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 is utilised in systems and synthetic biology through qualitative vs quantitative analysis. Here, we choose two well known case studies: quorum sensing in P. aeruginosas and pulse generator. The paper reports verification analysis of two systems carried out using some model checking tools, integrated to the
As unconventional computation matures and non-standard programming frameworks are demonstrated, the need for formal verification will become more prevalent. This is so because "programming" in unconventional substrates is difficult. In this paper we show how conventional verification tools can be used to verify unconventional programs implementing a logical XOR gate.
Summary. In this paper it is surveyed the set of formal verification methods and testing approaches utilised for applications based on P systems.P systems (also called membrane systems) represent a class of parallel and distributed computing devices which are inspired by the structure and the functioning of living cells [11], [12]. The model has been used for theoretical investigations as well as a vehicle to represent different problems from various domains [13]. A rich set of software tools have been produced to implement various simulators [7].As a consequence of using membrane systems to specify, model and simulate various systems, certain methods and techniques have been employed to verify they work properly.Formal methods have been used for various types of systems and using different formalisms. Petri nets based methods have been studied with respect to translating various classes of P systems into this formalism. Tools and techniques developed for Petri nets become available for the description, analysis, and verification of behavioral properties of membrane systems, and in particular for the investigation of the structure of the behavior of P systems [10]. It also allows to study causality and (a)synchrony, as basic properties of such systems.Structural operational semantic allowing to systematically translate certain classes of P systems into a specific rewriting logic formalism called Maude [6], [2], has been provided. This approach allows to formally verify properties of the systems specified with these classes of P systems by using linear temporal logic model checking approaches [1].For probabilistic and stochastic P systems special relationships with classes of stochastic process algebras and Petri nets have been investigated and a special purpose model checking approach based on Prism has been studied [3].
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