21 papers · ranked by Valyu relevance
Patrick T. Thompson, Christian D. Powell, Hunter N.B. Moseley
In recent years, United States federal funding agencies, including the National Institutes of Health (NIH) and the National Science Foundation (NSF), have implemented public access policies to make research supported by funding from these federal agencies freely available to the public. Enforcement is primarily through…
P. Travis Thompson, Christian D. Powell, Hunter N. B. Moseley, Yuji Zhang
'Yuji Zhang'] In recent years, United States federal funding agencies, including the National Institutes of Health (NIH) and the National Science Foundation (NSF), have implemented public access policies to make research supported by funding from these federal agencies freely available to the public. Enforcement is…
Serghei Mangul, Thiago Mosqueiro, Richard J. Abdill, Dat Duong + 13 more
'Keith Mitchell' 'Varuni Sarwal' 'Brian Hill' 'Jaqueline Brito' 'Russell Jared Littman' 'Benjamin Statz' 'Angela Ka-Mei Lam' 'Gargi Dayama' 'Laura Grieneisen' 'Lana S. Martin' 'Jonathan Flint' 'Eleazar Eskin' 'Ran Blekhman'] Developing new software tools for analysis of large-scale biological data is a key component of…
Caroline Jay, Robert Haines, Daniel S. Katz
Software now lies at the heart of scholarly research. Here we argue that as well as being important from a methodological perspective, software should, in many instances, be recognised as an output of research, equivalent to an academic paper. The article discusses the different roles that software may play in research…
Derek Groen, Xiaohu Guo, James A. Grogan, Ulf Schiller + 1 more
'James M. Osborne'] Academic software development practices often differ from those of commercial development settings, yet only limited research has been conducted on assessing software development practises in academia. Here we present a case study of software development practices in four open-source scientific…
Lucien Hinderling, Hannah S. Heil, Alfredo Rates, Philipp Seidel + 26 more
Smart microscopy is transforming life sciences by automating experimental imaging workflows and enabling real-time adaptation based on feedback from images and other data streams. This shift increases throughput, improves reproducibility, and expands the functional capabilities of microscopes. However, the current…
Héctor D. García-Verdugo, Cristian Román-Palacios, Francis Ouellette
Effective collaboration, essential for success in academic environments, often requires efficient team communication and access to a team-oriented digital infrastructure. Despite the significance of efficient and effective collaboration within the academy, a standardized and structured suite for collaboration remains…
Serghei Mangul, Thiago Mosqueiro, Dat Duong, Keith Mitchell + 12 more
Developing new software tools for analysis of large-scale, biological data is a key component of advancing computational, data-enabled research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the…
Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler + 40 more
Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon…
Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler + 40 more
Hartwig Anzt1,2,† , Felix Bach1,† , Stephan Druskat3,4,5,† , Frank Löer6,7,8,† , Axel Loewe9,,† , Bernhard Y. Renard10,11† , Gunnar Seemann12,13,† , Alexander Struck14,† , Elke Achhammer15, Piush Aggarwal16, Franziska Appel17, Michael Bader18, Lutz Brusch19, Christian Busse20, Gerasimos Chourdakis21, Piotr W.…
Teresa Gomez-Diaz, Tomas Recio
Background: Evaluation of the quality of research software is a challenging and relevant issue, still not sufficiently addressed by the scientific community. Methods: Our contribution begins by defining, precisely but widely enough, the notions of research software and of its authors followed by a study of the…
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…
Zhouming Wu, Dakota Murray
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 demands. Software, near-ubiquitous in modern research and traceable across the…
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…
Eva Maxfield Brown, Lindsey Schwartz, Richard Lewei Huang, Nicholas Weber
'Nicholas Weber'] Software is an important tool for scholarly work, but software produced for research is in many cases not easily identifiable or discoverable. A potential first step in linking research and software is software identification. In this paper we present two datasets to study the identification and…
Anne-Christin Hauschild, Roman Martin, Sabrina Celine Holst, Joachim Wienbeck + 1 more
'Joachim Wienbeck' 'Dominik Heider'] Title: Summary The long-lasting trend of medical informatics is to adapt novel technologies in the medical context. In particular, incorporating artificial intelligence to support clinical decision-making can significantly improve monitoring, diagnostics, and prognostics for the…
David W. Schindler, Benjamin Zapilko, Frank Krüger
Knowledge about the software used in scientific investigations is necessary for different reasons, including provenance of the results, measuring software impact to attribute developers, and bibliometric software citation analysis in general. Additionally, providing information about whether and how the software and…
Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree + 10 more
Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of…
Kai Li, Pei‐Ying Chen, Erjia Yan
The rise of software as a research object is mirrored in the increasing interests towards quantitative studies of scientific software. However, due to the inconsistent practice of citing software, most of the existing studies analyzing the impact of scientific software are based on identification of software name…
Authors not listed
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolated, traditional model of software development. The traditional approach often led to redundant engineering effort, high…
Authors not listed
Despite the promise of self-driving laboratories to accelerate discovery, their widespread implementation is hindered by prohibitive cost and technical complexity. We introduce BrickSDLab, a fully functional self-driving lab platform built entirely from LEGO® components, designed to bridge this accessibility gap.…