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Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy…

Biomolecules · Quantitative Biology 2016-03-01 Simon Mitternacht

Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science…

Digital Libraries · Computer Science 2022-05-04 Martin Hunt , Steven Clark , Daniel Mejia , Saaketh Desai , Alejandro Strachan

Science advances not only through the accumulation of facts but also through the evolution of tools. Crucially, tools are rarely used in isolation. They form tool portfolios, combinations shaped by a discipline's workflows and analytical…

Digital Libraries · Computer Science 2026-04-28 Zhouming Wu , Dakota Murray

Context: Over the past decade Software Engineering research has seen a steady increase in survey-based studies, and there are several guidelines providing support for those willing to carry out surveys. The need for auditing survey research…

Software Engineering · Computer Science 2019-01-29 Jefferson Seide Molléri , Kai Petersen , Emilia Mendes

The use of statistical software in academia and enterprises has been evolving over the last years. More often than not, students, professors, workers, and users, in general, have all had, at some point, exposure to statistical software.…

Applications · Statistics 2019-08-21 Rui Portocarrero Sarmento , Vera Costa

This paper proposes a software repository model together with associated tooling and consists of several complex, open-source GUI driven applications ready to be used in empirical software research. We start by providing the rationale for…

Software Engineering · Computer Science 2017-02-28 Arthur-Jozsef Molnar

We present SPUX - a modular framework for Bayesian inference enabling uncertainty quantification and propagation in linear and nonlinear, deterministic and stochastic models, and supporting Bayesian model selection. SPUX can be coupled to…

Computation · Statistics 2021-05-14 Jonas Šukys , Marco Bacci

In traditional usability studies, researchers talk to users of tools to understand their needs and challenges. Insights gained via such interviews offer context, detail, and background. Due to costs in time and money, we are beginning to…

Human-Computer Interaction · Computer Science 2018-02-01 Kelly Mack , John Lee , Kevin Chang , Karrie Karahalios , Aditya Parameswaran

Social network platforms have increased and become very popular in the last decade; they allow people to create an online account to then interact with others creating a complicated net of connections. LinkedIn is one of the most used…

Human-Computer Interaction · Computer Science 2020-06-09 Alessandro Ecclesie Agazzi

Information access systems, such as search engines, recommender systems, and conversational assistants, have become integral to our daily lives as they help us satisfy our information needs. However, evaluating the effectiveness of these…

Human-Computer Interaction · Computer Science 2026-04-21 Krisztian Balog , ChengXiang Zhai

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…

Information Retrieval · Computer Science 2022-01-20 Timo Breuer , Nicola Ferro , Maria Maistro , Philipp Schaer

There has been a large focus in recent years on making assets in scientific research findable, accessible, interoperable and reusable, collectively known as the FAIR principles. A particular area of focus lies in applying these principles…

Human-Computer Interaction · Computer Science 2021-11-02 Robin A Richardson , Remzi Celebi , Sven van der Burg , Djura Smits , Lars Ridder , Michel Dumontier , Tobias Kuhn

JISA is a software library, written in Java, aimed at providing an easy, flexible and standardised means of creating experimental control software for physical sciences researchers. Specifically, with an emphasis on enabling measurement…

Instrumentation and Detectors · Physics 2023-08-28 William Alexander Wood , Thomas Marsh , Henning Sirringhaus

MSstatsQC [3] is an open-source software that provides longitudinal system suitability monitoring tools in the form of control charts for proteomic experiments. It includes simultaneous tools for the mean and dispersion of suitability…

Human-Computer Interaction · Computer Science 2020-03-27 Sara Mohammad Taheri , Omkar Terse , Eralp Dogu , Magy Seif El-Nasr , Olga Vitek

The development and enhancement of methods for evaluating software accessibility is a relevant challenge in modern software engineering, as ensuring equal access to digital services is a key factor in improving their efficiency and…

Software Engineering · Computer Science 2025-09-30 Mykola Kuz , Ivan Yaremiy , Hanna Yaremii , Mykola Pikuliak , Ihor Lazarovych , Mykola Kozlenko , Denys Vekeryk

Usability engineering and usability testing are concepts that continue to evolve. Interesting research studies and new ideas come up every now and then. This paper tests the hypothesis of using an EDA based physiological measurements as a…

Human-Computer Interaction · Computer Science 2014-09-02 Arwa Alamoudi , Noura Alomar , Rawan Alabdulrahman , Sarah Alkoblan , Wea'am Alrashed

In diverse industrial and academic environments, the quality of the software has been evaluated using different analytic studies. The contribution of the present work is focused on the development of a methodology in order to improve the…

Software Engineering · Computer Science 2012-09-13 Leticia Dávila-Nicanor , Pedro Mejía-Alvarez

Scientific inference is often undermined by the vast but rarely explored "multiverse" of defensible modelling choices, which can generate results as variable as the phenomena under study. We introduce RobustiPy, an open-source Python…

Methodology · Statistics 2026-05-20 Daniel Valdenegro , Jiani Yan , Duiyi Dai , Charles Rahal

The key to speeding up applications is often understanding where the elapsed time is spent, and why. This document reviews in depth the full array of performance analysis tools and techniques available on Linux for this task, from the…

Performance · Computer Science 2007-05-23 Michel R. Dagenais , Karim Yaghmour , Charles Levert , Makan Pourzandi

Previous work established that open source software (OSS) projects can benefit from the involvement of UX professionals, who offer user-centric perspectives and contributions to improve software usability. However, their participation in…

Human-Computer Interaction · Computer Science 2025-03-05 Arghavan Sanei , Jinghui Cheng