Rights statement: This is the author’s version of a work that was accepted for publication in Biosystems. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biosystems, 139, 2016 DOI: 10.1016/j.biosystems.2015.12.006
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Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
}
TY - JOUR
T1 - Rosen's (M,R) system in Unified Modelling Language
AU - Zhang, Ling
AU - Williams, Richard
AU - Gatherer, Derek
N1 - This is the author’s version of a work that was accepted for publication in Biosystems. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biosystems, 139, 2016 DOI: 10.1016/j.biosystems.2015.12.006
PY - 2016/1
Y1 - 2016/1
N2 - Robert Rosen's (M,R) system is an abstract biological network architecture that is allegedly non-computable on a Turing machine. If (M,R) is truly non-computable, there are serious implications for the modelling of large biological networks in computer software. A body of work has now accumulated addressing Rosen's claim concerning (M,R) by attempting to instantiate it in various software systems. However, a conclusive refutation has remained elusive, principally since none of the attempts to date have unambiguously avoided the critique that they have altered the properties of (M,R) in the coding process, producing merely approximate simulations of (M,R) rather than true computational models. In this paper, we use the Unified Modelling Language (UML), a diagrammatic notation standard, to express (M,R) as a system of objects having attributes, functions and relations. We believe that this instantiates (M,R) in such a way than none of the original properties of the system are corrupted in the process. Crucially, we demonstrate that (M,R) as classically represented in the relational biology literature is implicitly a UML communication diagram. Furthermore, since UML is formally compatible with object-oriented computing languages, instantiation of (M,R) in UML strongly implies its computability in object-oriented coding languages.
AB - Robert Rosen's (M,R) system is an abstract biological network architecture that is allegedly non-computable on a Turing machine. If (M,R) is truly non-computable, there are serious implications for the modelling of large biological networks in computer software. A body of work has now accumulated addressing Rosen's claim concerning (M,R) by attempting to instantiate it in various software systems. However, a conclusive refutation has remained elusive, principally since none of the attempts to date have unambiguously avoided the critique that they have altered the properties of (M,R) in the coding process, producing merely approximate simulations of (M,R) rather than true computational models. In this paper, we use the Unified Modelling Language (UML), a diagrammatic notation standard, to express (M,R) as a system of objects having attributes, functions and relations. We believe that this instantiates (M,R) in such a way than none of the original properties of the system are corrupted in the process. Crucially, we demonstrate that (M,R) as classically represented in the relational biology literature is implicitly a UML communication diagram. Furthermore, since UML is formally compatible with object-oriented computing languages, instantiation of (M,R) in UML strongly implies its computability in object-oriented coding languages.
KW - UML
KW - Unified Modelling Language
KW - object oriented design
KW - systems biology
KW - Turing machine
KW - Computability
KW - Impredicativity
U2 - 10.1016/j.biosystems.2015.12.006
DO - 10.1016/j.biosystems.2015.12.006
M3 - Journal article
C2 - 26723228
VL - 139
SP - 29
EP - 36
JO - BioSystems
JF - BioSystems
SN - 0303-2647
ER -