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BMC Syst Biol. 2013 Nov 17;7:128. doi: 10.1186/1752-0509-7-128.

Rosen's (M,R) system in process algebra.

Author information

1
MRC-University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow G11 5JR, UK. d.gatherer@lancaster.ac.uk.

Abstract

BACKGROUND:

Robert Rosen's Metabolism-Replacement, or (M,R), system can be represented as a compact network structure with a single source and three products derived from that source in three consecutive reactions. (M,R) has been claimed to be non-reducible to its components and algorithmically non-computable, in the sense of not being evaluable as a function by a Turing machine. If (M,R)-like structures are present in real biological networks, this suggests that many biological networks will be non-computable, with implications for those branches of systems biology that rely on in silico modelling for predictive purposes.

RESULTS:

We instantiate (M,R) using the process algebra Bio-PEPA, and discuss the extent to which our model represents a true realization of (M,R). We observe that under some starting conditions and parameter values, stable states can be achieved. Although formal demonstration of algorithmic computability remains elusive for (M,R), we discuss the extent to which our Bio-PEPA representation of (M,R) allows us to sidestep Rosen's fundamental objections to computational systems biology.

CONCLUSIONS:

We argue that the behaviour of (M,R) in Bio-PEPA shows life-like properties.

PMID:
24237684
PMCID:
PMC3879122
DOI:
10.1186/1752-0509-7-128
[Indexed for MEDLINE]
Free PMC Article

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