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Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.
Biodivers Data J
January 2025
Laboratório de Computação Avançada para Biodiversidade (COMBIO). Museu Paraense Emílio Goeldi, Belém, Brazil Laboratório de Computação Avançada para Biodiversidade (COMBIO). Museu Paraense Emílio Goeldi Belém Brazil.
Background: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.
New Information: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise.
Immersive virtual reality (VR) environments are a powerful tool to explore cognitive processes ranging from memory and navigation to visual processing and decision making-and to do so in a naturalistic yet controlled setting. As such, they have been employed across different species, and by a diverse range of research groups. Unfortunately, designing and implementing behavioral tasks in such environments often proves complicated.
View Article and Find Full Text PDFA Digital Tool for Clinical Evidence-Driven Guideline Development by Studying Properties of Trial Eligible and Ineligible Populations: Development and Usability Study.
J Med Internet Res
January 2025
Advanced Care Research Centre, Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom.
Background: Clinical guideline development preferentially relies on evidence from randomized controlled trials (RCTs). RCTs are gold-standard methods to evaluate the efficacy of treatments with the highest internal validity but limited external validity, in the sense that their findings may not always be applicable to or generalizable to clinical populations or population characteristics. The external validity of RCTs for the clinical population is constrained by the lack of tailored epidemiological data analysis designed for this purpose due to data governance, consistency of disease or condition definitions, and reduplicated effort in analysis code.
View Article and Find Full Text PDFOPTO: Automated Optimization for Solid-State NMR Spectroscopy.
J Am Chem Soc
January 2025
Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
NMR spectroscopy presents boundless opportunities for understanding the structure, dynamics, and function for a broad range of scientific applications. Solid-state NMR (SSNMR), in particular, provides novel insights into biological and material systems that are not amenable to other approaches. However, a major bottleneck is the extent of user training and the difficulty of obtaining reproducible, high-quality experimental results, especially for the sophisticated multidimensional pulse sequences that are essential to provide site-resolved measurements in large biomolecules.
View Article and Find Full Text PDFOpen Chrono-Morph viewer: visualize big bioimage time series containing heterogeneous volumes.
Bioinformatics
January 2025
Department of Biomedical Engineering, Stevens Institute of Technology, Hoboken, NJ 07030, USA.
Summary: Time-lapse 3D imaging is fundamental for studying biological processes but requires software able to handle terabytes of voxel data. Although many multidimensional viewing applications exist, they mostly lack support for heterogeneous voxel counts, datatypes, and modalities in a single timeline. Open Chrono-Morph Viewer provides a straightforward graphical user interface to quickly investigate multi-timescale datasets represented as separate volume files in the common NRRD format for compatibility between toolchains.
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