24 papers · ranked by Valyu relevance
Simon Bray, Matthias Bernt, Nicola Soranzo, Marius van den Beek + 7 more
There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. In…
Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo + 7 more
'Marius van den Beek' 'Bérénice Batut' 'Helena Rasche' 'Martin Čech' 'Peter J.A. Cock' 'Björn Grüning' 'Anton Nekrutenko'] There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing…
Julian Frattini, Michael Unterkalmsteiner, Davide Fucci, Daniel Méndez
'Daniel Méndez'] Abstract. Tools constitute an essential contribution to natural language processing for requirements engineering (NLP4RE) research. They are executable instruments that make research usable and applicable in practice. In this chapter, we first introduce a systematic classification of NLP4RE tools to…
Harsha Kathard, Rizwana Mallick, Tracey-lee Cloete, Anthea Hansen + 1 more
'Lehana Thabane'] Background Given the dire need for health and rehabilitation services internationally, exacerbated during the COVID-19 pandemic, there is a critical need to develop tools to support service delivery. This need is palpable in the Global South where tools developed in Eurocentric contexts are not always…
Bethany Laursen, Bianca Vienni-Baptista, Gabriele Bammer, Antonietta Di Giulio + 3 more
'Antonietta Di Giulio' 'Theres Paulsen' 'Melissa Robson-Williams' 'Sibylle Studer'] A growing number of inter- and transdisciplinary (ITD) toolkits provide methods, processes, concepts, heuristics, frameworks, and other resources for designing and implementing ITD research. A brief overview of the currently fragmented…
Oscar Nierstrasz, Tudor Gîrba
Moldable development supports decision-making by making software systems explainable. This is done by making it cheap to add numerous custom tools to your software, turning it into a live, explorable domain model. Based on several years of experience of applying moldable development to both open-source and industrial…
Meiying Qin, Jake Brawer, Brian Scassellati
Using human tools can significantly benefit robots in many application domains. Such ability would allow robots to solve problems that they were unable to without tools. However, robot tool use is a challenging task. Tool use was initially considered to be the ability that distinguishes human beings from other animals.…
Havan Yusuf, Alison Hillman, Jan Arend Stegeman, Angus Cameron + 1 more
'Skye Badger'] Introduction Digital clinical decision support (CDS) tools are of growing importance in supporting healthcare professionals in understanding complex clinical problems and arriving at decisions that improve patient outcomes. CDS tools are also increasingly used to improve antimicrobial stewardship (AMS)…
Zoë Goldsborough, Meredith Carlson, Leonie Reetz, Margaret C. Crofoot + 1 more
Percussive tool use for extractive foraging allows animals to access otherwise inaccessible resources and forage more efficiently, with potentially important implications for their fitness. The development of tool use proficiency has been well-documented in nut-cracking chimpanzees and robust capuchins, and in…
Zoë Goldsborough, Meredith K.W. Carlson, Leonie S. Reetz, Margaret C. Crofoot + 1 more
Percussive tool use for extractive foraging allows animals to access otherwise inaccessible resources and forage more efficiently, with potentially important implications for their fitness. The development of tool use proficiency has been well-documented in nut-cracking chimpanzees and robust capuchins, and in…
Paul P. Gardner
The development of accurate bioinformatic software tools is crucial for the effective analysis of complex biological data. This study examines the relationship between the academic department affiliations of authors and the accuracy of the bioinformatic tools they develop. By analyzing a corpus of previously…
Pierre R. Mercuriali, Carlos Hernandez Corbato, Geeske H.J. Langejans
To contribute to current discussions on the complexity of extinct and modern non-human and human primate tasks, we explore if ontologies are helpful as a means of representing tool tasks. We thus hope to help illuminate how primates approach tool tasks internally, such as breaking open a nutshell between a wooden anvil…
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…
Mark Marron
The practice of programming is undergoing a revolution with the introduction of AI assisted development (copilots) and the creation of new programming languages that are designed explicitly for tooling, analysis, and automation. Integrated Development Environments (IDEs) as they are currently conceptualized have not…
Authors not listed
The widespread adoption of open-source cheminformatics toolkits remains constrained by technical implementation barriers, including complex installation procedures, dependency management, and integration challenges. Here, we present Cheminformatics Microservice V3, a significant update to the existing platform that…
Cora Coleman, William G. Griswold, Nick Mitchell
Despite the increased importance of Cloud tooling, and many large-scale studies of Cloud users, research has yet to answer what tool modalities (e.g. CLI or web console) developers prefer. In formulating our studies, we quickly found that preference varies heavily based on the programming task at hand. To address this…
Eric Deutsch, Luis Mendoza, David Shteynberg, Michael Hoopmann + 3 more
The Trans-Proteomic Pipeline mass spectrometry data analysis suite has been in continual development and refinement since its first tools PeptideProphet and ProteinProphet were published twenty years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search…
Glaucia Melo
—The growing demand for software developers and the increasing development complexity have emphasized the need for support in software engineering projects. This is especially relevant in light of advancements in artificial intelligence, such as conversational systems. A significant contributor to the complexity of…
Elizabeth Bjarnason, Patrik Åberg, Nauman bin Ali
Context Software selection in large-scale software development continues to be ad hoc and ill-structured. Previous proposals for software component selection tend to be technology-specific and/or do not consider business or ecosystem concerns. Objective Our main aim is to develop an industrially relevant…
Erin Looney, Andre Buscariolli, Maria Yang, Geoffrey Raymond + 2 more
Hardware-based startups risk having longer times-to-market, deterring investment in critical fields such as cleantech, medical devices, and automation. We interviewed 55 leaders at hardware startups, mapped their development timelines, and found prototyping to be the longest development step (median of 19 weeks per…
Authors not listed
While virtual libraries of synthetically accessible compounds have exploded in size to many billions, our capacity to extract valuable drug leads from these vast databases remains limited by computational resources. To overcome this, we developed SLICE SMARTS and Logic In ChEmistry), a powerful new tool designed for…
Authors not listed
ThinkFactory 2025 was a virtual workshop jointly hosted by the Acceleration Consortium and CMAC to facilitate discussion on harmonizing and accelerating self-driving laboratories. The three-hour event brought together more than 50 participants for plenary and breakout discussion across four themed tracks: AI and…
Glaucia Melo, Luis Fernando Lins, Paulo Alencar, Don A. Cowan
—Software Development (SD) is remarkably dynamic and is critically dependent on the knowledge acquired by the project's software developers as the project progresses. Software developers need to understand large amounts of information related to the tasks at hand. This information (context) is often not explicit, as it…
VP Nagraj, Stephen D Turner, Neal Magee
Containerization enables portable, reproducible, and scalable scientific computing. However, container development, documentation, and deployment practices can vary widely, even within a single domain. Understanding patterns of how containers are implemented in real-world settings can inform community guidelines…