A Modular Model of the Apoptosis Machinery

  • E. O. Kutumova
  • I. N. Kiselev
  • R. N. Sharipov
  • I. N. Lavrik
  • Fedor A. Kolpakov
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 736)

Abstract

Using a modular principle of computer hardware as a metaphor, we defined and implemented in the BioUML platform a module concept for biological pathways. BioUML provides a user interface to create modular models and convert them automatically into plain models for further simulations. Using this approach, we created the apoptosis model including 13 modules: death stimuli (TRAIL, CD95L, and TNF-α)-induced activation of caspase-8; survival stimuli (p53, EGF, and NFB) regulation; the mitochondria level; cytochrome C- and Smac-induced activation of caspase-3; direct activation of effector caspases by caspase-8 and − 12; PARP and apoptosis execution phase modules. Each module is based on earlier published models and extended by data from the Reactome and TRANSPATH databases. The model ability to simulate the apoptosis-related processes was checked; the modules were validated using experimental data. Availability: http://www.biouml.org/apoptosis.shtml.

Keywords

Metaphor 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • E. O. Kutumova
    • 1
    • 2
  • I. N. Kiselev
    • 1
    • 2
  • R. N. Sharipov
    • 3
    • 1
  • I. N. Lavrik
    • 4
  • Fedor A. Kolpakov
    • 1
    • 2
  1. 1.Institute of Systems Biology, LtdNovosibirskRussia
  2. 2.Design Technological Institute of Digital Techniques SB RASNovosibirskRussia
  3. 3.Institute of Cytology and Genetics SB RASNovosibirskRussia
  4. 4.German Cancer Research Center (DKFZ)HeidelbergGermany

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