vis.uni-stuttgart.deVisualization 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.
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Projects
- SFB 716 "Dynamic simulation of systems with large particle numbers"
Subproject D.4 "Interactive Visualization of Protein-Solvent Systems' Dynamic and Complex Properties"
The aim of this subproject is to develop new visualization approaches for the interactive exploration of protein-solvent-systems. Particular attention is paid to the specific properties of the solvent, as these can not be analyzed adequately with available visualization tools. - Center Systems Biology Project Area A Compartimentation
Subproject A4 "4D-spatial-temporal dynamics in cellular signal transduction processes: Modeling, computational analysis and visualization" (completed December 2009)
Publications
2013
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Vehlow, Corinna; Hasenauer, Jan; Theis, Fabian J.; Weiskopf, Daniel: Visualizing Edge-Edge Relations in Graphs. In: Proceedings of IEEE Pacific Visualization Symposium (2013) (to appear).
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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) (to appear).
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2012
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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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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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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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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, 2012.
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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
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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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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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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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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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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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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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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
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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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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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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
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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
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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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