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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…

Other Quantitative Biology · Quantitative Biology 2023-04-19 Pedro Mendes

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…

Software Engineering · Computer Science 2025-07-09 S. Lee , C. Myers , A. Yang , T. Zhang , S. J. L. Billinge

Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution, or even off the primary developer's computer. We present ten…

Software Engineering · Computer Science 2017-07-05 Morgan Taschuk , Greg Wilson

Reproducibility of computationally-derived scientific discoveries should be a certainty. As the product of several person-years' worth of effort, results -- whether disseminated through academic journals, conferences or exploited through…

Computational Engineering, Finance, and Science · Computer Science 2015-06-17 Tom Crick , Benjamin A. Hall , Samin Ishtiaq

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…

Software Engineering · Computer Science 2024-11-05 Venkat S. Malladi , Maria Yazykova , Olesya Melnichenko , Yulia Dubinina

Scientific data governance should prioritize maximizing the utility of data throughout the research lifecycle. Research software systems that enable analysis reproducibility inform data governance policies and assist administrators in…

With the recognized crisis of credibility in scientific research, there is a growth of reproducibility studies in computer science, and although existing surveys have reviewed reproducibility from various perspectives, especially very…

Software Engineering · Computer Science 2023-12-19 José Armando Hernández , Miguel Colom

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific…

Independent computational reproducibility of scientific results is rapidly becoming of pivotal importance in scientific progress as computation itself plays a more and more central role in so many branches of science. Historically,…

Quantitative Methods · Quantitative Biology 2016-08-25 Les Hatton , Gregory Warr

This paper introduces reproducible research, and explains its importance, benefits and challenges. Some important tools for conducting reproducible research in Transportation Research are also introduced. Moreover, the source code for…

Digital Libraries · Computer Science 2021-05-17 Zuduo Zheng

High-quality research software is a cornerstone of modern scientific progress, enabling researchers to analyze complex data, simulate phenomena, and share reproducible results. However, creating such software requires adherence to best…

Software Engineering · Computer Science 2025-07-23 Nasir U. Eisty , David E. Bernholdt , Alex Koufos , David J. Luet , Miranda Mundt

One of the main goals of Open Science is to make research more reproducible. There is no consensus, however, on what exactly "reproducibility" is, as opposed for example to "replicability", and how it applies to different research fields.…

Digital Libraries · Computer Science 2024-10-15 Sebastian Barzaghi , Alice Bordignon , Bianca Gualandi , Silvio Peroni

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…

Digital Libraries · Computer Science 2020-02-27 Nicholas J Tierney , Karthik Ram

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…

Quantitative Methods · Quantitative Biology 2018-10-10 Daniel G. Hurley , Joseph Cursons , Matthew Faria , David M. Budden , Vijay Rajagopal , Edmund J. Crampin

This paper investigates the reproducibility of computational science research and identifies key challenges facing the community today. It is the result of the First Summer School on Experimental Methodology in Computational Science…

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…

Digital Libraries · Computer Science 2018-08-24 Christian Schulz

Freely and openly shared low-cost electronic applications, known as open electronics, have sparked a new open-source movement, with much un-tapped potential to advance scientific research. Initially designed to appeal to electronic…

Quantitative Methods · Quantitative Biology 2022-07-14 Michael Oellermann , Jolle W. Jolles , Diego Ortiz , Rui Seabra , Tobias Wenzel , Hannah Wilson , Richelle Tanner

The reproducibility of scientific research has become a point of critical concern. We argue that openness and transparency are critical for reproducibility, and we outline an ecosystem for open and transparent science that has emerged…

Computers and Society · Computer Science 2018-09-27 Russell A. Poldrack , Krzysztof J. Gorgolewski , Gael Varoquaux

In recent years, funding agencies and journals increasingly advocate for open science practices (e.g. data and method sharing) to improve the transparency, access, and reproducibility of science. However, quantifying these practices at…

Digital Libraries · Computer Science 2023-10-06 Hancheng Cao , Jesse Dodge , Kyle Lo , Daniel A. McFarland , Lucy Lu Wang

Although it is possible to increase confidence in Free and Open Source Software (FOSS) by reviewing its source code, trusting code is not the same as trusting its executable counterparts. These are typically built and distributed by…

Software Engineering · Computer Science 2021-04-14 Chris Lamb , Stefano Zacchiroli