Related papers: Systematically Examining Reproducibility: A Case S…
The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. I analyze a computational model of the segment polarity network…
In vitro fertilization (IVF) is a widely utilized assisted reproductive technology, yet predicting its success remains challenging due to the multifaceted interplay of clinical, demographic, and procedural factors. This study develops a…
Synthetic Biology is the new engineering-based approach to biology that includes applications of designing complex biological devices. At present, it is not yet clear what will emerge as the defining principles of Synthetic Biology. One…
Reproducibility is a crucial aspect of scientific research that involves the ability to independently replicate experimental results by analysing the same data or repeating the same experiment. Over the years, many works have been proposed…
Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…
High-Performance Computing (HPC) platforms enable scientific software to achieve breakthroughs in many research fields such as physics, biology, and chemistry, by employing Research Software Engineering (RSE) techniques. These include 1)…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
The Common Objects in Context (COCO) dataset has been instrumental in benchmarking object detectors over the past decade. Like every dataset, COCO contains subtle errors and imperfections stemming from its annotation procedure. With the…
The Open Knowledgebase of Interatomic Models (OpenKIM) project is a framework intended to facilitate access to standardized implementations of interatomic models for molecular simulations along with computational protocols to evaluate them.…
Deep learning techniques hold immense promise for advancing medical image analysis, particularly in tasks like image segmentation, where precise annotation of regions or volumes of interest within medical images is crucial but manually…
Scientific investigations that incorporate next generation sequencing involve analyses of high-dimensional data where the need to organize, collate and interpret the outcomes are pressingly important. Currently, data can be collected at the…
In this work we introduce repro_eval - a tool for reactive reproducibility studies of system-oriented information retrieval (IR) experiments. The corresponding Python package provides IR researchers with measures for different levels of…
Data analysis for scientific experiments and enterprises, large-scale simulations, and machine learning tasks all entail the use of complex computational pipelines to reach quantitative and qualitative conclusions. If some of the activities…
BCI algorithm development has long been hampered by two major issues: small sample sets and a lack of reproducibility. We offer a solution to both of these problems via a software suite that streamlines both the issues of finding and…
Background: Empirical studies on widely used model-based development tools such as MATLAB/Simulink are limited despite the tools' importance in various industries. Aims: The aim of this paper is to investigate the reproducibility of…
This paper presents a reproducible and process-aware pipeline for predictive monitoring of clinical pathways. The approach integrates data lifting, temporal reconstruction, event log construction, prefix-based representations, and…
Those seeking to reproduce a computational experiment often need to manually look at the code to see how to build necessary libraries, configure parameters, find data, and invoke the experiment; it is not automatic. Automatic…
Large-scale plasma simulations are critical for designing and developing next-generation fusion energy devices and modeling industrial plasmas. BIT1 is a massively parallel Particle-in-Cell code designed for specifically studying plasma…
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…
Efficient design of genomic perturbation experiments is crucial for accelerating drug discovery and therapeutic target identification, yet exhaustive perturbation of the human genome remains infeasible due to the vast search space of…