Related papers: Facilitating Bioinformatics Reproducibility
Reproducibility remains a central challenge in computational social science, where complex workflows, evolving software ecosystems, and inconsistent documentation hinder researchers ability to re-execute published methods. This study…
Scientific advancement relies on the ability to share and reproduce results. When data analysis or calculations are carried out using software written by scientists there are special challenges around code versions, quality and code…
Biomedical information extraction (BioIE) is important to many applications, including clinical decision support, integrative biology, and pharmacovigilance, and therefore it has been an active research. Unlike existing reviews covering a…
Assessment of replicability is critical to ensure the quality and rigor of scientific research. In this paper, we discuss inference and modeling principles for replicability assessment. Targeting distinct application scenarios, we propose…
Software is now a vital scientific instrument, providing the tools for data collection and analysis across disciplines from bioinformatics and computational physics, to the humanities. The software used in research is often home-grown and…
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,…
Computational methods and associated software implementations are central to every field of scientific investigation. Modern biological research, particularly within systems biology, has relied heavily on the development of software tools…
With the increased interest in computational sciences, machine learning (ML), pattern recognition (PR) and big data, governmental agencies, academia and manufacturers are overwhelmed by the constant influx of new algorithms and techniques…
Machine Learning (ML) has become essential in several industries. In Computational Science and Engineering (CSE), the complexity of the ML lifecycle comes from the large variety of data, scientists' expertise, tools, and workflows. If data…
Software production research is quickly evolving on two parallel approaches: conventional and bio-inspired. The bio-inspired approaches are generally developed and presented as enhancements of the conventional ones. However the conventional…
Scientific code is not production software. Scientific code participates in the evaluation of a scientific hypothesis. This imposes specific constraints on the code that are often overlooked in practice. We articulate, with a small example,…
Provenance is information recording the source, derivation, or history of some information. Provenance tracking has been studied in a variety of settings; however, although many design points have been explored, the mathematical or semantic…
As the demand for large scale AI models continues to grow, the optimization of their training to balance computational efficiency, execution time, accuracy and energy consumption represents a critical multidimensional challenge. Achieving…
PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0):…
Data provenance strives for explaining how the computation was performed by recording a trace of the execution. The provenance trace is useful across a wide-range of workflows to improve the dependability, security, and efficiency of…
Despite much creative work on methods and tools, reproducibility -- the ability to repeat the computational steps used to obtain a research result -- remains elusive. One reason for these difficulties is that extant tools for capturing…
The ability to verify research results and to experiment with methodologies are core tenets of science. As research results are increasingly the outcome of computational processes, software plays a central role. GNU Guix is a software…
Analytic software tools and workflows are increasing in capability, complexity, number, and scale, and the integrity of our workflows is as important as ever. Specifically, we must be able to inspect the process of analytic workflows to…
With the advent of open source software, a veritable treasure trove of previously proprietary software development data was made available. This opened the field of empirical software engineering research to anyone in academia. Data that is…
Generative artificial intelligence (GenAI) has become a transformative approach in bioinformatics that often enables advancements in genomics, proteomics, transcriptomics, structural biology, and drug discovery. To systematically identify…