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Item A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data(The Eurographics Association, 2019) Schäfer, Marco; Krone, Michael; Byska, Jan and Krone, Michael and Sommer, BjörnThe interactive visualization of molecular surfaces can help users to understand the dynamic behavior of proteins in molecular dynamics simulations. These simulations play an important role in biochemical and pharmaceutical research, e.g. in drug design. The efficient calculation of molecular surfaces in a fast and memory-saving way is a challenging task. For example, to gain a detailed understanding of complex diseases like Alzheimer, conformational changes and spatial interactions between molecules have to be investigated. Molecular surfaces, such as Solvent Excluded Surfaces (SES), are instrumental for identifying structures such as tunnels or cavities that critically influence transport processes and docking events, which might induce enzymatic reactions. Therefore, we developed a highly parallelized algorithm that exploits the massive computing power of modern graphics hardware. Our analytical algorithm is suitable for the real-time computation of dynamic SES based on many time steps, as it runs interactively on a single consumer GPU for more than 20 k atoms.Item A Web-based Visual Analytics Application for Biological Networks(The Eurographics Association, 2020) Krone, Michael; Dräger, Andreas; Cobanoglu, Ebru; Harke, Manuel Otto; Hoene, Miriam; Weigert, Cora; Lehmann, Rainer; ByÅ¡ka, Jan and Jänicke, StefanModern high-throughput methods enable rapidly obtaining transcriptomics data, which includes information about the expression rate of genes. The expression rates are usually given as fold change, which describes the over- or under-expression of each gene. Each gene can be part of one or more biological pathways. A pathway models the interactions between molecules in an organism that lead to a particular chemical change. Consequently, many applications in medical research need to analyze the impact of gene expression changes on the biological pathways of an organism. It allows concluding diseases or other conditions of the organism. We present a web-based visual analytics application that facilitates exploring the network of biological pathways corresponding to a given set of genes. The network is constructed from pathways derived from an external database. Users can interactively zoom and filter the network and get details on demand. Our application is currently work in progress and is developed in close collaboration with medical researchers. In subsequent steps, we strive to add more features, such as the ability to compare data from different individuals or to visualize time series data. Furthermore, we want to extend our application to visualize not just transcriptomics but multi-omics data.Item MolVa 2020: Frontmatter(The Eurographics Association, 2020) ByÅ¡ka, Jan; Krone, Michael; Sommer, Björn; ByÅ¡ka, Jan and Krone, Michael and Sommer, BjörnItem Evaluation of Visualizations for Interface Analysis of SPH(The Eurographics Association, 2014) Krone, Michael; Huber, Markus; Scharnowski, Katrin; Hirschler, Manuel; Kauker, Daniel; Reina, Guido; Nieken, Ulrich; Weiskopf, Daniel; Ertl, Thomas; N. Elmqvist and M. Hlawitschka and J. KennedyWe present a GPU-accelerated visualization application that employs methods from computer graphics and visualizationto analyze SPH simulations from the field of material science. To this end, we extract the isosurfacethat separates the stable phases in a fluid mixture via the kernel function that was used by the simulation. Ourapplication enables the analysis of the separation process using interactive 3D renderings of the data and an additionalline chart that shows the computed surface area over time. This also allows us to validate the correctnessof the simulation method, since the surface area can be compared to the power law that describes the change inarea over time. Furthermore, we compare the isosurface that is based on the simulation kernel with an establishedmethod to extract smooth high-quality SPH surfaces. The comparison focuses on demonstrating the applicabilityfor data analysis in the context of material science, which is based on the resulting surface area and how wellthe two phases are separated with respect to the original particles. The evaluation was carried out together withexperts in material science.Item Interactive Exploration of Polymer-Solvent Interactions(The Eurographics Association, 2011) Thomaß, Bertram; Walter, Jonathan; Krone, Michael; Hasse, Hans; Ertl, Thomas; Peter Eisert and Joachim Hornegger and Konrad PolthierThe interaction of three-dimensional linked hydrophilic polymers with surrounding solvents in time-dependent data sets is of great interest for domain experts and current research in molecular dynamics. These polymers are called hydrogels, and their most characteristic property is their swelling in aqueous solutions by absorbing the solvent. Their conformation transition can be studied by investigations of the interaction of the single polymer strand and the solvent directly around the polymer at an atomistic level. We present new visualization techniques to interactively study time-dependent data sets from molecular dynamics simulations-with special regard to polymer-solvent interactions like local concentrations and hydrogen bonds-as well as filtering methods to facilitate analysis. Such methods that visualize polymer-solvent interactions on a hydration shell around a polymer are not available in current tools and can greatly facilitate the visual analysis, which helps domain experts to extract additional information about hydrogel characteristics and gain new insights from the simulation results. While our visual analysis methods presented in this paper clearly facilitate the analysis of hydrogels and lead to new insight, the presented concepts are applicable to other domains like proteins or polymers in general that interact with solvents.Item Visual Analysis of Multivariate Intensive Care Surveillance Data(The Eurographics Association, 2020) Brich, Nicolas; Schulz, Christoph; Peter, Jörg; Klingert, Wilfried; Schenk, Martin; Weiskopf, Daniel; Krone, Michael; KozlÃková, Barbora and Krone, Michael and Smit, Noeska and Nieselt, Kay and Raidou, Renata GeorgiaWe present an approach for visual analysis of high-dimensional measurement data with varying sampling rates in the context of an experimental post-surgery study performed on a porcine surrogate model. The study aimed at identifying parameters suitable for diagnosing and prognosticating the volume state-a crucial and difficult task in intensive care medicine. In intensive care, most assessments not only depend on a single measurement but a plethora of mixed measurements over time. Even for trained experts, efficient and accurate analysis of such multivariate time-dependent data remains a challenging task. We present a linked-view post hoc visual analysis application that reduces data complexity by combining projection-based time curves for overview with small multiples for details on demand. Our approach supports not only the analysis of individual patients but also the analysis of ensembles by adapting existing techniques using non-parametric statistics. We evaluated the effectiveness and acceptance of our application through expert feedback with domain scientists from the surgical department using real-world data: the results show that our approach allows for detailed analysis of changes in patient state while also summarizing the temporal development of the overall condition. Furthermore, the medical experts believe that our method can be transferred from medical research to the clinical context, for example, to identify the early onset of a sepsis.Item MolVa 2021: Frontmatter(The Eurographics Association, 2021) ByÅ¡ka, Jan; Krone, Michael; Sommer, Björn; ByÅ¡ka, Jan and Krone, Michael and Sommer, BjörnItem Interactive CPU-based Ray Tracing of Solvent Excluded Surfaces(The Eurographics Association, 2019) Rau, Tobias; Zahn, Sebastian; Krone, Michael; Reina, Guido; Ertl, Thomas; KozlÃková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata GeorgiaDepictions of molecular surfaces such as the Solvent Excluded Surface (SES) can provide crucial insight into functional molecular properties, such as the molecule's potential to react. The interactive visualization of single and multiple molecule surfaces is essential for the data analysis by domain experts. Nowadays, the SES can be rendered at high frame rates using shader-based ray casting on the GPU. However, rendering large molecules or larger molecule complexes requires large amounts of memory that has the potential to exceed the memory limitations of current hardware. Here we show that rendering using CPU ray tracing also reaches interactive frame rates without hard limitations to memory. In our results large molecule complexes can be rendered with only the precomputation of each individual SES, and no further involved representation or transformation. Additionally, we provide advanced visualization techniques like ambient occlusion opacity mapping (AOOM) to enhance the comprehensibility of the molecular structure. CPU ray tracing not only provides very high image quality and global illumination, which is beneficial for the perception of spatial structures, it also opens up the possibility to visualize larger data sets and to render on any HPC cluster. Our results demonstrate that simple instancing of geometry keeps the memory consumption for rendering large molecule complexes low, so the examination of much larger data is also possible.Item VisGap 2020: Frontmatter(The Eurographics Association, 2020) Gillmann, Christina; Krone, Michael; Reina, Guido; Wischgoll, Thomas; Gillmann, Christina and Krone, Michael and Reina, Guido and Wischgoll, ThomasItem visMOP - A Visual Analytics Approach for Multi-omics Pathways(The Eurographics Association and John Wiley & Sons Ltd., 2023) Brich, Nicolas; Schacherer, Nadine; Hoene, Miriam; Weigert, Cora; Lehmann, Rainer; Krone, Michael; Bujack, Roxana; Archambault, Daniel; Schreck, TobiasWe present an approach for the visual analysis of multi-omics data obtained using high-throughput methods. The term ''omics'' denotes measurements of different types of biologically relevant molecules, like the products of gene transcription (transcriptomics) or the abundance of proteins (proteomics). Current popular visualization approaches often only support analyzing each of these omics separately. This, however, disregards the interconnectedness of different biologically relevant molecules and processes. Consequently, it describes the actual events in the organism suboptimally or only partially. Our visual analytics approach for multi-omics data provides a comprehensive overview and details-on-demand by integrating the different omics types in multiple linked views. To give an overview, we map the measurements to known biological pathways and use a combination of a clustered network visualization, glyphs, and interactive filtering. To ensure the effectiveness and utility of our approach, we designed it in close collaboration with domain experts and assessed it using an exemplary workflow with real-world transcriptomics, proteomics, and lipidomics measurements from mice.