Related papers: PlayMolecule Viewer: a toolkit for the visualizati…
In today's world of big data, computational analysis has become a key driver of biomedical research. Recent exponential growth in the volume of available omics data has reshaped the landscape of contemporary biology, creating demand for a…
Deep Learning (DL) developers come from different backgrounds, e.g., medicine, genomics, finance, and computer science. To create a DL model, they must learn and use high-level programming languages (e.g., Python), thus needing to handle…
In the present work we have selected a collection of statistical and mathematical tools useful for the exploration of multivariate data and we present them in a form that is meant to be particularly accessible to a classically trained…
Multilayer relationships among entities and information about entities must be accompanied by the means to analyze, visualize, and obtain insights from such data. We present open-source software (muxViz) that contains a collection of…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
We present Digital Collections Explorer, a web-based, open-source exploratory search platform that leverages CLIP (Contrastive Language-Image Pre-training) for enhanced visual discovery of digital collections. Our Digital Collections…
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…
WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schr\"odinger and Liouville-von Neumann-equations in one or more…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
We present VLMEvalKit: an open-source toolkit for evaluating large multi-modality models based on PyTorch. The toolkit aims to provide a user-friendly and comprehensive framework for researchers and developers to evaluate existing…
Every molecule ever synthesised can be drawn as a 2D skeletal diagram, yet in modern property prediction this universally available representation has received less focus in favour of molecular graphs, 3D conformers, or billion-parameter…
Converting peptide sequences into useful representations for downstream analysis is a common step in computational modeling and cheminformatics. Furthermore, peptide drugs (e.g., Semaglutide, Degarelix) often take advantage of the diverse…
Scientific data visualization plays a crucial role in research by enabling the direct display of complex information and assisting researchers in identifying implicit patterns. Despite its importance, the use of Large Language Models (LLMs)…
We present the Virtual Beamline (VBL) application, an interactive web-based platform for visualizing high-intensity laser-matter interactions using particle-in-cell (PIC) simulations, with future potential for experimental data…
Hillview is a distributed spreadsheet for browsing very large datasets that cannot be handled by a single machine. As a spreadsheet, Hillview provides a high degree of interactivity that permits data analysts to explore information quickly…
A java-based graphical tool for drawing Feynman diagrams is presented. It differs from similar existing tools in various respects. For example, it is based on models, consisting of particles (lines) and (optionally) vertices, each of which…