2014
DOI: 10.1021/sb500134w
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Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems

Abstract: Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems. ACS Synthetic Biology, 4 (1): 83-92. AbstractComputational models are perceived as an attractive alternative to mathematical models, e.g. ordinary differential equations. These models incorporate a set of methods for specifying, modelling, testing and simulating biological systems. In addition, they can be analysed using algorithmic techniques, e.g. formal verification. This paper shows how formal verification i… Show more

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Cited by 17 publications
(12 citation statements)
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References 34 publications
(64 reference statements)
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“…Namely, they allow one to describe all chains of reactions, observe various interactions between species and determine various dependencies between molecules. In [22], two biological systems, the quorum sensing in P. aeruginosas and the synthetic pulse generator, and in [21] some genetic Boolean gates have been qualitatively analysed using the NuSMV and Spin model checkers. However, the ideas and methodology presented in these papers were not fully automated.…”
Section: Discussionmentioning
confidence: 99%
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“…Namely, they allow one to describe all chains of reactions, observe various interactions between species and determine various dependencies between molecules. In [22], two biological systems, the quorum sensing in P. aeruginosas and the synthetic pulse generator, and in [21] some genetic Boolean gates have been qualitatively analysed using the NuSMV and Spin model checkers. However, the ideas and methodology presented in these papers were not fully automated.…”
Section: Discussionmentioning
confidence: 99%
“…The model checking framework now works in a fully automated fashion and is integrated into the kPWorkbench platform. Thus, this work can be considered progress on the conceptually presented methodology introduced in [22,21].…”
Section: Discussionmentioning
confidence: 99%
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“…The basis of such models is state machines, which can be used to model numerous variables and relate different system states (configurations) to one another [21]. There have been various attempts to model biological systems from a computational point of view, including the use of Boolean networks [31], Petri nets [45], the π-calculus [39], interacting state machines [25], L-systems [38] and variants of P systems (membrane systems) [5,17,23,29,33,42]. These techniques are useful for investigating the qualitative features, as are their stochastic counterparts (e.g., stochastic Petri Nets [26] and stochastic P systems [8,43]) are useful for investigating the quantitative features of computation models.…”
Section: Introductionmentioning
confidence: 99%
“…quorum sensing [18], genetic Boolean gates [23] and synthetic pulse generators [1], to some classical computational problems, e.g. sorting [6], broadcasting [10] and subset sum [5].…”
Section: Introductionmentioning
confidence: 99%