Related papers: Systematically Examining Reproducibility: A Case S…
Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Recording the provenance of scientific computation results is key to the support of traceability, reproducibility and quality assessment of data products. Several data models have been explored to address this need, providing…
The high-performance computing (HPC) community has adopted incentive structures to motivate reproducible research, with major conferences awarding badges to papers that meet reproducibility requirements. Yet, many papers do not meet such…
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,…
Brain Computer Interface (BCI) technologies have the potential to improve the lives of millions of people around the world, whether through assistive technologies or clinical diagnostic tools. Despite advancements in the field, however, at…
Replicability and reproducibility of experimental results are primary concerns in all the areas of science and IR is not an exception. Besides the problem of moving the field towards more reproducible experimental practices and protocols,…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area…
Computational reproducibility is fundamental to trustworthy science, yet remains difficult to achieve in practice across various research workflows, including Jupyter notebooks published alongside scholarly articles. Environment drift,…
Reproducibility is a fundamental requirement of the scientific process since it enables outcomes to be replicated and verified. Computational scientific experiments can benefit from improved reproducibility for many reasons, including…
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…
In real-world recommender systems, such as in the music domain, repeat consumption is a common phenomenon where users frequently listen to a small set of preferred songs or artists repeatedly. The key point of modeling repeat consumption is…
Research in ultrasound imaging is limited in reproducibility by two factors: First, many existing ultrasound pipelines are protected by intellectual property, rendering exchange of code difficult. Second, most pipelines are implemented in…
We propose an approach for improved reproducibility that includes capturing and relating provenance characteristics and performance metrics, in a hybrid queriable system, the ProvEn server. The system capabilities are illustrated on two use…
Building Performance Simulation (BPS) uses advanced computational and data science methods. Reproducibility, the ability to obtain the same results by using the same data and methods, is essential in BPS research to ensure the reliability…
This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE). The workshop's discussion-oriented agenda…
Reproducibility in research remains hindered by complex systems involving data, models, tools, and algorithms. Studies highlight a reproducibility crisis due to a lack of standardized reporting, code and data sharing, and rigorous…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…