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JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept

  • Mary Ann Blätke
  • Anna Dittrich
  • Monika Heiner
  • Fred Schaper
  • Wolfgang Marwan
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7605)

Abstract

We present a detailed model of the JAK-STAT pathway in IL-6 signaling as non-trivial case study demonstrating a new database-supported modular modeling method. A module is a self-contained and autonomous Petri net, centred around an individual protein. The modelling approach allows to easily generate and modify coherent, executable models composed from a collection of modules and provides numerous options for advanced biomodel engineering.

Keywords

Coarse Transition Executable Model Numerous Option Degradation Module Biomolecular Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Blätke, M., et al.: JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems- and synthetic biology (submitted, 2012), http://arxiv.org/abs/1206.0959v1
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    Heiner, M., Gilbert, D., Donaldson, R.: Petri Nets for Systems and Synthetic Biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 215–264. Springer, Heidelberg (2008)CrossRefGoogle Scholar
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    Heinrich, P., et al.: Principles of interleukin (il)-6-type cytokine signalling and its regulation. Biochemical Journal 374, 1–20 (2003)CrossRefMathSciNetGoogle Scholar
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    Rohr, C., Marwan, W., Heiner, M.: Snoopy - a unifying Petri net framework to investigate biomolecular networks. Bioinformatics 26(7), 974–975 (2010)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Mary Ann Blätke
    • 1
  • Anna Dittrich
    • 1
  • Monika Heiner
    • 2
  • Fred Schaper
    • 1
  • Wolfgang Marwan
    • 1
  1. 1.Otto-von-Guericke-UniversitätMagdeburgGermany
  2. 2.Brandenburg Technical UniversityCottbusGermany

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