Lumpability abstractions of rule-based systems Conference Paper

Author(s): Feret, Jérôme; Henzinger, Thomas A; Koeppl, Heinz; Petrov, Tatjana
Title: Lumpability abstractions of rule-based systems
Title Series: EPTCS
Affiliation IST Austria
Abstract: The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.
Conference Title: MECBIC: Membrane Computing and Biologically Inspired Process Calculi
Conference Dates: August 23th, 2010
Conference Location: Jena, Germany
ISBN: 2075-2180
Publisher: Open Publishing Association  
Location: Jena
Date Published: 2010-08-19
Start Page: 137
End Page: 156
Notes: Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support from, the Swiss Initiative in Systems Biology.
Open access: yes (repository)
IST Austria Authors
  1. Thomas A. Henzinger
    405 Henzinger
  2. Tatjana Petrov
    11 Petrov
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