Visualisation in bio-informatics

The development of modern acquisition technologies for biological processes comes along with a vast amount of data. This data may result from experimental measurements as well as simulations of processes of single molecules, the expression of genes, or models of complete populations. Analysis of such data is challenging, as it is oftentimes fraught with uncertainty and errors, heterogeneous, and high-dimensional. Therefore, modern and adequate visualization techniques are essential ingredients for the analysis of such data.



Visual analysis for gene expression data


Visualization of gene expression values of genes of the yeast Saccharomyces cerevisiae that are influenced by the cell cycle. Due to the coloring of gene profiles based on a statistical parameter, typical periodic patterns emerge.

DNA carries the genetic information of individuals, build of two linear strands of nucleic acids. A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. Based on modern high-throughput methods, by now many genomes of different organisms have been decoded completely.

Gene expression is the process by which information from a gene is transcriped into mRNA and is used in the synthesis functional gene products (translation), such as proteins. Proteins are involved in almost all functions of cells. Gene expression is a highly complex, precisely regulated process that allows the cell to react dynamically on environmental changes as well as its own changing needs. The mechanism of gene expression therefore operates as on/off-switch to control which genes of the cell are expressed, but also as volume control to increase or decrease the degree of gene expression.

During the last years, different technologies have been developed that facilitate the parallel measurement of gene expression of mRNA and proteins on genome-wide scale. Common technologies are microarrays and modern sequences techniques, which facilitate the analysis of gene expression of many different genes for different experimental conditions at a time. The aim of such measurements is oftentimes the comparison of gene expression between different cell types, e.g., the analysis of histoid-specific genes, the expression in healthy and diseased tissue, the influence of environmental changes on the gene expression, or the dependence of gene expression on the stage of the cell cycle. As a result, we obtain expression data for several thousands of genes under numerous different conditions, those manual analysis is not feasible due to the huge amount of data.

 



Visual Analysis of genome wide association studies (GWAS)


Using iHAT to find sequence positions correlated with virulence in 15 sequences of the neuraminidase protein of H5N1 influenza virus samples. The virulence is represented as meta information of the sequences.

In the search for single-nucleotide polymorphisms (SNPs), genome wide association studies have become an important technique for the identification of associations between genotype and phenotype of a diverse set of sequence-based data. Genome wide association studies (GWAS) are used to study the variation of genes between individuals (the genotype), and their association with a variety of complex traits (the phenotype), e.g. diabetes, heart disease, or arthritis. GWAS have become an established method to alleviate the identification of genetic risk factors of diseases, as they make use of recent technologies that allow a rapid and cost-effective analysis of genetic differences. The huge amount of data produced by GWAS implies a great challenge for data analysis and visualization. The identification of dependencies and correlations calls for adequate visual representations of the data as well as suitable interactions that enable a change of the view onto the data. The latter comprises focus and context techniques as well as techniques to show relevant or hide irrelevant information, e.g., the aggregation of information that can be meaningfully hierarchically organized.

We developed the tool iHAT as visual analytics tool for genome wide association studies. iHAT supports the visualization of multiple sequence alignments, associated metadata, and hierarchical clusterings.

 



Visual analysis of biological networks

Networks play a central role in the investigation of organisms. They are oftentimes used to model processes in biological systems, to represent interactions between and dependencies of biological entities, such as genes, transcripts, proteins, or metabolites. One mayor application domain of network-based analysis and visualization is the field of systems biology that tries to gain a holistic understanding of transformation and signaling processes in living organisms. Based on the ever increasing knowledge in biology, such networks become more and more complex and bigger. To tackle this problem of complexity and size and to facilitate the analysis and interpretation of such complex interaction networks, the development of suitable and appropriate visualization is indispensable.

For the visualization of biochemical reaction networks, usually standard graph drawing approaches are not suitable as they do not respect the conventions of the bioscience community. For that reason, lots of attention has been devoted to the development of automatic graph drawing methods for such networks. As a result, miscellaneous layout algorithms and a graphical notation standard (Systems Biology Graphical Notation) have been developed. Layout algorithms for biological networks need to evaluate different meta-information, e.g., the cell compartments within that the reactions take place.

Further challenges for the visualization of such networks are the temporal component as well as uncertainty of measured or simulated meta-data describing the biochemical reactions. The temporal component may be related to either the change structure of the graph, as e.g., some reactions occur only at particular time points during the cell cycle, or to the properties of reactions/interactions that may change, e.g., the expression level of genes. Uncertainties of contained within the meta-data describing elements or relations within the graph, such as expression values of genes (nodes) or fluxes between chemical species (edges), should be highlighted visually. We developed a the tool iVUN for the visual analysis of uncertain biochemical reaction networks.



Publikationen

  1. Krone, Michael ; Frieß, Florian ; Scharnowski, Katrin ; Reina, Guido ; Fademrecht, Silvia ; Kulschewski, Tobias ; Pleiss, Jürgen ; Ertl, Thomas: Molecular Surface Maps. In: IEEE Transactions on Visualization and Computer Graphics (Proceedings of the Scientific Visualization 2016), IEEE Transactions on Visualization and Computer Graphics (Proceedings of the Scientific Visualization 2016). Bd. 23 (2017a), Nr. 1
  2. Alharbi, Naif ; Alharbi, Mohammad ; Martinez, Xavier ; Krone, Michael ; Rose, Alexander ; Baaden, Marc ; Laramee, Robert S. ; Chavent, Matthieu: Molecular Visualization of Computational Biology Data: A Survey of Surveys. In: EuroVis 2017 Short Papers, EuroVis 2017 Short Papers, 2017
  3. Krone, Michael ; Reina, Guido ; Zahn, Sebastian ; Tremel, Tina ; Bahnmüller, Carsten ; Ertl, Thomas: Implicit Sphere Shadow Maps. In: IEEE PacificVis - Visualization Notes, IEEE PacificVis - Visualization Notes. Bd. 4, 2017b
  4. Hermosilla, Pedro ; Krone, Michael ; Guallar, Victor ; Vázquez, Pere-Pau ; Vinacua, Àlvar ; Ropinski, Timo: Interactive GPU-based Generation of Solvent Excluded Surfaces. In: The Visual Computer (Proceedings of CGI’2017), The Visual Computer (Proceedings of CGI’2017). Bd. 33, Springer (2017), Nr. 6
  5. Sancho-Chavarria, Lilliana ; Beck, Fabian ; Mata-Montero, Erick ; Weiskopf, Daniel: Visual Comparison of Biological Taxonomies: A Task Characterization. In: EuroVis 2016 Posters, EuroVis 2016 Posters, 2016. — Rezensiertes Poster
  6. Müller, Christoph ; Krone, Michael ; Scharnowski, Katrin ; Reina, Guido ; Ertl, Thomas: An Evaluation of the Utility of Large High-Resolution Displays for Comparative Scientific Visualisation. In: International Journal of Software and Informatics, International Journal of Software and Informatics. Bd. 9 (2016), Nr. 3
  7. Krone, Michael ; Kozlíková, Barbora ; Lindow, Norbert ; Baaden, Marc ; Baum, Daniel ; Parulek, Julius ; Hege, Hans-Christian ; Viola, Ivan: Visual Analysis of Biomolecular Cavities: State of the Art. In: Computer Graphics Forum, Computer Graphics Forum. Bd. 35, Whiley (2016), Nr. 3
  8. Mwalongo, Finian ; Krone, Michael ; Becher, Michael ; Reina, Guido ; Ertl, Thomas: GPU-based Remote Visualization of Dynamic Molecular Data on the Web. In: Graphical Models, Graphical Models. Bd. 88, Elsevier (2016)
  9. Kozlíková, Barbora ; Krone, Michael ; Falk, Martin ; Lindow, Norbert ; Baaden, Marc ; Baum, Daniel ; Viola, Ivan ; Parulek, Julius ; u. a.: Visualization of Molecular Structure: State of the Art Revisited. In: Computer Graphics Forum, Computer Graphics Forum. (2016)
  10. Vehlow, Corinna ; Kao, David P. ; Bristow, Michael R. ; Hunter, Lawrence E. ; Weiskopf, Daniel ; Görg, Carsten: Visual analysis of biological data-knowledge networks. In: BMC Bioinformatics, BMC Bioinformatics. Bd. 16 (2015), Nr. 135
  11. Kozlíková, Barbora ; Krone, Michael ; Lindow, Norbert ; Falk, Martin ; Baaden, Marc ; Baum, Daniel ; Viola, Ivan ; Parulek, Julius ; u. a.: Visualization of Molecular Structure: State of the Art. In: Eurographics Conference on Visualization (EuroVis) - STARs, Eurographics Conference on Visualization (EuroVis) - STARs, 2015
  12. Lawonn, Kai ; Krone, Michael ; Ertl, Thomas ; Preim, Bernhard: On the Reproducibility of Line Integral Convolution for Real-Time Illustration of Molecular Surface Shape and Salient Regions. In: EuroRV3: EuroVis Workshop on Reproducibility, Verification, and Validation in Visualization, EuroRV3: EuroVis Workshop on Reproducibility, Verification, and Validation in Visualization. Bd. 3, 2015. — Rezensiertes Abstract
  13. Grottel, Sebastian ; Krone, Michael ; Müller, Christoph ; Reina, Guido ; Ertl, Thomas: MegaMol – A Prototyping Framework for Particle-based Visualization. In: IEEE Transactions on Visualization and Computer Graphics, IEEE Transactions on Visualization and Computer Graphics. Bd. 21, IEEE (2015), Nr. 2
  14. Rau, Benjamin ; Frieß, Florian ; Krone, Michael ; Müller, Christoph ; Ertl, Thomas: Enhancing Visualization of Molecular Simulations using Sonification. In: International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR). Bd. 1 : IEEE, 2015
  15. Mwalongo, Finian ; Krone, Michael ; Becher, Michael ; Reina, Guido ; Ertl, Thomas: Remote Visualization of Dynamic Molecular Data using WebGL. In: ACM ; ACM (Hrsg.) ; ACM (Hrsg.): International Conference on 3D Web Technology (Web3D), International Conference on 3D Web Technology (Web3D). Bd. 20, 2015
  16. Müller, Christoph ; Krone, Michael ; Scharnowski, Katrin ; Reina, Guido ; Ertl, Thomas: On the Utility of Large High-Resolution Displays for Comparative Scientific Visualisation. In: International Symposium on Visual Information Communication and Interaction (VINCI), International Symposium on Visual Information Communication and Interaction (VINCI). Bd. 8 : ACM, 2015
  17. Scharnowski, Katrin ; Krone, Michael ; Reina, Guido ; Ertl, Thomas: On the Reproducibility of our Biomolecular Visualization. In: Aigner, W. ; Rosenthal, P. ; Scheidegger, C. ; Aigner, W. ; Rosenthal, P. ; Scheidegger, C. (Hrsg.) ; Aigner, W. ; Rosenthal, P. ; Scheidegger, C. (Hrsg.): EuroRV3: EuroVis Workshop on Reproducibility, Verification, and Validation in Visualization, EuroRV3: EuroVis Workshop on Reproducibility, Verification, and Validation in Visualization. Bd. 3 : The Eurographics Association, 2015. — Rezensiertes Abstract
  18. Krone, Michael ; Müller, Christoph ; Ertl, Thomas ; Kauker, Daniel ; Silva, Augusto Cravo ; Salsa, Diana ; Gräber, Manuel ; Kallert, Manuela: Remote Rendering and User Interaction on Mobile Devices for Scientific Visualization. In: International Symposium on Visual Information Communication and Interaction (VINCI), International Symposium on Visual Information Communication and Interaction (VINCI). Bd. 8 : ACM, 2015
  19. Krone, Michael: Interactive Visual Analysis of Biomolecular Simulations, Universität Stuttgart, PhD dissertation, 2015
  20. Ertl, Thomas ; Krone, Michael ; Kesselheim, Stefan ; Scharnowski, Katrin ; Reina, Guido ; Holm, Christian: Visual Analysis for Space-Time Aggregation of Biomolecular Simulations. In: for Chemistry, R. S. (Hrsg.) Faraday Discussions, Faraday Discussions. Bd. 169 (2014)
  21. Scharnowski, Katrin ; Krone, Michael ; Reina, Guido ; Kulschewski, Tobias ; Pleiss, Jürgen ; Ertl, Thomas: Comparative Visualization of Molecular Surfaces Using Deformable Models. In: Computer Graphics Forum, Computer Graphics Forum. Bd. 33 (2014), Nr. 3
  22. Heinrich, Julian ; Krone, Michael ; Weiskopf, Daniel ; O’Donoghue, Seán: Visualising Intrinsic Disorder and Conformational Variation in Protein Ensembles. In: for Chemistry, R. S. (Hrsg.) Faraday Discussions, Faraday Discussions. Bd. 169 (2014)
  23. 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, Computer Graphics Forum. Bd. 33 (2014), Nr. 3
  24. Krone, Michael ; Kauker, Daniel ; Reina, Guido ; Ertl, Thomas: Visual Analysis of Dynamic Protein Cavities and Binding Sites. In: IEEE PacificVis - Visualization Notes, IEEE PacificVis - Visualization Notes. Bd. 1, 2014
  25. Mwalongo, Finian ; Krone, Michael ; Karch, Grzegorz Karol ; Becher, Michael ; Reina, Guido ; Ertl, Thomas: Visualization of Molecular Structures using State-of-the-Art Techniques in WebGL. In: International Conference on 3D Web Technology (Web3D’14), International Conference on 3D Web Technology (Web3D’14). Bd. 19, 2014
  26. Vehlow, Corinna ; Hasenauer, Jan ; Kramer, Andrei ; Raue, Andreas ; Hug, Sabine ; Timmer, Jens ; Radde, Nicole ; Theis, Fabian J. ; u. a.: iVUN: interactive Visualization of Uncertain biochemical reaction Networks. In: Bioinformatics, B. (Hrsg.) BMC Bioinformatics, BMC Bioinformatics. Bd. 14 (2013)
  27. Falk, Martin: Visualization and mesoscopic simulation in systems biology, Visualization Research Center, Universität Stuttgart, PhD dissertation, 2013
  28. Falk, Martin ; Krone, Michael ; Ertl, Thomas: Atomistic Visualization of Mesoscopic Whole-Cell Simulations using Ray-Casted Instancing. In: Computer Graphics Forum, Computer Graphics Forum. Bd. 32 (2013), Nr. 8
  29. Falk, Martin ; Krone, Michael ; Ertl, Thomas: Atomistic Visualization of Mesoscopic Whole-Cell Simulations. In: EG Workshop on Visual Computing for Biology and Medicine (VCBM), EG Workshop on Visual Computing for Biology and Medicine (VCBM), 2012
  30. 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, EuroVis 2012 Short Papers. Bd. 1, 2012
  31. Bartlett, Christopher ; Cheong, Soo ; Hou, Liping ; Paquette, Jesse ; Lum, Pek ; Jaeger, Guenter ; Battke, Florian ; Vehlow, Corinna ; u. a.: An eQTL biological data visualization challenge and approaches from the visualization community. In: Bioinformatics, B. (Hrsg.) BMC Bioinformatics, BMC Bioinformatics. Bd. 2012 (2012), Nr. 13
  32. Vehlow, Corinna ; Hasenauer, Jan ; Kramer, Andrei ; Heinrich, Julian ; Radde, Nicole ; Allgöwer, Frank ; Weiskopf, Daniel: Uncertainty-Aware Visual Analysis of Biochemical Reaction Networks. In: IEEE ; IEEE (Hrsg.) ; IEEE (Hrsg.): IEEE Symposium on Biological Data Visualization, IEEE Symposium on Biological Data Visualization. Bd. 2012, 2012
  33. Heinrich, Julian ; Vehlow, Corinna ; Battke, Florian ; Jaeger, Guenter ; Weiskopf, Daniel ; Nieselt, Kay: iHAT: interactive Hierarchical Aggregation Table for Genetic Association Data. In: Bioinformatics, B. (Hrsg.) BMC Bioinformatics, BMC Bioinformatics. Bd. 2012 (2012), Nr. 13
  34. 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, Proceedings Workshop on Computational Systems Biology, 2011
  35. Vehlow, Corinna ; Preim, Bernhard ; Lappe, Michael: Visualization of Anisotropic Contact Potentials within Protein Structures. In: IEEE ; IEEE (Hrsg.) ; IEEE (Hrsg.): IEEE Symposium on Biological Data Visualization, IEEE Symposium on Biological Data Visualization. Bd. 2011 : IEEE, 2011c
  36. Vehlow, Corinna ; Heinrich, Julian ; Battke, Florian ; Weiskopf, Daniel ; Nieselt, Kay: iHAT: interactive Hierarchical Aggregation Table. In: IEEE ; IEEE (Hrsg.) ; IEEE (Hrsg.): IEEE Symposium on Biological Data Visualization, IEEE Symposium on Biological Data Visualization. Bd. 2011, 2011a
  37. 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), Proceedings of International Symposium on Visual Computing (ISVC) : Springer, 2011
  38. 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), Proceedings of IEEE Symposium on Biological Data Visualization (biovis’11), 2011b
  39. 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: Fages, F. ; Fages, F. (Hrsg.) ; Fages, F. (Hrsg.): International Conference on Computational Methods in Systems Biology (CMSB 2011), International Conference on Computational Methods in Systems Biology (CMSB 2011) : ACM, 2011b
  40. Vehlow, Corinna ; Heinrich, Julian ; Battke, Florian ; Weiskopf, Daniel ; Nieselt, Kay: iHAT: interactive Hierarchical Aggregation Table. In: IEEE ; IEEE (Hrsg.) ; IEEE (Hrsg.): IEEE Symposium on Biological Data Visualization, IEEE Symposium on Biological Data Visualization. Bd. 2011, 2011b
  41. Krone, Michael ; Falk, Martin ; Rehm, Sascha ; Pleiss, Jürgen ; Ertl, Thomas: Interactive Exploration of Protein Cavities. In: Computer Graphics Forum, Computer Graphics Forum. Bd. 30 (2011a), Nr. 3
  42. 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), IEEE Symposium on Biological Data Visualization (BioVis 2011), 2011a
  43. Falk, Martin ; Grottel, Sebastian ; Ertl, Thomas: Interactive Image-Space Volume Visualization for Dynamic Particle Simulations. In: Proceedings of The Annual SIGRAD Conference, Proceedings of The Annual SIGRAD Conference : Linköping University Electronic Press, 2010a
  44. 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), IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI ’10), 2010b
  45. 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, International Conference On Bioinformatics and Computational Biology. Bd. 2010 : ACM, 2010
  46. Krone, Michael ; Bidmon, Katrin ; Ertl, Thomas: Interactive Visualization of Molecular Surface Dynamics. In: IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2009), IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2009). Bd. 15 (2009), Nr. 6
  47. 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), IEEE Pacific Visualization Symposium (PacificVis 2009), 2009
  48. Krone, Michael ; Bidmon, Katrin ; Ertl, Thomas: GPU-based Visualisation of Protein Secondary Structure. In: Proceedings of TP.CG’08, Proceedings of TP.CG’08, 2008