Abstract
We extend our previous work on the exploration of static metabolic networks to evolving, and therefore dynamic, pathways. We apply our visualization software to data from a simulation of early metabolism. Thereby, we show that our technique allows us to test and argue for or against different scenarios for the evolution of metabolic pathways. This supports a profound and efficient analysis of the structure and properties of the generated metabolic networks and its underlying components, while giving the user a vivid impression of the dynamics of the system. The analysis process is inspired by Ben Shneiderman’s mantra of information visualization. For the overview, user-defined diagrams give insight into topological changes of the graph as well as changes in the attribute set associated with the participating enzymes, substances and reactions. This way, “interesting features” in time as well as in space can be recognized. A linked view implementation enables the navigation into more detailed layers of perspective for in-depth analysis of individual network configurations.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Palsson, B.O.: Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, New York (2006)
Gagneur, J., Klamt, S.: Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5 (2004)
Yang, K., Ma, W., Liang, H., Ouyang, Q., Tang, C., Lai, L.: Dynamic simulations on the arachidonic acid metabolic network. PLoS Comput. Biol. 3, e55 (2007)
Steuer, R., Gross, T., Selbig, J., Blasius, B.: Structural kinetic modeling of metabolic networks. Proc. Natl. Acad. Sci. 103, 11868–11873 (2006)
Caetano-Anollés, G., Yafremava, L.S., Gee, H., Caetano-Anollés, D., Kim, H.S., Mittenthal, J.E.: The origin and evolution of modern metabolism. The International Journal of Biochemistry & Cell Biology 41, 285–297 (2009)
Ullrich, A., Flamm, C.: Functional evolution of ribozyme-catalyzed metabolisms in a graph-based toy-universe. In: Heiner, M., Uhrmacher, A.M. (eds.) CMSB 2008. LNCS (LNBI), vol. 5307, pp. 28–43. Springer, Heidelberg (2008)
Rohrschneider, M., Heine, C., Reichenbach, A., Kerren, A., Scheuermann, G.: A novel grid-based visualization approach for metabolic networks with advanced focus & context view. In: Eppstein, D., Gansner, E.R. (eds.) GD 2009. LNCS, vol. 5849, pp. 268–279. Springer, Heidelberg (2010)
Kerren, A., Ebert, A., Meyer, J. (eds.): Human-Centered Visualization Environments. LNCS, vol. 4417. Springer, Heidelberg (2007)
Di Battista, G., Eades, P., Tamassia, R., Tollis, I.G.: Graph Drawing: Algorithms for the Visualization of Graphs. Prentice Hall, New Jersey (1999)
Görg, C., Pohl, M., Qeli, E., Xu, K.: Visual Representations. In: [8], pp. 163–230
Klukas, C., Schreiber, F.: Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics 23, 344–350 (2007)
Rao, R., Card, S.K.: The table lens: merging graphical and symbolic representations in an interactive focus+context visualization for tabular information. In: Conference Companion on Human Factors in Computing Systems, CHI 1994, p. 222. ACM, New York (1994)
Albrecht, M., Kerren, A., Klein, K., Kohlbacher, O., Mutzel, P., Paul, W., Schreiber, F., Wybrow, M.: On open problems in biological network visualization. In: Eppstein, D., Gansner, E.R. (eds.) GD 2009. LNCS, vol. 5849, pp. 256–267. Springer, Heidelberg (2010)
Oldiges, M., Noack, S., Wahl, A., Qeli, E., Freisleben, B., Wiechert, W.: From enzyme kinetics to metabolic network modeling - visualization tool for enhanced kinetic analysis of biochemical network models. Eng. Life Sci. 6 (2006)
Branke, J.: Dynamic graph drawing. In: Drawing Graphs: Methods and Models, London, UK, pp. 228–246. Springer, Heidelberg (2001)
Misue, K., Eades, P., Lai, W., Sugiyama, K.: Layout adjustment and the mental map. Journal of Visual Languages and Computing 6, 183–210 (1995)
Diehl, S., Görg, C., Kerren, A.: Preserving the mental map using foresighted layout. In: Proc. of Joint Eurographics-IEEE TVCG Symp. on Vis., VisSym 2001, pp. 175–184. Springer, Heidelberg (2001)
Frishman, Y., Tal, A.: Online dynamic graph drawing. IEEE TVCG 14, 727–740 (2008)
Roberts, J.C.: Exploratory visualization with multiple linked views. In: MacEachren, A., Kraak, M.J., Dykes, J. (eds.) Exploring Geovisualization. Elseviers, Amsterdam (2004)
Moody, J., McFarland, D., Bender-deMoll, S.: Dynamic network visualization. American Journal of Sociology 110 (2005)
Faulon, J.L., Sault, A.G.: Stochastic generator of chemical structure. 3. Reaction network generation. J. Chem. Inf. Comp. Sci. 41, 894–908 (2001)
Wiener, H.: Structural determination of paraffin boiling points. Journal of the American Chemical Society 69, 17–20 (1947)
Ullrich, A., Flamm, C.: A sequence-to-function map for ribozyme-catalyzed metabolisms. In: ECAL. LNCS, vol. 5777. Springer, Heidelberg (2009)
Brandes, U., Eiglsperger, M., Herman, I., Himsolt, M., Marshall, M.S.: Graphml progress report: Structural layer proposal. In: Mutzel, P., Jünger, M., Leipert, S. (eds.) GD 2001. LNCS, vol. 2265, pp. 501–512. Springer, Heidelberg (2002)
Weininger, D.: SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31–36 (1988)
Sugiyama, K., Tagawa, S., Toda, M.: Methods for visual understanding of hierarchical systems. IEEE Trans. Systems, Man, and Cybernetics 11, 109–125 (1981)
Gansner, E.R., Koutsofios, E., North, S.C., Vo, K.P.: A technique for drawing directed graphs. IEEE Trans. Software Eng. 19, 214–230 (1993)
Shneiderman, B.: The eyes have it: A task by data type taxonomy for information visualizations. In: VL, pp. 336–343 (1996)
Horowitz, N.H.: On the evolution of biochemical syntheses. Proc. Natl. Acad. Sci. USA 31, 153–157 (1945)
Cordon, F.: Tratado evolucionista de biologa. Aguilar Ediciones, Madrid (1990)
Jensen, R.A.: Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409–425 (1976)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Rohrschneider, M., Ullrich, A., Kerren, A., Stadler, P.F., Scheuermann, G. (2010). Visual Network Analysis of Dynamic Metabolic Pathways. In: Bebis, G., et al. Advances in Visual Computing. ISVC 2010. Lecture Notes in Computer Science, vol 6453. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-17289-2_31
Download citation
DOI: https://doi.org/10.1007/978-3-642-17289-2_31
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-17288-5
Online ISBN: 978-3-642-17289-2
eBook Packages: Computer ScienceComputer Science (R0)