25 papers · ranked by Valyu relevance
Pietro Braione, Giovanni Denaro, Luca Gugliemo, Elson Kurian + 2 more
Context. Since the eighties, the combination of program analysis techniques has been increasingly recognized as a promising approach to overcome the limitations of standalone methods. While individual techniques, based on either static or dynamic analysis, address important challenges in software dependability, their…
Michael Pradel, Cristian Cadar, Islem Bouzenia
Numerous software analysis tools exist today, yet applying them to diverse open-source projects remains challenging due to environment setup, dependency resolution, and tool configuration. LLM-based agents offer a potential solution, yet no prior work has systematically studied their effectiveness on the specific task…
Flash Sheridan
Static source code analysis is a powerful tool for finding and fixing bugs when deployed properly; it is, however, all too easy to deploy it in a way that looks good superficially, but which misses important defects, shows many false positives, and brings the tool into disrepute. This article is a guide to the process…
Katalin Ferenc, Konrad Otto, Francisco Gomes de Oliveira Neto, Marcela Dávila López + 2 more
Software quality in computational tools impacts research output in a variety of scientific disciplines. Biology is one of these fields, especially for High Throughput Sequencing (HTS) data, such tools play an important role. This study therefore characterises the overall quality of a selection of tools which are…
Ra’Fat Al-Msie’deen
Reverse engineering tools are required to handle the complexity of software products and the unique requirements of many different tasks, like software analysis and visualization. Thus, reverse engineering tools should adapt to a variety of cases. Static Code Analysis (SCA) is a technique for analyzing and exploring…
David Schindler, Felix Bensmann, Stefan Dietze, Frank Krüger + 1 more
Science across all disciplines has become increasingly data-driven, leading to additional needs with respect to software for collecting, processing and analysing data. Thus, transparency about software used as part of the scientific process is crucial to understand provenance of individual research data and insights…
Muhammad Laiq, Nauman bin Ali, Jürgen Börstler, Emelie Engström
Software analytics (SA) is frequently proposed as a tool to support practitioners in software engineering (SE) tasks. We have observed that several secondary studies on SA have been published. Some of these studies have overlapping aims and some have even been published in the same calendar year. This presents an…
Jones Yeboah, Saheed Popoola
open-source projects Authors: ['Jones Yeboah' 'Saheed Popoola'] This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting, reproduction on…
Sena Isik, Gunes Unal
Rodent behavioral analysis is a major specialization in experimental psychology and behavioral neuroscience. Rodents display a wide range of species-specific behaviors, not only in their natural habitats but also under behavioral testing in controlled laboratory conditions. Detecting and categorizing these different…
Md Shafiqur Rahman Jabin, Ding Pan
Objective To identify a subset of software issues occurring in daily Swedish healthcare practice and devise a set of local solutions to overcome the challenges. Methods A sample of 46 incident reports was collected from one of Sweden's national incident reporting repositories, ranging from June 2019 to December 2021.…
Eva Martín del Pico, Josep Lluis Gelpi, Salvador Capella-Gutiérrez
Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is challenging to reproduce and verify most of the time. It could be undocumented, opaque, may even contain unknown errors that affect the outcome, or be directly unavailable, and impossible to…
Yitong Ma, Yaron Antebi
Flow cytometry enables quantitative measurements of fluorescence in single cells. The technique was widely used for immunology to identify populations with different surface protein markers. More recently, the usage of flow cytometry has been extended to additional readouts, including intracellular proteins and…
Ishara Devendra, Chaman Wijesiriwardana, Prasad Wimalaratne
—Software security visualization is an interdisciplinary field that combines the technical complexity of cybersecurity, including threat intelligence and compliance monitoring, with visual analytics, transforming complex security data into easily digestible visual formats. As software systems get more complex and the…
Aws A. Magableh, Hana’a Bani Ata, Ahmad A. Saifan, Adnan Rawashdeh
Nowadays, large numbers of organizations may opt for Aspect-Oriented Programming (AOP), which is an enhancement to Object-Oriented Programming (OOP). This is due to the addition of a number of concepts that have assisted in the production of more flexible and reusable components. One of the most important elements…
Sophie Lathouwers, Yujie Liu, Vadim Zaytsev
In software engineering, models are used for many different things. In this paper, we focus on program verification, where we use models to reason about the correctness of systems. There are many different types of program verification techniques which provide different correctness guarantees. We investigate the domain…
Mikaela Cashman, Myra B. Cohen, Alexis L. Marsh, Robert W. Cottingham
Biology is a quest; an ongoing inquiry about the nature of life. How do the different forms of life interact? What makes up an ecosystem? How does a tiny bacterium work? To answer these questions biologists turn increasingly to sophisticated computational tools. Many of these tools are highly configurable, allowing…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…
Authors not listed
Step-by-step thinking is essential in all domains of chemical sciences and engineering. While machine learning tools are broadly used, algorithms that automate reasoning are far less common. We elaborate on seven categories of human reasoning activities and connect each to applications in chemical science and…
Xinliang Zheng, Yi Xie
In order to further promote the standardization of seismic performance design of bridge structures, one must ensure the quality of bridge design and improve design efficiency. First, based on the basic principle of the probabilistic pushover method, the randomness of the structural pushover curve is attributed to the…
Raquel Lopez-Rios de Castro, Alejandro Santana-Bonilla, Robert M. Ziolek, Christian D. Lorenz
Molecular dynamics simulations have become an essential tool in the study of soft matter and biological macromolecules. The large amount of high-dimensional data produced by such simulations does not immediately elucidate the atomistic mechanisms that underlie complex materials and molecular processes. Analysis of…
Jeremy Li, Alex Rubinsteyn, Sergey Feldman, Timothy O’Donnell + 18 more
Scientific computing has become a central component of modern scientific discovery. Yet many computational tools are developed by small, specialized teams under incentives that encourage the release of rapidly prototyped tooling without commensurate attention to engineering concerns, including performance and…
Oliver Rodríguez
Here, I introduce Soft Potato, an open source electrochemical simulator and toolkit that contains typical electrochemical equations and simulations to aid researchers streamline their data analysis when dealing with large datasets. As examples, I show here how to use it to calculate steady state voltammograms from…
Authors not listed
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms…
Authors not listed
Traditional and non-classical machine learning models for solid-state structure prediction have predominantly relied on compositional features (derived from properties of constituent elements) to predict the existence of structure and its properties. However, the lack of structural information can be a source of…
Authors not listed
Self-driving laboratories (SDLs) promise accelerated scientific discovery and product development by closing the loop between robotic execution and AI/ML-driven decision making. In practice, however, SDL orchestration remains fragmented; workflows are typically encoded as laboratory-specific scripts or bespoke…