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Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years sustainable software development practices have made progress in being considered as an integral component of research.…

Software Engineering · Computer Science 2023-12-21 Akash Dhruv , Anshu Dubey

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,…

General Literature · Computer Science 2019-04-25 Fabien Benureau , Nicolas Rougier

The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…

Software Engineering · Computer Science 2014-09-17 Tom Crick , Benjamin A. Hall , Samin Ishtiaq

Reproducibility is widely acknowledged as a fundamental principle in scientific research. Currently, the scientific community grapples with numerous challenges associated with reproducibility, often referred to as the ''reproducibility…

Software Engineering · Computer Science 2024-09-16 Benjamin A. Antunes , David R. C. Hill

Replication of scientific experiments is critical to the advance of science. Unfortunately, the discipline of Computer Science has never treated replication seriously, even though computers are very good at doing the same thing over and…

General Literature · Computer Science 2013-04-15 Ian P. Gent

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…

Software Engineering · Computer Science 2023-08-03 Lázaro Costa , Susana Barbosa , Jácome Cunha

Reproducibility, the ability to recompute results, and replicability, the chances other experimenters will achieve a consistent result, are two foundational characteristics of successful scientific research. Consistent findings from…

Applications · Statistics 2015-06-23 Jeffrey T. Leek , Roger D. Peng

The main goal of this document is to help the research community to understand the basic concepts of software distribution: Free software, Open source software, licenses. This document also includes a procedure for research software and…

Computers and Society · Computer Science 2014-09-12 Teresa Gomez-Diaz

Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…

The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…

Other Quantitative Biology · Quantitative Biology 2022-10-07 Griffin Chure

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…

Software Engineering · Computer Science 2019-03-15 Mario Rosado de Souza , Robert Haines , Markel Vigo , Caroline Jay

Reproducibility is one of the core dimensions that concur to deliver Trustworthy Artificial Intelligence. Broadly speaking, reproducibility can be defined as the possibility to reproduce the same or a similar experiment or method, thereby…

Artificial Intelligence · Computer Science 2023-02-27 Riccardo Albertoni , Sara Colantonio , Piotr Skrzypczyński , Jerzy Stefanowski

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…

Databases · Computer Science 2019-09-04 Maria Luiza Mondelli , A. Townsend Peterson , Luiz M. R. Gadelha

The high incidence of irreproducible research has led to urgent appeals for transparency and equitable practices in open science. For the scientific disciplines that rely on computationally intensive analyses of large data sets, a granular…

This paper investigates the conceptual relationship between openness and reproducibility using a model-centric approach, heavily informed by probability theory and statistics. We first clarify the concepts of reliability, auditability,…

Other Statistics · Statistics 2019-10-30 Bert Baumgaertner , Berna Devezer , Erkan O. Buzbas , Luis G. Nardin

Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, and open source. While open science is becoming generally accepted as a norm in other…

Software Engineering · Computer Science 2021-02-10 Daniel Méndez Fernández , Daniel Graziotin , Stefan Wagner , Heidi Seibold

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…

Other Quantitative Biology · Quantitative Biology 2020-07-28 Jaqueline J. Brito , Jun Li , Jason H. Moore , Casey S. Greene , Nicole A. Nogoy , Lana X. Garmire , Serghei Mangul

Contemporary debates on "open science" mostly focus on the pub- lic accessibility of the products of scientific and academic work. In contrast, this paper presents arguments for "opening" the ongoing work of science. That is, this paper is…

Physics Education · Physics 2017-02-17 Pratim Sengupta , Marie-Claire Shanahan

Computer science is also an experimental science. This is particularly the case for parallel computing, which is in a total state of flux, and where experiments are necessary to substantiate, complement, and challenge theoretical modeling…

Distributed, Parallel, and Cluster Computing · Computer Science 2013-08-19 Sascha Hunold , Jesper Larsson Träff

Small to medium-scale data science experiments often rely on research software developed ad-hoc by individual scientists or small teams. Often there is no time to make the research software fast, reusable, and open access. The consequence…

Software Engineering · Computer Science 2022-11-10 Moritz Schubotz , Ankit Satpute , Andre Greiner-Petter , Akiko Aizawa , Bela Gipp