Article
Computer Science, Interdisciplinary Applications
Carlos Erazo Ramirez, Yusuf Sermet, Frank Molkenthin, Ibrahim Demir
Summary: HydroLang is an open-source computational web framework for hydrology and water resources research and education. It employs client-side web technologies and standards to carry out various routines aimed at acquiring, managing, transforming, analyzing, and visualizing hydrological datasets. The framework consists of four major modules and has been demonstrated through two case studies. Its modular architecture and open-source nature allow for easy customization and encourage community involvement for future enhancements.
ENVIRONMENTAL MODELLING & SOFTWARE
(2022)
Article
Biochemistry & Molecular Biology
Phillip Seitzer, Bryson Bennett, Eugene Melamud
Summary: The manuscript describes a major update to the MAVEN software program, MAVEN2, which now supports LC-MS/MS analysis of metabolomics and lipidomics samples. The update includes algorithms for MS/MS spectral matching and efficient search of large-scale fragmentation libraries. The study also introduces a novel in-silico lipidomics library and compares it to existing libraries.
Article
Computer Science, Interdisciplinary Applications
Nirbhaya Shaji, Florbela Nunes, M. Ines Rocha, Elsa Ferreira Gomes, Helena Castro
Summary: This report introduces a graphical user interface called MigraR, which translates the coordinate positions of moving cells into measurable parameters of cell migration, and plots cell trajectories and migration metrics. By simplifying the data analysis process, this interface helps cell biologists without data analysis experience to quantify and visualize cell migration datasets.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Computer Science, Interdisciplinary Applications
Chris Kelly, Julian Fawkes, Rachel Habermehl, Davi de Ferreyro Monticelli, Naomi Zimmerman
Summary: This paper presents the PLUME Dashboard, a free and open-source software package designed for mobile air quality monitoring. It provides real-time data display, peak identification, baseline subtraction, and alerts based on wind direction and vehicle speed. The functionality of the software is demonstrated using real-world data collected in Canada.
ENVIRONMENTAL MODELLING & SOFTWARE
(2023)
Article
Chemistry, Multidisciplinary
Mamdouh Alenezi
Summary: The evolution of software systems and understanding their internal quality is crucial in software engineering. This study analyzed the evolution of object-oriented open-source software systems in terms of size, internal quality metrics, showing significant differences among systems in LOC, significant correlations between internal quality metrics, and positive effects of complexity and inheritance on LOC. Coupling and Cohesion did not show significant effects on LOC.
APPLIED SCIENCES-BASEL
(2021)
Article
Chemistry, Analytical
Sean M. Colby, Christine H. Chang, Jessica L. Bade, Jamie R. Nunez, Madison R. Blumer, Daniel J. Orton, Kent J. Bloodsworth, Ernesto S. Nakayasu, Richard D. Smith, Yehia M. Ibrahim, Ryan S. Renslow, Thomas O. Metz
Summary: DEIMoS is a Python tool for high-dimensional mass spectrometry data analysis that provides features such as feature detection, feature alignment, and calibration. It operates on N-dimensional data and can improve detection sensitivity and data alignment confidence while reducing artifacts in tandem mass spectra. The demonstration with metabolomics data shows the advantages of using DEIMoS in each data processing step.
ANALYTICAL CHEMISTRY
(2022)
Article
Engineering, Biomedical
Ina Vernikouskaya, Dagmar Bertsche, Wolfgang Rottbauer, Volker Rasche
Summary: With the increase in availability and variety of imaging modalities, new methods of intraoperative support have become available for all kinds of interventions. The introduced software system provides a common foundation for rapid prototyping of new approaches in the field of XR fluoroscopic guidance, with basic functionality including data import, projection geometry calculation, rigid 3D-3D registration, and template matching-based tracking algorithms.
INTERNATIONAL JOURNAL OF COMPUTER ASSISTED RADIOLOGY AND SURGERY
(2021)
Article
Statistics & Probability
Nascif Abousalh-Neto, Meijian Guan, Ruth Hummel
Summary: JMP is a commercial software designed for interactive data analysis, featuring a high-level, visual interface suitable for teaching and model building. It is also extensible, allowing the embedding and deployment to open-source environments. This paper explores use cases illustrating how JMP users can benefit from open-source software while still leveraging JMP's streamlined interface and robust capabilities.
Article
Psychology, Mathematical
Kristoffer Geyer, David A. Ellis, Heather Shaw, Brittany I. Davidson
Summary: Psychological science has been studying the impact of new technology on individuals and society for years, but self-report methods have limitations in capturing nuances of human-computer interaction. Commercial apps offer objectivity, but lack flexibility for researchers looking for an 'open' platform.
BEHAVIOR RESEARCH METHODS
(2022)
Review
Biochemical Research Methods
Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simon, Kay Faaberg, Emily Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski, Sook Jung, Kelly Lager, Dorrie Main, Monica Poelchau, Risharde Ramnath, Peter Richter, Joe West, Stephen Ficklin
Summary: Online, open access biological knowledge databases are central repositories for research communities, facing challenges in growth, complexity and data integration. Shared infrastructure frameworks and Tripal platform address development burden, interoperability and sustainability.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Computer Science, Software Engineering
Damian A. Tamburri, Fabio Palomba, Rick Kazman
Summary: Software engineering success relies on balancing distance, culture, global engineering practices and more. This paper introduces an automated approach, CodeFace4Smells, to identify four community smell types. A large-scale empirical study on 60 open-source communities reveals that community smells are highly diffused in open-source and perceived by developers as significant issues for software community evolution.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Computer Science, Software Engineering
Georgia M. Kapitsaki, Georgia Charalambous
Summary: This paper introduces findOSSLicense, a license recommender that helps users choose the appropriate open source license for their software under creation. The recommendation process is based on a hybrid recommender that considers user needs and system flexibility, and involves analysis of existing open source licenses.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Clinical Neurology
Jackson N. Cagle, Kara A. Johnson, Leonardo Almeida, Joshua K. Wong, Adolfo Ramirez-Zamora, Michael S. Okun, Kelly D. Foote, Coralie de Hemptinne
Summary: The BRAVO platform is a user-friendly tool developed for in-depth visualization and analysis of brain signals and DBS data, which is of great importance for clinicians and researchers.
Article
Computer Science, Information Systems
Marc Oriol, Carlos Mueller, Jordi Marco, Pablo Fernandez, Xavier Franch, Antonio Ruiz-Cortes
Summary: Recent surveys show that the use of Open Source Software (OSS) is increasingly important for organizations. However, choosing the right OSS or contributing to its development is a complex task. There is a lack of useful OSSECO analysis tools for potential adopters or contributors.
INTERNET OF THINGS
(2023)
Article
Pathology
Young-gon Kim, Man Jin Kim, Jee-Soo Lee, Jung Ae Lee, Ji Yun Song, Sung Im Cho, Sung-Sup Park, Moon-Woo Seong
Summary: Despite the prevalence of next-generation sequencing, the development of tools for Sanger sequencing has lagged behind. SnackVar, a novel software, can accurately identify various types of variants and may provide a cost-effective option for clinical laboratories performing Sanger sequencing.
JOURNAL OF MOLECULAR DIAGNOSTICS
(2021)
