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Summary: The advent of Web-based tools that assist in the analysis and visualization of macromolecules require application programming interfaces (APIs) designed for modern web frameworks. To this end, we have developed a Node.js module…
Over the past decade, deep learning (DL) research in computer vision has been growing rapidly, with many advances in DL-based image analysis methods for biomedical problems. In this work, we introduce MMV_Im2Im, a new open-source python…
Backgr: Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology.…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…
In modern computing, RDBMS are great to store different types of data. To a developer, one of the major objectives is to provide a very low cost and easy to use solution to an existing problem. While commercial databases are more easy to…
Digital biomarkers (DBMs) are a growing field and increasingly tested in the therapeutic areas of psychiatric and neurodegenerative disorders. Meanwhile, isolated silos of knowledge of audiovisual DBMs use in industry, academia, and clinics…
Summary: In anticipation of the individualized proteomics era and the need to integrate knowledge from disease studies, we have augmented our peptide identification software RAId DbS to take into account annotated single amino acid…
Data sharing is a key factor for ensuring reproducibility and transparency of scientific experiments, and neuroimaging is no exception. The vast heterogeneity of data formats and imaging modalities utilised in the field makes it a very…
The field of structural bioinformatics has seen significant advances with the use of Molecular Dynamics (MD) simulations of biological systems. The MD methodology has allowed to explain and discover molecular mechanisms in a wide range of…
The increasing interest in developing Artificial Intelligence applications in the medical domain, suffers from the lack of high-quality data set, mainly due to privacy-related issues. In addition, the recent increase in Vision Language…
Can web-based image processing and visualization tools easily integrate into existing websites without significant time and effort? Our Boostlet.js library addresses this challenge by providing an open-source, JavaScript-based web framework…
We introduce 3DB: an extendable, unified framework for testing and debugging vision models using photorealistic simulation. We demonstrate, through a wide range of use cases, that 3DB allows users to discover vulnerabilities in computer…
AI models for drug discovery and chemical literature mining must interpret molecular images and generate outputs consistent with 3D geometry and stereochemistry. Most molecular language models rely on strings or graphs, while…
Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current…
Sophisticated visualization tools are essential for the presentation and exploration of human neuroimaging data. While two-dimensional orthogonal views of neuroimaging data are conventionally used to display activity and statistical…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
For several decades, chemical knowledge has been published in written text, and there have been many attempts to make it accessible, for example, by transforming such natural language text to a structured format. Although the discovered…
Massive Multi-Omics Microbiome Database (M3DB) is a data warehousing and analytics solution designed to handle diverse, complex, and unprecedented volumes of sequence and taxonomic classification data obtained in a typical microbiome…