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Visualization of Protein Dynamics and Systems Biology

  • Molecular dynamics simulations play a major role in biologica, pharmaceutcal und medical research. In particular, the analysis of protein properties in different solvents is of interest for many processes. The simulation produces large, time-dependent data sets - so-called trajectories. The visualization of these trajectories enables the interactive investigation of the simulated properties. Furthermore, the automated extraction of freatures from the raw data and the fitting visualization of these features is important. Here, the abstract illustration of solvent properties plays a major role. In order to ensure an interactive analysis and high-quality visualizations, parallel algorithms are particularly developed. These algorithms take advantage of the features of current multi-core CPUs and programmable GPUs.
  • In systems biology, correlations play an important role and visualizations are a great way to make these visible. Hence, the focus of this work lies in the visualization and the interactive exploration of data from this environment. The data to be visualized will be generated by in silico simulations. Special emphasis is placed on the development of methods, which are carried out on graphic processing units (GPUs). The parallel architecture of GPUs is of interest, because it has the potential to allow high speed-ups of computations.

    The aim of this work is to develop a mesoscopic simulation of selected intra-cellular and extra-cellular processes and visualizations which are able to represent the simulation results in meaningful ways. In particular, cellular signal transduction processes will be studied.
Signal concentration of a virtual cell
Signal concentration of a virtual cell
Microscopic-like image for comparison with wet lab experiment
Microscopic-like image for comparison with wet lab experiment

Projects

Publications

2014

Visual Analysis for Space-Time Aggregation of Biomolecular Simulations
Ertl, Thomas; Krone, Michael; Kesselheim, Stefan; Scharnowski, Katrin; Reina, Guido; Holm, Christian: Visual Analysis for Space-Time Aggregation of Biomolecular Simulations. In: Faraday Discussions (2014) (to appear).
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Visualising Intrinsic Disorder and Conformational Variation in Protein Ensembles
Heinrich, Julian; Krone, Michael; Weiskopf, Daniel; O'Donoghue, Seán: Visualising Intrinsic Disorder and Conformational Variation in Protein Ensembles. In: Faraday Discussions (2014) (to appear).
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Line Integral Convolution for Real-Time Illustration of Molecular Surface Shape and Salient Regions
Lawonn, Kai; Krone, Michael; Ertl, Thomas; Preim, Bernhard: Line Integral Convolution for Real-Time Illustration of Molecular Surface Shape and Salient Regions. In: Computer Graphics Forum: No. 3 (2014) (to appear).
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Comparative Visualization of Molecular Surfaces Using Deformable Models
Scharnowski, Katrin; Krone, Michael; Reina, Guido; Kulschewski, Tobias; Pleiss, Jürgen; Ertl, Thomas: Comparative Visualization of Molecular Surfaces Using Deformable Models. In: Computer Graphics Forum: No. 3 (2014) (to appear).
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Visual Analysis of Dynamic Protein Cavities and Binding Sites
Krone, Michael; Kauker, Daniel; Reina, Guido; Ertl, Thomas: Visual Analysis of Dynamic Protein Cavities and Binding Sites. In: IEEE PacificVis - Visualization Notes, 2014.
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2013

Atomistic Visualization of Mesoscopic Whole-Cell Simulations using Ray-Casted Instancing
Falk, Martin; Krone, Michael; Ertl, Thomas: Atomistic Visualization of Mesoscopic Whole-Cell Simulations using Ray-Casted Instancing. In: Computer Graphics Forum: No. 8 (2013), pp. 195-206.
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iVUN: interactive Visualization of Uncertain biochemical reaction Networks
Vehlow, Corinna; Weiskopf, Daniel; Hasenauer, Jan; Kramer, Andrei; Radde, Nicole; Theis, Fabian J.: iVUN: interactive Visualization of Uncertain biochemical reaction Networks. In: BMC Bioinformatics (2013), p. S2.
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Visualization and mesoscopic simulation in systems biology
Falk, Martin: Visualization and mesoscopic simulation in systems biology. Diss., Visualization Research Center, Universität Stuttgart, 2013.
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2012

An eQTL biological data visualization challenge and approaches from the visualization community
Bartlett, Christopher; Cheong, Soo; Hou, Liping; Paquette, Jesse; Lum, Pek; Jaeger, Guenter; Battke, Florian; Vehlow, Corinna; Heinrich, Julian; Nieselt, Kay; Sakai, Ryo; Aerts, Jan; Ray, William: An eQTL biological data visualization challenge and approaches from the visualization community. In: BMC Bioinformatics: No. 13 (2012), pp. 1-16.
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iHAT: interactive Hierarchical Aggregation Table for Genetic Association Data
Heinrich, Julian; Vehlow, Corinna; Battke, Florian; Jaeger, Guenter; Weiskopf, Daniel; Nieselt, Kay: iHAT: interactive Hierarchical Aggregation Table for Genetic Association Data. In: BMC Bioinformatics: No. 13 (2012), pp. 1-12.
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Atomistic Visualization of Mesoscopic Whole-Cell Simulations
Falk, Martin; Krone, Michael; Ertl, Thomas: Atomistic Visualization of Mesoscopic Whole-Cell Simulations. In: EG Workshop on Visual Computing for Biology and Medicine (VCBM), pp. 123-130, 2012.
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Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories
Krone, Michael; Stone, John E.; Ertl, Thomas; Schulten, Klaus: Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. In: EuroVis 2012 Short Papers, pp. 67-71, 2012.
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Uncertainty-Aware Visual Analysis of Biochemical Reaction Networks
Vehlow, Corinna; Hasenauer, Jan; Kramer, Andrei; Heinrich, Julian; Radde, Nicole; Allgöwer, Frank; Weiskopf, Daniel: Uncertainty-Aware Visual Analysis of Biochemical Reaction Networks. In: IEEE Symposium on Biological Data Visualization, pp. 91-98, 2012.
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2011

Interactive Exploration of Protein Cavities
Krone, Michael; Falk, Martin; Rehm, Sascha; Pleiss, Jürgen; Ertl, Thomas: Interactive Exploration of Protein Cavities. In: Computer Graphics Forum: No. 3 (2011), pp. 673-682.
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Visualization of Anisotropic Contact Potentials within Protein Structures
Vehlow, Corinna; Preim, Bernhard; Lappe, Michael: Visualization of Anisotropic Contact Potentials within Protein Structures. In: IEEE Symposium on Biological Data Visualization (2011), pp. 31-38.
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Modeling and Visualization of Receptor Clustering on the Cellular Membrane
Falk, Martin; Daub, Markus; Schneider, Guido; Ertl, Thomas: Modeling and Visualization of Receptor Clustering on the Cellular Membrane. In: IEEE Symposium on Biological Data Visualization (BioVis 2011), pp. 9-15, 2011.
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Parallelized Agent-based Simulation on CPU and Graphics Hardware for Spatial and Stochastic Models in Biology
Falk, Martin; Klann, Michael; Ott, Michael; Koeppl, Heinz; Ertl, Thomas: Parallelized Agent-based Simulation on CPU and Graphics Hardware for Spatial and Stochastic Models in Biology. In: International Conference on Computational Methods in Systems Biology (CMSB 2011), pp. 73-82, 2011.
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Hasenauer, Jan; Heinrich, Julian; Doszczak, Malgorzata; Scheurich, Peter; Allgöwer, Frank: Visualization methods and support vector machines as tools for determining markers in models of heterogeneous populations: Proapoptotic signaling as a case study. In: Proceedings Workshop on Computational Systems Biology, pp. 61-64, 2011.
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BiCluster Viewer: A Visualization Tool for Analyzing Gene Expression Data
Heinrich, Julian; Seifert, Julian; Burch, Michael; Weiskopf, Daniel: BiCluster Viewer: A Visualization Tool for Analyzing Gene Expression Data. In: Proceedings of International Symposium on Visual Computing (ISVC), p. 641–652, 2011.
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Parallel Contour-Buildup Algorithm for the Molecular Surface
Krone, Michael; Grottel, Sebastian; Ertl, Thomas: Parallel Contour-Buildup Algorithm for the Molecular Surface. In: Proceedings of IEEE Symposium on Biological Data Visualization (biovis'11), pp. 17-22, 2011.
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iHAT: interactive Hierarchical Aggregation Table
Vehlow, Corinna; Heinrich, Julian; Battke, Florian; Weiskopf, Daniel; Nieselt, Kay: iHAT: interactive Hierarchical Aggregation Table. In: IEEE Symposium on Biological Data Visualization, pp. 63-69, 2011.
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2010

Interactive Image-Space Volume Visualization for Dynamic Particle Simulations
Falk, Martin; Grottel, Sebastian; Ertl, Thomas: Interactive Image-Space Volume Visualization for Dynamic Particle Simulations. In: Proceedings of The Annual SIGRAD Conference, pp. 35-43, 2010.
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3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations
Falk, Martin; Klann, Michael; Reuss, Matthias; Ertl, Thomas: 3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI '10), pp. 1301-1304, 2010.
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Parallel Computation and Interactive Visualization of Time-varying Solvent Excluded Surfaces
Krone, Michael; Dachsbacher, Carsten; Ertl, Thomas: Parallel Computation and Interactive Visualization of Time-varying Solvent Excluded Surfaces. In: International Conference On Bioinformatics and Computational Biology, pp. 402-405, 2010.
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2009

Visualization of Signal Transduction Processes in the Crowded Environment of the Cell
Falk, Martin; Klann, Michael; Reuss, Matthias; Ertl, Thomas: Visualization of Signal Transduction Processes in the Crowded Environment of the Cell. In: IEEE Pacific Visualization Symposium (PacificVis 2009), pp. 169-176, 2009.
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2008

GPU-based Visualisation of Protein Secondary Structure
Krone, Michael; Bidmon, Katrin; Ertl, Thomas: GPU-based Visualisation of Protein Secondary Structure. In: Proceedings of TP.CG'08, pp. 115-122, 2008.
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