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The vast majority of scientific contributions in the field of computational systems biology are based on mathematical models. These models can be broadly classified as either dynamic (kinetic) models or steady-state (constraint-based)…

Other Quantitative Biology · Quantitative Biology 2025-04-17 Moritz E. Beber

Background: Reaching out to professional software developers is a crucial part of empirical software engineering research. One important method to investigate the state of practice is survey research. As drawing a random sample of…

Software Engineering · Computer Science 2017-07-05 Sebastian Baltes , Stephan Diehl

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

Artificial Neural Networks (ANNs) replaced conventional software systems in various domains such as machine translation, natural language processing, and image processing. So, why do we need an repository for artificial neural networks?…

Machine Learning · Computer Science 2020-03-31 Javad Ghofrani , Ehsan Kozegar , Mohammad Divband Soorati , Arezoo Bozorgmehr , Hongfei Chen , Maximilian Naake

The availability of large idea repositories (e.g., the U.S. patent database) could significantly accelerate innovation and discovery by providing people with inspiration from solutions to analogous problems. However, finding useful…

Computation and Language · Computer Science 2017-06-20 Tom Hope , Joel Chan , Aniket Kittur , Dafna Shahaf

The World Wide Web and the Semantic Web are designed as a network of distributed services and datasets. In this network and its genesis, collaboration played and still plays a crucial role. But currently we only have central collaboration…

Databases · Computer Science 2019-03-01 Natanael Arndt , Michael Martin

The use of packaged libraries can significantly shorten the software development cycle by improving the quality and readability of code. In this paper, we present a recommendation engine called Librarian for open source libraries. A…

Software Engineering · Computer Science 2023-02-08 Lili Tao , Alexandru-Petre Cazan , Senad Ibraimoski , Sean Moran

In this article, we present the challenge of software citation as a method to ensure credit for and identification, discovery, and reuse of software in scientific and engineering research. We discuss related work and key challenges/research…

Computers and Society · Computer Science 2016-11-04 Kyle E. Niemeyer , Arfon M. Smith , Daniel S. Katz

Case studies are a popular and noteworthy type of research study in software engineering, offering significant potential to impact industry practices by investigating phenomena in their natural contexts. This potential to reach a broad…

Software Engineering · Computer Science 2024-02-14 Sergio Rico

Decomposing large systems into smaller components with limited privileges has long been recognized as an effective means to minimize the impact of exploits. Despite historical roots, demonstrated benefits, and a plethora of research efforts…

Cryptography and Security · Computer Science 2024-10-14 Hugo Lefeuvre , Nathan Dautenhahn , David Chisnall , Pierre Olivier

Quantum computing is rapidly advancing, but quantum software development faces significant challenges, including a steep learning curve, high hardware error rates, and a lack of mature engineering practices. This study conducts a…

Software Engineering · Computer Science 2025-10-02 Krishna Upadhyay , Vinaik Chhetri , A. B. Siddique , Umar Farooq

Developers that use version control systems can work in parallel with other developers and merge their versions afterwards. Sometimes these merges fail, demanding manual intervention to resolve conflicts. Some studies aim at analyzing the…

Software Engineering · Computer Science 2018-11-26 Tayane Silva Fernandes de Moura , Leonardo Gresta Paulino Murta

Process Mining is a branch of Data Science that aims to extract process-related information from event data contained in information systems, that is steadily increasing in amount. Many algorithms, and a general-purpose open source…

Databases · Computer Science 2019-08-01 Alessandro Berti

Open source software is a rapidly evolving center for distributed work, and understanding the characteristics of this work across its different contexts is vital for informing policy, economics, and the design of enabling software. The…

Software Engineering · Computer Science 2025-04-24 Wenyi Lu , Enock Kasaadah , S M Rakib Ul Karim , Matt Germonprez , Sean Goggins

Many software engineering studies or tasks rely on categorizing software engineering artifacts. In practice, this is done either by defining simple but often imprecise heuristics, or by manual labelling of the artifacts. Unfortunately,…

Software Engineering · Computer Science 2021-03-03 Hlib Babii , Julian Aron Prenner , Laurin Stricker , Anjan Karmakar , Andrea Janes , Romain Robbes

Current paper reports the advantages of the application of GitHub and LaTeX for the MSc thesis writing. The existing code-based program implemented in GitHub portal provides a great tool for scientists and students for data sharing and…

Computers and Society · Computer Science 2018-12-27 Polina Lemenkova

Open source software has an increasing importance in our modern society, providing basic services to other software systems and also supporting the rapid development of a variety of end-user applications. Recently, world-wide code sharing…

Software Engineering · Computer Science 2018-05-04 Thais Mombach , Marco Tulio Valente , Cuiting Chen , Magiel Bruntink , Gustavo Pinto

We make a case for "planetary computing" -- infrastructure to handle the ingestion, transformation, analysis and publication of global data products for furthering environmental science and enabling better informed policy-making. We draw on…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-06-04 Patrick Ferris , Michael Dales , Sadiq Jaffer , Amelia Holcomb , Eleanor Toye Scott , Thomas Swinfield , Alison Eyres , Andrew Balmford , David Coomes , Srinivasan Keshav , Anil Madhavapeddy

Research software refers to software development tools that accelerate discovery and simplifies access to digital infrastructures. However, although research software platforms can be built increasingly more innovative and powerful than…

Software Engineering · Computer Science 2018-12-27 Doug Mulholland , Paulo Alencar , Donald Cowan

Considerable scientific work involves locating, analyzing, systematizing, and synthesizing other publications. Its results end up in a paper's "background" section or in standalone articles, which include meta-analyses and systematic…

Digital Libraries · Computer Science 2023-12-05 Diomidis Spinellis