Related papers: Facilitating Bioinformatics Reproducibility
The reproducibility of computational pipelines is an expectation in biomedical science, particularly in critical domains like human health. In this context, reporting next generation genome sequencing methods used in precision medicine…
Laboratory research is a complex, collaborative process that involves several stages, including hypothesis formulation, experimental design, data generation and analysis, and manuscript writing. Although reproducibility and data sharing are…
Visualisation facilitates the understanding of scientific data both through exploration and explanation of visualised data. Provenance contributes to the understanding of data by containing the contributing factors behind a result. With the…
In this paper, we replicated a Bayesian educational research project, which explores the association between broadband access and online course enrollment in the US. We summarized key findings from our replication and compared them with the…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Over the past few years, deep learning methods have been applied for a wide range of Software Engineering (SE) tasks, including in particular for the important task of automatically predicting and localizing faults in software. With the…
Scientific workflows are becoming increasingly popular for compute-intensive and data-intensive scientific applications. The vision and promise of scientific workflows includes rapid, easy workflow design, reuse, scalable execution, and…
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…
One of the challenges in machine learning research is to ensure that presented and published results are sound and reliable. Reproducibility, that is obtaining similar results as presented in a paper or talk, using the same code and data…
Recent reproducibility case studies have raised concerns showing that much of the deposited research has not been reproducible. One of their conclusions was that the way data repositories store research data and code cannot fully facilitate…
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…
Being able to duplicate published research results is an important process of conducting research whether to build upon these findings or to compare with them. This process is called "replicability" when using the original authors'…
Reproducibility, the ability to reproduce the results of published papers or studies using their computer code and data, is a cornerstone of reliable scientific methodology. Studies where results cannot be reproduced by the scientific…
Open science initiatives seek to make research outputs more transparent, accessible, and reusable, but ensuring that published findings can be independently reproduced remains a persistent challenge. In this paper we describe an AI-driven…
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…
The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of…
In the field of computational science and engineering, workflows often entail the application of various software, for instance, for simulation or pre- and postprocessing. Typically, these components have to be combined in arbitrarily…
Reproducibility should be a cornerstone of science as it enables validation and reuse. In recent years, the scientific community and the general public became increasingly aware of the reproducibility crisis, i.e. the wide-spread inability…
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…
Reproducibility is essential to reliable scientific discovery in high-throughput experiments. In this work we propose a unified approach to measure the reproducibility of findings identified from replicate experiments and identify putative…