Skip to main content

BioPath — Exploration and Visualization of Biochemical Pathways

  • Chapter
Graph Drawing Software

Part of the book series: Mathematics and Visualization ((MATHVISUAL))

Abstract

Biochemical reactions in organisms form large and complex networks. Examples are given by the Biochemical Pathways atlas [17] and the well known Boehringer Biochemical Pathways poster [16], see Figure 1. Biochemists are familiar with visual representations of reactions and reaction networks. Automatic visualizations help in understanding the complex relations between the components of the networks and in extracting information from the data. They are very useful for building sophisticated research tools.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Becker, M. Y., Rojas, I. (2001) A graph layout algorithm for drawing metabolic pathways. Bioinformatics 17(5), 461–467

    Article  Google Scholar 

  2. Brandenburg, F. J., Gruber, B., Himsolt, M., Schreiber, F. (1998) Automatische Visualisierung biochemischer Information. In: R. Hofestädt (ed.) Proceedings of the Workshop Molekulare Bioinformatik, Gl Jahrestagung, Shaker Verlag, 24–38

    Google Scholar 

  3. Ellis, L. B., Hershberger, C. D., Wackett, L. P. (2000) The University of Minnesota Biocatalysis/Biodegradation Database: Microorganisms, Genomics and Prediction. Nucleic Acids Research 28(1), 377–379

    Article  Google Scholar 

  4. Forster, M., Pick, A., Raitner, M., Schreiber, F., Brandenburg, F. J. (2002) The System Architecture of the BioPath System. In Silico Biology 2(3), 415–426

    Google Scholar 

  5. Fruchterman, T., Reingold, E. (1991) Graph Drawing by Force-directed Placement. Software — Practice and Experience 21(11), 1129–1164

    Article  Google Scholar 

  6. Garey, M. R., Johnson, D. S. (1979) Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman, New York

    MATH  Google Scholar 

  7. Himsolt, M. (2000) Graphlet: Design and Implementation of a Graph Editor. Software — Practice and Experience 30(11), 1303–1324

    Article  MATH  Google Scholar 

  8. Hofestädt, R., Thelen, S. (1998) Qualitative Modeling of Biochemical Networks. In Silico Biology 1, 39–53

    Google Scholar 

  9. (1992) International Union of Biochemistry and Molecular Biology Nomenclature Commitee (1992) Enzyme Nomenclature. Academic Press

    Google Scholar 

  10. Kanehisa, M., Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acid Research 28(1), 27–30

    Article  Google Scholar 

  11. Kanne, C.-C. (2000) BioPath database schema. Internal documentation

    Google Scholar 

  12. Kanne, C.-C, Schreiber, F., Trümbach, D. (1999) Electronic Biochemical Pathways. In: J. Kratochvil (ed.) Graph Drawing’ 99, Lecture Notes in Computer Science 1731, Springer-Verlag, 418–419

    Google Scholar 

  13. Karp, P. D., Paley, S. M. (1994) Automated Drawing of Metabolic Pathways. In: H. Lim, C. Cantor, and R. Bobbins (eds.) Proceedings of the 3rd International Conference on Bioinformatics and Genome Research, 225–238

    Google Scholar 

  14. Karp, P. D., Riley, M., Saier, M., Paulsen, I. T., Paley, S. M., Pellegrini-Toole, A. (2000) The EcoCyc and MetaCyc database. Nucleid Acids Research 28, 56–59

    Article  Google Scholar 

  15. Mendes, P. (2000) Advanced Visualization of Metabolic Pathways in PathDB. In: Proceedings of the 8th Conference on Plant and Animal Genome

    Google Scholar 

  16. Michal, G. (1993) Biochemical Pathways (Poster). Boehringer Mannheim, Penzberg

    Google Scholar 

  17. Michal, G. (1999) Biochemical Pathways. Spektrum Akademischer Verlag, Heidelberg

    Google Scholar 

  18. Michal, G. (2000) Personal Communication.

    Google Scholar 

  19. Misue, K., Eades, P., Lai, W., Sugiyama, K. (1995) Layout Adjustment and the Mental Map. Journal of Visual Languages and Computing 6, 183–210

    Article  Google Scholar 

  20. http://www.ebi.ac.uk/research/pfmp/.

    Google Scholar 

  21. Reddy, V. N., Mavrovouniotis, M. L., Liebman, M. N. (1993) Petri Net Representations of Metabolic Pathways. In: L. Hunter, D. Searls, and J. Shavlik (eds.) Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB’93), 328–336

    Google Scholar 

  22. Stryer, L. (1995) Biochemie. Spektrum Akademischer Verlag, Heidelberg

    Google Scholar 

  23. Sugiyama, K., Tagawa, S., Toda, M. (1981) Methods for Visual Understanding of Hierarchical System Structures. IEEE Transactions on Systems, Man and Cybernetics SMC-11(2), 109–125

    Article  MathSciNet  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Brandenburg, F.J., Forster, M., Pick, A., Raitner, M., Schreiber, F. (2004). BioPath — Exploration and Visualization of Biochemical Pathways. In: Jünger, M., Mutzel, P. (eds) Graph Drawing Software. Mathematics and Visualization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18638-7_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-18638-7_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-62214-4

  • Online ISBN: 978-3-642-18638-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics