Modelling and validating an engineering application in kernel P systems

© 2018, Springer International Publishing AG. This paper illustrates how kernel P systems (kP systems) can be used for modelling and validating an engineering application, in this case a cruise control system of an electric bike. The validity of the system is demonstrated via formal verification, carried out using the kPWorkbench tool. Furthermore, we show how the kernel P system model can be tested using automata and X-machine based techniques

Design and Analysis of Genetically Constructed Logic Gates

Synthetic biology, comprising many aspects including in vivo, in vitro and in silico techniques, models and methods, programming paradigms and tools, is a rapidly growing field with promising potential in building new synthetically constructed devices and systems. Synthetic biology features unconventional biological systems that do not naturally exist in nature. In this paper, we discuss a software platform, Infobiotics Workbench, developed to perform in silico experiments for synthetic biology systems. We utilise the tool on an unconventional system, a genetic logic gate

Comparative Analysis of Statistical Model Checking Tools

Statistical model checking is a powerful and flexible approach for formal verification of computational models like P systems, which can have very large search spaces. Various statistical model checking tools have been developed, but choosing between them and using the most appropriate one requires a significant degree of experience, not only because different tools have different modelling and property specification languages, but also because they may be designed to support only a certain subset of property types. Furthermore, their performance can vary depending on the property types and membrane systems being verified. In this paper we evaluate the performance of various common statistical model checkers against a pool of biological models. Our aim is to help users select the most suitable SMC tools from among the available options, by comparing their modelling and property specification languages, capabilities and performances

Spiking neural P systems: matrix representation and formal verification

YesStructural and behavioural properties of models are very important in development of complex systems and applications. In this paper, we investigate such properties for some classes of SN P systems. First, a class of SN P systems associated to a set of routing problems are investigated through their matrix representation. This allows to make certain connections amongst some of these problems. Secondly, the behavioural properties of these SN P systems are formally verified through a natural and direct mapping of these models into kP systems which are equipped with adequate formal verification methods and tools. Some examples are used to prove the effectiveness of the verification approach.EPSRC research grant EP/R043787/1; DOST-ERDT research grants; Semirara Mining Corp; UPD-OVCRD

An integrated model checking toolset for kernel P systems

P systems are the computational models introduced in the context of membrane computing, a computational paradigm within the more general area of unconventional computing. Kernel P (kP) systems are defined to unify the specification of different variants of P systems, motivated by challenging theoretical aspects and the need to model different problems. kP systems are supported by a software framework, called kPWORKBENCH, which integrates a set of related simulation and verification methodologies and tools. In this paper, we present an extension to kPWORKBENCH with a new model checking framework supporting the formal verification of kP system models. This framework supports both LTL and CTL properties. To make the property specification an easier task, we propose a property language, composed of natural language statements. We demonstrate our proposed methodology with an example

An Assessment on the Hidden Ecological Factors of the Incidence of Malaria

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).Confounding effects of climatic factors temporally contribute to the prevalence of malaria. In this study, we explore a new framework for assessment and identification of hidden ecological factors to the incidence of malaria. A statistical technique, partial least squares path modeling and exploratory factor analysis, is employed to identify hidden ecological factors. Three hidden factors are identified: Factor I is related to minimum temperature and relative humidity, Factor II is related to maximum temperature and solar radiation and Factor III is related to precipitation and wind speed, respectively. Factor I is identified as the most influential hidden ecological factor of malaria incidence in the study area, as evaluated by communality and Dillon-Goldstein’s indices

Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems

YesComputational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations). These models incorporate a set of methods for specifying, modeling, testing, and simulating biological systems. In addition, they can be analyzed using algorithmic techniques (e.g., formal verification). This paper shows how formal verification is utilized 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 Infobiotics Workbench platform, where system models are based on stochastic P systems.EPSR

Work Zone Simulator Analysis: Driver Performance and Acceptance of Alternate Merge Sign Configurations

Improving work zone road safety is an issue of great interest due to the high number of crashes observed in work zones. Departments of Transportation (DOTs) use a variety of methods to inform drivers of upcoming work zones. One method used by DOTs is work zone signage configuration. It is necessary to evaluate the efficiency of different configurations, by law, before implementation of new signage designs that deviate from national standards. This research presents a driving simulator based study, funded by the Missouri Department of Transportation (MoDOT) that evaluates a driver’s response to work zone sign configurations. This study has compared the Conventional Lane Merge (CLM) configurations against MoDOT’s alternate configurations. Study participants within target populations, chosen to represent a range of Missouri drivers, have attempted four work zone configurations, as part of a driving simulator experience. The test scenarios simulated both right and left work zone lane closures for both the CLM and MoDOT alternatives. Travel time was measured against demographic characteristics of test driver populations. Statistical data analysis was used to investigate the effectiveness of different configurations employed in the study. The results of this study were compared to results from a previous MoDOT to compare result of field and simulation study about MoDOT’s alternate configurations

Work Zone Simulator Analysis: Driver Performance and Acceptance of Missouri Alternate Lane Shift Configurations

The objective of this project is to evaluate MoDOT’s alternate lane shift sign configuration for work zones. The single signproposed by MoDOT provides the traveler with enough information to let them know that all lanes are available to shift around thework zone, whereas the MUTCD signs require drivers to see two signs. This research simulation project evaluates the drivers’ laneshifting performance and acceptance of the alternate lane shift sign proposed by MoDOT to be used on work zones as compared tothe MUTCD lane shift signs. Based on the study results, no difference was observed between MUTCD lane shift sign andMoDOT lane shift sign lane shift patterns with respect to driving patterns. In summary, statistical data analysis clearlydemonstrated that there was not a noticeable, statistical difference between lane change patterns of drivers in the MoDOT alternatesigns with MUTCD signs in the work zone

Towards a Formal Verification Methodology for Collective Robotic Systems

We introduce a UML-based notation for graphically modeling systems’ security aspects in a simple and intuitive way and a model-driven process that transforms graphical specifications of access control policies in XACML. These XACML policies are then translated in FACPL, a policy language with a formal semantics, and the resulting policies are evaluated by means of a Java-based software tool