparent. This increases trust in the work, and allows for independent reproduction of results. However, a large proportion of data from…
Although a standard in natural science, reproducibility has been only episodically applied in experimental computer science. Scientific papers often present a large number of tables, plots and pictures that summarize the obtained results,…
To reproduce eScience, several challenges need to be solved: scientific workflows need to be automated; the involved software versions need to be provided in an unambiguous way; input data needs to be easily accessible; High-Performance…
Scientific knowledge increasingly depends on complex computational processes where both hardware and software layers can influence research outcomes. As computational complexity grows, classical-quantum integration provides a lens for…
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)…
In recent years, the research community, but also the general public, has raised serious questions about the reproducibility and replicability of scientific work. Since many studies include some kind of computational work, these issues are…