2 research outputs found
Lumpability Abstractions of Rule-based Systems
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 mathematical 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 combinatorial 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.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors
In this paper, we survey five different computational modeling methods. For
comparison, we use the activation cycle of G-proteins that regulate cellular
signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving
example. Starting from an existing Ordinary Differential Equations (ODEs)
model, we implement the G-protein cycle in the stochastic Pi-calculus using
SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using
Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also
provide a high-level notation to abstract away from communication primitives
that may be unfamiliar to the average biologist, and we show how to translate
high-level programs into stochastic Pi-calculus processes and chemical
reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005