Customizable visualization on demand for hierarchically organized information in biochemical networks

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6026 LNCS, Issue , 2010, Pages 163-174

  Droste, Peter ^a   Von Lieres, Eric ^a   Wiechert, Wolfgang ^a   Nöh, Katharina ^a  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

Biochemical networks; Hierarchical data organization; Scientific information visualization; Systems biology; Visualization on demand

Indexed keywords

BIOCHEMICAL NETWORK; BIOLOGICAL PROCESS; COMPLEX INTERACTION; CUSTOMIZABLE; HIERARCHICAL DATA ORGANIZATION; HIGH-THROUGHPUT TECHNIQUE; INTERACTIVE VISUALIZATIONS; MEASUREMENT DATA; MOLECULAR COMPONENTS; NETWORK TOPOLOGY; ON-DEMAND; QUALITATIVE INFORMATION; QUANTITATIVE DATA; SCIENTIFIC INFORMATION; SIMULATION RESULT; STRUCTURED NETWORKS; SYSTEM STATE; SYSTEMS BIOLOGY;

BIOLOGY; ELECTRIC NETWORK TOPOLOGY; ENZYME KINETICS; HIERARCHICAL SYSTEMS; INFORMATION ANALYSIS; INFORMATION SYSTEMS; VISUALIZATION;

DATA VISUALIZATION;

EID: 77952359755     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-12712-0_15     Document Type: Conference Paper

References (16)

1. Droste, P.: Omix - Editor and Visualization Tool for Biochemical Networks - User Manual. Institute of Biotechnology 2, Forschungszentrum Jülich, Jülich (2008)
2. Droste, P.: Omix Visualization Language - Technical Manual. Institute of Biotechnology 2, Forschungszentrum Jülich, Jülich (2008)
3. Droste, P., Nöh, K., Noack, S., Wiechert, W.: Customizable visualization of Multi-Omics data in the context of biochemical networks. In: Banissi, E., et al. (eds.) Int. Conference on Visualization, Visualization in Built and Rural Environments, BioMedical Visualization, Geometric Modeling and Imaging, pp. 21-25. IEEE, Inc., Los Alamitos (2009)
4. Gottschalk, G.: Bacterial Metabolism. Cambridge University Press, Cambridge (1986)
5. Junker, B.H., Klukas, C., Schreiber, F.: VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7 (2006)
6. Klamt, S., Stelling, J., Ginkel, M., Gilles, E.D.: FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19, 261-269 (2003) (Pubitemid 36181912)
7. Klamt, S., Saez-Rodriguez, J., Gilles, E.D.: Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 1(2) (2007)
8. Kremling, A., Jahreis, K., Lengeler, J.W., Gilles, E.D.: The organization of metabolic reaction networks: A signal-oriented approach to cellular models. Metabolic Engineering 2, 190-200 (2000)
9. Neuweger, H., Persicke, M., Albaum, S.P., Bekel, T., Dondrup, M., Huser, A.T., Winnebald, J., Schneider, J., Kalinowski, J., Goesmann, A.: Visualizing post genomics data-sets on customized pathway maps by ProMeTra - aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biology 3 (2009)
10. Palsson, B.O.: Systems Biology: Properties of Reconstructed Networks. Cambridge (2006)
11. Parr, T.J., Quong, R.W.: ANTLR: A Predicated-LL(k) Parser Generator. Software - Practice and Experience 25 (1995)
12. Pavlopoulos, G.A., Wegener, A.-L., Schneider, R.: A survey of visualization tools for biological network analysis. BioData Mining 1(12) (2008)
13. Qeli, E., Wahl, A., Degenring, D., Wiechert, W., Freisleben, B.: MetVis: A tool for designing and animating metabolic networks. In: Proceedings of the 2003 European Simulation and Modelling Conference, pp. 333-338. Eurosis Press, Naples (2003)
14. Reuss, M., Aguilera-Vázquez, L., Mauch, K.: Reconstruction of dynamic network models from metabolite measurements. In: Nielsen, J., Jewett, M.C. (eds.) Metabolomics. Topics in Current Genetics, vol.18, pp. 97-127. Springer, Heidelberg (2007)
15. Rost, U., Kummer, U.: Visualisation of biochemical network simulations with SimWiz. IEE Systems Biology 1, 184-189 (2004)
16. Sudermann, M., Hallett, M.: Tools for visually exploring biological networks. BMC Bioinformatics 23, 2651-2659 (2007)