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Flux Visualization Using VANTED/FluxMap

  • Christian Krach
  • Astrid Junker
  • Hendrik Rohn
  • Falk Schreiber
  • Björn H. Junker
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1191)

Abstract

The calculation of metabolic fluxes has been shown to be a valuable asset in systems biology. Several procedures are commonly used to achieve this. Flux balance analyses or metabolic flux analyses usually result in a list of reaction rates (fluxes) provided in a spreadsheet format. This makes it difficult to quickly assess general characteristics of the solution. A fast and easy mapping of these results to a graphical map template facilitates an easy visual data inspection. Here, we describe a protocol that helps in setting up user-specific network templates, mapping flux results to it, and creating multiple exportable flux maps at one time.

Key words

Visualization VANTED FluxMap Java Automation 

References

  1. 1.
    Kitano H (2002) Systems biology: a brief overview. Science 295(5560):1662–1664PubMedCrossRefGoogle Scholar
  2. 2.
    Allen DK, Libourel IGL, Shachar-Hill Y (2009) Plant, Cell Environ 32:1241–1257CrossRefGoogle Scholar
  3. 3.
    Masakapalli SK, Le Lay P, Huddleston JE, Pollock NL, Kruger NJ, Ratcliffe RG (2010) Subcellular flux analysis of central metabolism in a heterotrophic Arabidopsis cell suspension using steady-state stable isotope labeling. Plant Physiol 152:602–619PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Grafahrend-Belau E, Schreiber F, Koschützki D, Junker BH (2009) Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol 149:585–598PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstück M, Czauderna T, Klukas C, Schreiber F (2012) VANTED v2: a framework for systems biology applications. BMC Syst Biol 6:139PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Rohn H, Hartmann A, Junker A, Junker BH, Schreiber F (2012) FluxMap: a VANTED add-on for the visual exploration of flux distributions in biological networks. BMC Syst Biol 6:33PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Junker BH, Klukas C, Schreiber F (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7(109):1–13Google Scholar
  8. 8.
    Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Database issue):D277–D280PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker BH, Schreiber F (2008) MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res 36(Database issue):D954–D958PubMedCentralPubMedGoogle Scholar
  10. 10.
    Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S (2012) MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res 40(Database issue): D1173–D1177PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Junker A, Rohn H, Czauderna T, Klukas C, Hartmann A, Schreiber F (2012) Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. Nat Protoc 7:579–593PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Christian Krach
    • 1
  • Astrid Junker
    • 1
  • Hendrik Rohn
    • 1
  • Falk Schreiber
    • 1
  • Björn H. Junker
    • 2
  1. 1.Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)GaterslebenGermany
  2. 2.Institute of PharmacyMartin-Luther-UniversityHalle/SaaleGermany

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