Related papers: PlayMolecule Viewer: a toolkit for the visualizati…
Objective: A proof-of-concept study aimed at designing and implementing VIEWER, a versatile toolkit for visual analytics of clinical data, and systematically evaluating its effectiveness across various clinical applications while gathering…
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…
Interactive data visualization is a major part of modern exploratory data analysis, with web-based technologies enabling a rich ecosystem of both specialized and general tools. However, current visualization tools often lack support for…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep…
Multiscale magnetic simulations, including micromagnetic and atomistic spin dynamics simulations, are widely used in the study of complex magnetic systems over a wide range of spatial and temporal scales. The advances in these simulation…
Visualizing spreadsheet content provides analytic insight and visual validation of large amounts of spreadsheet data. Oculus Excel Visualizer is a point and click data visualization experiment which directly visualizes Excel data and…
Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which…
Biologists are leading current research on genome characterization (sequencing, alignment, transcription), providing a huge quantity of raw data about many genome organisms. Extracting knowledge from this raw data is an important process…
Information visualization applications have become ubiquitous, in no small part thanks to the ease of wide distribution and deployment to users enabled by the web browser. Scientific visualization applications, relying on native code…
Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…
In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular…
In this paper we show how advanced visualization tools can help the researcher in investigating and extracting information from data. The focus is on VisIVO, a novel open source graphics application, which blends high performance…
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…
Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
This paper introduces Polyphorm, an interactive visualization and model fitting tool that provides a novel approach for investigating cosmological datasets. Through a fast computational simulation method inspired by the behavior of Physarum…
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…