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At least 19 recordsLinked to original sources
PubMed1978

Computer-graphic representation of mandibular movements in three dimensions. Part I. The horizontal plane.

A computer-graphics simulation was developed to display the effects of mandibular movement patterns of both the maxillary and mandibular teeth in the occlusal plane. The many parameters affecting mandibular movement patterns may be varied selectively. The effects of these parameters on the pathways of movement described by the supporting cusps during occlusion can be graphically observed in the horizontal plane.

Art↗
PubMed1978

Interactive computer surface graphics approach to study of the active site of bovine trypsin.

A descriptive medium for the presentation of protein structure has been developed and used to evaluate the structure of the active site of bovine trypsin (EC 3.4.21.4). This technique, involving advanced computer graphics technology, permits the facile display of a representation of the molecular surface of proteins of known structure and employs color to code the structural or chemical features of this surface. Benzamidine derivatives were inserted into the benzamidine-binding site of trypsin and the binary inhibitor-trypsin complex was evaluated by using the computer-generated structure. On the basis of qualitative assessments of the contribution of electrostatic and hydrophobic forces to the binding energy associated with complex formation, we made predictions concerning the effects of interaction of benzamidine substituents and amino acid side chains upon the binding energy associated with inhibitor-protein binding. The computer display of the molecular surfaces of the binary complex of substituted benzamidines and trypsin permitted unique insight into the identity and chemical properties of the atoms that participate at the interface of the molecular surfaces of the inhibitor and the protein. The computer-generated molecular surface display can potentially be combined with quantitative definition of the physical forces involved in the interaction of molecular surfaces. This technology should facilitate the study of the structure-activity relationship of substrates, inhibitors, and drugs that bind to proteins of known three-dimensional structure.

Animals↗
PubMed1976

Morphological correlates of synaptic transmission in lamprey spinal cord.

The dye Procion brown was used to identify in the light and electron microscope, synaptic contacts made between monosynaptically coupled neurons in the lamprey spinal cord whose synaptic interaction had been recorded. Synaptic contacts were made on different dendrites of the postsynaptic cell at different distances from the soma. Some of the contacts were made on dentritic spines and some on the smooth shaft of the dentrites. Serial sections through synaptic contacts made on dendritic processess of the postsynaptic cells were used for three-dimensional reconstruction of the synapses using computer graphics techniques. The computer reconstructions and detailed examination of the serial EM micrographs revealed the large proliferation of membrane involved in making these en passant synapses as well as the morphological changes due to stimulation of the presynaptic axon. These changes include depletion of synaptic vesicles and formation of complex vesicles and synaptic cisternae. Besides chemical synaptic contacts, four electrotonic contacts were located, confirming the mixed electrochemical synaptic response recorded from the postsynaptic cell. The mean quantum content was estimated and compared with the estimate of the available transmitter pool, assuming the quantal release hypothesis applies at these synapses. The total transmitter pool was estimated by counting all synaptic vesicles in all synaptic contacts. It was estimated that about 6% of the total transmitter pool is available for release at these synapses. This compares with less than 1% at the neuromuscular junction and about 20% at sympathetic synapses. These results support the hypothesis that synaptic vesicles may be recycled as described by Heuser and Reese (22) at the neuromuscular junction. Ongoing studies are investigating the effect on a variety of synaptic junctions to stimulation for different periods of time of presynaptic axons. The methods described in this study can also be used to test the models of synaptic interaction on dendritic trees described by Rall (39) and Jack and Redman (24).

Action Potentials↗
PubMed1978

Computer assisted unit data acquistion/reduction.

A computer system for unit data acquisition and reduction (CAUDAR) is presented. This system digitally processes uninterrupted, continuous unit data with attention to waveform detail. Several units in a multiunit field are recognized by evaluation of spike waveform and amplitude. High-speed computer graphics provides almost instantaneous figures of good quality for illustration. The system affords a great economy of the user's time because the computer performs all data processing.

Computers↗
PubMed1977

Serial electrocardiograms in hypertensive cardiovascular disease.

A graphic method for depicting serial changes in electrocardiograms is described and demonstrated for patients being treated in an antihypertension clinic. For these patients, the diagnostic categories, normal, left ventricular hypertrophy, and biventricular hypertrophy, are of primary interest. For each electrocardiogram, 14 measurements are used to compute posterior probabilities for each of the three categories. A triangular grid is used to plot each set of probabilities for an electrocardiogram as one point, which by its position in the triangle can be related to the three categories simultaneously. Points representing successive electrocardiograms can be plotted in the same triangle, giving a pattern of change with time. This pattern of change has been corroborated with associated clinical information on a number of patients. This display, which can be produced quickly and efficiently on a computer graphics terminal, should be considered as a possible tool in evaluating the status of individual hypertensive patients in terms of increase or decrease of ventricular hypertrophy and the efficacy of therapeutic measures.

Aged↗
PubMed1977

Morphanalysis of craniofacial dysharmony.

The first stage in the morphanalysis of craniofacial dysharmony involves induction. In this process, individual analytic morphograms are combined to form analytic histograms, which in turn are connected to form analytic histomorphograms, which provide three-dimensional statements about the variation in craniofacial structures in a population. The second stage involves deduction, in which the analytic morphograms of a particular patient are compared with appropriate analytic histomorphograms, so that a diagnosis of the three-dimensional nature of the dysharmony can be made. Craniofacial morphanalysis is performed manually in small scale enquiries but the methods have been converted to computer-graphic technology for large-scale studies. A clinical morphanalysis service is currently conducted and a standard reference atlas is being prepared.

Adolescent↗
PubMed2025

monarchr: an R package for querying biomedical knowledge graphs.

SUMMARY: Biomedical knowledge graphs (KGs) aggregate and provide a wealth of information, linking genes and their variants, diseases, phenotypes, and much more. While these data are available in raw and API-hosted form, to date, functionality for working with KGs in the R programming language has been limited. We introduce monarchr, a package for querying and manipulating KG data. Support for the expansive Monarch Initiative KG is built in, and monarchr can accommodate any KG in the Knowledge Graph eXchange (KGX) format. This tidy-inspired interface offers researchers an intuitive, iterative approach to querying and visualizing KG data. AVAILABILITY AND IMPLEMENTATION: Source code, documentation, and installation instructions are available at https://github.com/monarch-initiative/monarchr.

Software↗
PubMed2026

Treemble: a graphical tool to generate Newick strings from phylogenetic tree images.

SUMMARY: Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable Newick format. There are, thus, thousands of published trees in the scientific literature that are unavailable for follow-up analyses, comparisons, and supertree construction. Experts can easily read such diagrams, but the manual construction of a Newick string from a diagram is laborious, error-prone, and time-consuming. Previous attempts to semi-automate the reading of tree images relied on image processing techniques. These often encounter difficulties as typical published tree diagrams contain various graphical elements and annotations that overlap the branches, such as error bars on internal nodes. Here we introduce Treemble, a user-friendly desktop application for generating Newick strings from tree images. The user simply clicks to mark node locations, assisted by a deep learning-based node detection tool, and Treemble algorithmically assembles the tree from the node coordinates alone. Treemble also facilitates the automatic reading of tip name labels and can be used for both rectangular and circular trees. AVAILABILITY AND IMPLEMENTATION: Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org. Source code is available at github.com/John-Allard/Treemble. The trained node detection model is available at huggingface.co/John-Allard/treemble-1.

Phylogeny↗
PubMed1976

Comparison of graphical and computerized methods for calculating binding parameters for two strongly bound drugs to human serum albumin.

The determination of drug-protein binding parameters (n's and K's) can lead to important information on the required therapeutic dosage regimen and possible clinical complications associated with competitive displacement of one drug by a concurrently administered agent. Graphical and computer estimates of the data are often incorrectly formulated, and and seldom are adequate data obtained at low binding ratios. Commonly used graphical procedures, inadequately formulated computer methods, and a statistically correct computer method were used to compare results obtained from a circular dichroic examination of dicumarol-human serum albumin and fenoprofen-human serum albumin interactions. Literature binding constants for dicumarol-albumin range from 1 X 10(5) to 30 times that figure, and it is shown here that a wide range in parameter estimates may be obtained depending on the method of data analysis. The parameter estimates in the case of fenoprofen-albumin are even more variable.

Binding Sites↗
PubMed2004

EnsMart: a generic system for fast and flexible access to biological data.

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets.

Animals↗
PubMed2026

phylobar: an R package for multiresolution compositional barplots in omics studies.

SUMMARY: Stacked barplots, though widely used in microbiome studies, can obscure important patterns in microbiome data. They omit rare taxa and can mask shifts that emerge at finer taxonomic levels. To address this issue, we introduce phylobar, an R package that interactively links stacked barplots with overview phylogenetic or taxonomic hierarchies. The interface allows users to collapse or expand subtrees, paint color palettes interactively, and search for specific taxa. This allows comparison across taxonomic resolutions that are hidden in static overviews. phylobar works with any omics data with hierarchical organization, including cell type hierarchies, as we demonstrate in a case study of immune cell composition in COVID-19 patients. AVAILABILITY AND IMPLEMENTATION: phylobar is available as an R package on GitHub. It uses the htmlwidgets library to link interactive D3 visualizations with R. The interactive plots can be embedded within R Markdown or Quarto notebooks, and views can be exported as vector graphics files. The package is open source and documented at https://mkdiro-O.github.io/phylobar.

Software↗
PubMed2026

Plotgardener App: a graphical interface for publication-ready genomic visualization.

SUMMARY: Plotgardener is an R package used for generating high-quality genomic visualizations. Despite its broad range of functions and versatility, its reliance on code presents a barrier for many potential users. To address this, we developed a macOS desktop application version of Plotgardener that enables users to create publication-ready genomic plots with no programming experience. The application employs a modular architecture comprising an Electron.js backend, a React frontend, and a Python parser that dynamically analyzes the Plotgardener package to ensure interface fields remain synchronized with package updates. By lowering the technical barrier to advanced genomic visualization, the Plotgardener desktop application broadens access to powerful visualization workflows for researchers and clinicians. AVAILABILITY: The current release of the Plotgardener App is an open source macOS desktop application built with Electron (Node.js), featuring a React frontend and a Python-based parser. The download link is available at https://phanstiellab.github.io/plotgardener/articles/guides/plotgardenerApp.html and on Zenodo (doi: https://doi.org/10.5281/zenodo.21684228). The source code is hosted on GitHub at https://github.com/rishabhsvemuri/ThePlotgardenerApp.

Genomics↗
PubMed2025

CSGL: chemical synthesis graph learning for molecule representation.

MOTIVATION: Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. RESULTS: Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. AVAILABILITY AND IMPLEMENTATION: https://github.com/li-2023/CSGL.

Machine Learning↗
PubMed2025

Tsbrowse: an interactive browser for ancestral recombination graphs.

SUMMARY: Ancestral recombination graphs (ARGs) represent the interwoven paths of genetic ancestry of a set of recombining sequences. The ability to capture the evolutionary history of samples makes ARGs valuable in a wide range of applications in population and statistical genetics. ARG-based approaches are increasingly becoming a part of genetic data analysis pipelines due to breakthroughs enabling ARG inference at biobank-scale. However, there is a lack of visualization tools, which are crucial for validating inferences and generating hypotheses. We present tsbrowse, an open-source, web-based Python application for the interactive visualization of the fundamental building blocks of ARGs, i.e. nodes, edges and mutations. We demonstrate the application of tsbrowse to various data sources and scenarios, and highlight its key features of browsability along the genome, user interactivity, and scalability to very large sample sizes. AVAILABILITY AND IMPLEMENTATION: Tsbrowse is installed as a Python package from PyPI (https://pypi.org/project/tsbrowse/), while a development version is maintained at https://github.com/tskit-dev/tsbrowse. Documentation is available at https://tskit.dev/tsbrowse/docs/. Source code is archived on Zenodo with DOI, https://doi.org/10.5281/zenodo.15683039.

Software↗
PubMed2026

Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.

SUMMARY: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks. Main features include an expressive way to specify visual encodings, and filtering of 3D genome structures based on genomic semantics and spatial aspects. Uchimata is designed to be highly integratable with biological tooling available in Python. AVAILABILITY AND IMPLEMENTATION: Uchimata is released under the MIT License. The Javascript library is available on NPM, while the widget is available as a Python package hosted on PyPI. The source code for both is available publicly on Github (https://github.com/hms-dbmi/uchimata and https://github.com/hms-dbmi/uchimata-py) and Zenodo (https://doi.org/10.5281/zenodo.17831959 and https://doi.org/10.5281/zenodo.17832045). The documentation with examples is hosted at https://hms-dbmi.github.io/uchimata/.

Software↗
PubMed2026

PangyPlot: multi-scale interactive visualization of pangenome variation graphs.

SUMMARY: Pangenome variation graphs integrate multiple samples into a unified representation, mitigating the reference bias inherent to linear genomes. However, these graphs can be large and structurally complex. Existing visualization tools are each confined to a fixed scale of resolution, requiring researchers to switch between multiple tools to examine variation at different levels of detail. PangyPlot is an interactive pangenome browser designed for multi-scale exploration of reference variation graphs from full chromosome to nucleotide-level sequence segments. PangyPlot anchors navigation to linear reference coordinates, organizes variation into hierarchical bubble structures, and uses a force-directed layout engine for automatic node arrangement. AVAILABILITY AND IMPLEMENTATION: An instance preloaded with data is available at https://pangyplot.research.sickkids.ca. Source code and documentation are openly available at https://github.com/strug-hub/pangyplot under the MIT License.

Software↗