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Passive acoustic monitoring has become an important data collection method, yielding massive datasets replete with biological, environmental and anthropogenic information. Automated signal detectors and classifiers are needed to identify events within these datasets, such as the presence of species-specific sounds or anthropogenic noise. These automated methods, however, are rarely a complete substitute for expert analyst review. The ability to visualize and annotate acoustic events efficiently can enhance scientific insights from large, previously intractable datasets. A MATLAB-based graphical user interface, called DetEdit, was developed to accelerate the editing and annotating of automated detections from extensive acoustic datasets. This tool is highly-configurable and multipurpose, with uses ranging from annotation and classification of individual signals or signal-clusters and evaluation of signal properties, to identification of false detections and false positive rate estimation. DetEdit allows users to step through acoustic events, displaying a range of signal features, including time series of received levels, long-term spectral averages, time intervals between detections, and scatter plots of peak frequency, RMS, and peak-to-peak received levels. Additionally, it displays either individual, or averaged sound pressure waveforms, and power spectra within each acoustic event. These views simultaneously provide analysts with signal-level detail and encounter-level context. DetEdit creates datasets of signal labels for further analyses, such as training classifiers and quantifying occurrence, abundances, or trends. Although designed for evaluating underwater-recorded odontocete echolocation click detections, DetEdit can be adapted to almost any stereotyped impulsive signal. Our software package complements available tools for the bioacoustic community and is provided open source at https://github.com/MarineBioAcousticsRC/DetEdit.
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http://dx.doi.org/10.1371/journal.pcbi.1007598 | DOI Listing |
Bioinformatics
September 2025
Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit GBsC-CSIC, University of Zaragoza, Zaragoza, 50018, Spain.
Motivation: The stability of protein interfaces influences protein dynamics and unfolding cooperativity. Although in some cases the dynamics of proteins can be deduced from their topology, much of the stability of an interface is related to the complementarity of the interacting parts. It is also important to note that proteins that display non-cooperative unfolding cannot be rationally stabilized unless the regions that unfold first are known.
View Article and Find Full Text PDFPLoS One
September 2025
School of Computer Science, Georgia Institute of Technology, Atlanta, Georgia, United States of America.
Background: When analyzing cells in culture, assessing cell morphology (shape), confluency (density), and growth patterns are necessary for understanding cell health. These parameters are generally obtained by a skilled biologist inspecting light microscope images, but this can become very laborious for high-throughput applications. One way to speed up this process is by automating cell segmentation.
View Article and Find Full Text PDFbioRxiv
August 2025
Structural Biology Initiative, Advanced Science Research Center at the CUNY Graduate Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
NMR spectroscopy is applied across a wide range of scientific disciplines to derive chemical, structural, and dynamical information for a broad and diverse range of molecular systems. The utility of the technique depends on robust computational protocols for processing, visualizing, and analyzing a wide range of experimental data types and transforming the data into useful chemical and structural information. Here we introduce NMRFx, a novel software application that integrates and augments features of our existing NMRViewJ and NMRFx Processor applications.
View Article and Find Full Text PDFJ Chem Inf Model
September 2025
Bioproduct Institute, Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
We introduce , a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS.
View Article and Find Full Text PDFFront Plant Sci
August 2025
School of Fishery, Zhejiang Ocean University, Zhoushan, China.
The identification and visualization of functional elements within biological sequences offers visual presentation for biologists to integrate annotation, and also helps them to produce high-quality figures for publication. Although there are now some standalone tools that can perform this function, these tools generally lack flexibility and cannot meet personalized needs. Based on the advantages of R language in graphic display, we have developed an R package: BioVizSeq (CRAN: https://cran.
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