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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

With the rise of Wikipedia as a first-stop source for scientific knowledge, it is important to compare its representation of that knowledge to that of the academic literature. Here we identify the 250 most heavily used journals in each of…

Digital Libraries · Computer Science 2017-01-17 Misha Teplitskiy , Grace Lu , Eamon Duede

So far, the relationship between open science and software engineering expertise has largely focused on the open release of software engineering research insights and reproducible artifacts, in the form of open-access papers, open data, and…

Software Engineering · Computer Science 2024-09-17 Cynthia C. S. Liem , Andrew M. Demetriou

GitHub is the world's largest collection of open source software. Therefore, it is important both to software developers and users to compare and track the popularity of GitHub repositories. In this paper, we propose a framework to assess…

Software Engineering · Computer Science 2017-03-22 Hudson Borges , Marco Tulio Valente , Andre Hora , Jailton Coelho

Scientific research is a key input into technological innovation, yet not all scientific knowledge is equally mobilized in patents. This paper examines how different scientific publishing models shape both the selection of scientific…

Digital Libraries · Computer Science 2026-04-09 Abdelghani Maddi , Chongjun Xi , Xiaoting Chen , Isabelle Dorsch , Marc-André Simard

A common assumption suggests that individuals tend to work with others who are similar to them. However, studies on team working and ability of the group to solve complex problems highlight that diversity plays a critical role during…

Social and Information Networks · Computer Science 2021-10-14 Dorota Celińska-Kopczyńska

Links are an essential feature of the World Wide Web, and source code repositories are no exception. However, despite their many undisputed benefits, links can suffer from decay, insufficient versioning, and lack of bidirectional…

Software Engineering · Computer Science 2019-02-18 Hideaki Hata , Christoph Treude , Raula Gaikovina Kula , Takashi Ishio

Fast-growing scientific publications present challenges to the scientific community. In this paper, we describe their implications to researchers. As references form explicit foundations for researchers to conduct a study, we investigate…

Digital Libraries · Computer Science 2023-07-14 Guoxiu He , Aixin Sun , Wei Lu

Traceability links are key information sources for software developers, connecting software artifacts. Such links play an important role, particularly between contribution artifacts and their corresponding source code. Through these links,…

Software Engineering · Computer Science 2026-02-24 Sota Nakashima , Masanari Kondo , Mahmoud Alfadel , Aly Ahmad , Toshihiro Nakae , Hidenori Matsuzaki , Yasutaka Kamei

The Software Engineering (SE) community has been embracing the open science policy and encouraging researchers to disclose artifacts in their publications. However, the status and trends of artifact practice and quality remain unclear,…

Software Engineering · Computer Science 2024-04-11 Mugeng Liu , Xiaolong Huang , Wei He , Yibing Xie , Jie M. Zhang , Xiang Jing , Zhenpeng Chen , Yun Ma

In open-source software development environments; textual, numerical and relationship-based data generated are of interest to researchers. Various data sets are available for this data, which is frequently used in areas such as software…

Software Engineering · Computer Science 2020-10-01 Abdulkadir Şeker , Banu Diri , Halil Arslan

To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage…

Computers and Society · Computer Science 2018-11-01 Dan Sholler , Karthik Ram , Carl Boettiger , Daniel S. Katz

Institutional repositories are deposits of different types of digital files for access, disseminate and preserve them. This paper aims to explain the importance of repositories in the academic field of engineering as a way to democratize…

Digital Libraries · Computer Science 2012-11-01 Jose Texier , Marisa De Giusti , Nestor Oviedo , Gonzalo Villarreal , Ariel Lira

Scientific software is essential to scientific innovation and in many ways it is distinct from other types of software. Abandoned (or unmaintained), buggy, and hard to use software, a perception often associated with scientific software can…

Software Engineering · Computer Science 2025-06-23 Addi Malviya Thakur , Reed Milewicz , Mahmoud Jahanshahi , Lavínia Paganini , Bogdan Vasilescu , Audris Mockus

GitHub, renowned for facilitating collaborative code version control and software production in software teams, expanded its services in 2017 by introducing GitHub Marketplace. This online platform hosts automation tools to assist…

Software Engineering · Computer Science 2024-07-09 SK Golam Saroar , Waseefa Ahmed , Elmira Onagh , Maleknaz Nayebi

Open source software projects usually acknowledge contributions with text files, websites, and other idiosyncratic methods. These data sources are hard to mine, which is why contributorship is most frequently measured through changes to…

Software Engineering · Computer Science 2021-07-06 Jean-Gabriel Young , Amanda Casari , Katie McLaughlin , Milo Z. Trujillo , Laurent Hébert-Dufresne , James P. Bagrow

From more than half a century ago indexing scientific articles has been studied intensively to provide a more efficient data retrieval and to conserve researchers invaluable time. In the last two decades with the emergence of the World Wide…

Digital Libraries · Computer Science 2014-01-07 Azam Majooni , Mona Masood , Amir Akhavan

An essential part of research and scientific communication is researchers' ability to reproduce the results of others. While there have been increasing standards for authors to make data and code available, many of these files are hard to…

Digital Libraries · Computer Science 2021-09-23 Layan Bahaidarah , Ethan Hung , Andreas F. De Melo Oliveira , Jyotsna Penumaka , Lukas Rosario , Ana Trisovic

How many times have you tried to re-implement a past CAV tool paper, and failed? Reliably reproducing published scientific discoveries has been acknowledged as a barrier to scientific progress for some time but there remains only a small…

Logic in Computer Science · Computer Science 2015-02-10 Tom Crick , Benjamin A. Hall , Samin Ishtiaq

Open digital public infrastructure needs community management to ensure accountability, sustainability, and robustness. Yet open-source projects often rely on centralized decision-making, and the determinants of successful community…

Computers and Society · Computer Science 2026-02-06 Mobina Noori , Mahasweta Chakraborti , Amy X Zhang , Seth Frey
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