InVADo: Interactive Visual Analysis of Molecular Docking Data.

Molecular docking is a key technique in various fields like structural biology, medicinal chemistry, and biotechnology. It is widely used for virtual screening during drug discovery, computer-assisted drug design, and protein engineering. A general molecular docking process consists of the target and ligand selection, their preparation, and the docking process itself, followed by the evaluation of the results.

ARGUS: Visualization of AI-Assisted Task Guidance in AR.

The concept of augmented reality (AR) assistants has captured the human imagination for decades, becoming a staple of modern science fiction. To pursue this goal, it is necessary to develop artificial intelligence (AI)-based methods that simultaneously perceive the 3D environment, reason about physical tasks, and model the performer, all in real-time. Within this framework, a wide variety of sensors are needed to generate data across different modalities, such as audio, video, depth, speech, and time-of-flight.

Perception of Line Attributes for Visualization.

Line attributes such as width and dashing are commonly used to encode information. However, many questions on the perception of line attributes remain, such as how many levels of attribute variation can be distinguished or which line attributes are the preferred choices for which tasks. We conducted three studies to develop guidelines for using stylized lines to encode scalar data.

OmicsTIDE: interactive exploration of trends in multi-omics data.

Motivation: The increasing amount of data produced by omics technologies has enabled researchers to study phenomena across multiple omics layers. Besides data-driven analysis strategies, interactive visualization tools have been developed for a more transparent analysis. However, most state-of-the-art tools do not reconstruct the impact of a single omics layer on the integration result.

Visualization Techniques of Time-Oriented Data for the Comparison of Single Patients With Multiple Patients or Cohorts: Scoping Review.

Background: Visual analysis and data delivery in the form of visualizations are of great importance in health care, as such forms of presentation can reduce errors and improve care and can also help provide new insights into long-term disease progression. Information visualization and visual analytics also address the complexity of long-term, time-oriented patient data by reducing inherent complexity and facilitating a focus on underlying and hidden patterns.

Objective: This review aims to provide an overview of visualization techniques for time-oriented data in health care, supporting the comparison of patients.

The Role of Community Health Workers Within the Continuum of Services for HIV, Viral Hepatitis, and Other STIs Amongst Men Who Have Sex with Men in Europe.

Little is known about Community Health Workers (CHWs) who work in non-clinical settings to provide sexual health support around HIV, viral hepatitis, and other sexually transmitted infections (STIs) to men who have sex with men (MSM) in Europe and neighbouring countries. This article describes for the first time, who CHWs are, and how they contribute to the continuum of services for HIV, viral hepatitis, and other STIs amongst MSM. The first European Community Health Worker Online Survey (ECHOES) developed in the framework of the EU-funded ESTICOM project ( www.

Nonclinical Sexual Health Support for HIV, Viral Hepatitis, and Other Sexually Transmitted Infections in Gay, Bisexual, and Other Men Who Have Sex With Men: Protocol for a European Community Health Worker Online Survey (ECHOES).

Background: The term "community health worker" (CHW) can apply to a wide range of individuals providing health services and support for diverse populations. Very little is known about the role of CHWs in Europe working in nonclinical settings who promote sexual health and prevent HIV and other sexually transmitted infections (STIs) among gay, bisexual, and other men who have sex with men (MSM).

Objective: This paper describes the development and piloting of the first European Community Health Worker Online Survey (ECHOES) as part of the broader European Union-funded ESTICOM (European Surveys and Trainings to Improve MSM Community Health) project.

Molecular Graphics: Bridging Structural Biologists and Computer Scientists.

Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit.

Enabling Detailed, Biophysics-Based Skeletal Muscle Models on HPC Systems.

Realistic simulations of detailed, biophysics-based, multi-scale models often require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are typically designed to allow for high flexibility and generality in model development. Flexibility and model development, however, are often a limiting factor for large-scale simulations.

From Virtual Reality to Immersive Analytics in Bioinformatics.

Bioinformatics-related research produces huge heterogeneous amounts of data. This wealth of information includes data describing metabolic mechanisms and pathways, proteomics, transcriptomics, and metabolomics. Often, the visualization and exploration of related structural - usually molecular - data plays an important role in the aforementioned contexts.

Interactive Molecular Graphics for Augmented Reality Using HoloLens.

Immersive technologies like stereo rendering, virtual reality, or augmented reality (AR) are often used in the field of molecular visualisation. Modern, comparably lightweight and affordable AR headsets like Microsoft's HoloLens open up new possibilities for immersive analytics in molecular visualisation. A crucial factor for a comprehensive analysis of molecular data in AR is the rendering speed.

10 Years of MegaMol: The Pain and Gain of Creating Your Own Visualization Framework.

This article discusses our experience in creating MegaMol, an open-source visualization framework for large particle-based data.

Feature-Based Volumetric Terrain Generation and Decoration.

Two-dimensional height fields are the most common data structure used for storing and rendering of terrain in offline rendering and especially real-time computer graphics. By its very nature, a height field cannot store terrain structures with multiple vertical layers such as overhanging cliffs, caves, or arches. This restriction does not apply to volumetric data structures.

Molecular Surface Maps.

We present Molecular Surface Maps, a novel, view-independent, and concise representation for molecular surfaces. It transfers the well-known world map metaphor to molecular visualization. Our application maps the complex molecular surface to a simple 2D representation through a spherical intermediate, the Molecular Surface Globe.

MegaMol--A Prototyping Framework for Particle-Based Visualization.

Visualization applications nowadays not only face increasingly larger datasets, but have to solve increasingly complex research questions. They often require more than a single algorithm and consequently a software solution will exceed the possibilities of simple research prototypes. Well-established systems intended for such complex visual analysis purposes have usually been designed for classical, mesh-based graphics approaches.

Visualising intrinsic disorder and conformational variation in protein ensembles.

Intrinsically disordered regions (IDRs) in proteins are still not well understood, but are increasingly recognised as important in key biological functions, as well as in diseases. IDRs often confound experimental structure determination-however, they are present in many of the available 3D structures, where they exhibit a wide range of conformations, from ill-defined and highly flexible to well-defined upon binding to partner molecules, or upon post-translational modifications. Analysing such large conformational variations across ensembles of 3D structures can be complex and difficult; our goal in this paper is to improve this situation by augmenting traditional approaches (molecular graphics and principal components) with methods from human-computer interaction and information visualisation, especially parallel coordinates.

Visual analysis for space-time aggregation of biomolecular simulations.

Conducting a current through a nanopore allows for the analysis of molecules inside the pore because a current modulation caused by the electrostatic properties of the passing molecules can be measured. This mechanism shows great potential for DNA sequencing, as the four different nucleotide bases induce different current modulations. We present a visualisation approach to investigate this phenomenon in our simulations of DNA within a nanopore by combining state-of-the-art molecular visualisation with vector field illustration.

GPU-powered tools boost molecular visualization.

Recent advances in experimental structure determination provide a wealth of structural data on huge macromolecular assemblies such as the ribosome or viral capsids, available in public databases. Further structural models arise from reconstructions using symmetry orders or fitting crystal structures into low-resolution maps obtained by electron-microscopy or small angle X-ray scattering experiments. Visual inspection of these huge structures remains an important way of unravelling some of their secrets.

Interactive visualization of molecular surface dynamics.

Molecular dynamics simulations of proteins play a growing role in various fields such as pharmaceutical, biochemical and medical research. Accordingly, the need for high quality visualization of these protein systems raises. Highly interactive visualization techniques are especially needed for the analysis of time-dependent molecular simulations.