Membrane Systems and Petri Net Synthesis

Automated synthesis from behavioural specifications is an attractive and powerful way of constructing concurrent systems. Here we focus on the problem of synthesising a membrane system from a behavioural specification given in the form of a transition system which specifies the desired state space of the system to be constructed. We demonstrate how a Petri net solution to this problem, based on the notion of region of a transition system, yields a method of automated synthesis of membrane systems from state spaces.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347

Quantitative Analysis of Opacity in Cloud Computing Systems

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Federated cloud systems increase the reliability and reduce the cost of the computational support. The resulting combination of secure private clouds and less secure public clouds, together with the fact that resources need to be located within different clouds, strongly affects the information flow security of the entire system. In this paper, the clouds as well as entities of a federated cloud system are assigned security levels, and a probabilistic flow sensitive security model for a federated cloud system is proposed. Then the notion of opacity --- a notion capturing the security of information flow --- of a cloud computing systems is introduced, and different variants of quantitative analysis of opacity are presented. As a result, one can track the information flow in a cloud system, and analyze the impact of different resource allocation strategies by quantifying the corresponding opacity characteristics

Modeling biological systems with delays in Bio-PEPA

Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed, or to provide abstraction of some behavior of the system resulting more compact models. In this paper we enrich the stochastic process algebra Bio-PEPA, with the possibility of assigning delays to actions, yielding a new non-Markovian process algebra: Bio-PEPAd. This is a conservative extension meaning that the original syntax of Bio-PEPA is retained and the delay specification which can now be associated with actions may be added to existing Bio-PEPA models. The semantics of the firing of the actions with delays is the delay-as-duration approach, earlier presented in papers on the stochastic simulation of biological systems with delays. These semantics of the algebra are given in the Starting-Terminating style, meaning that the state and the completion of an action are observed as two separate events, as required by delays. Furthermore we outline how to perform stochastic simulation of Bio-PEPAd systems and how to automatically translate a Bio-PEPAd system into a set of Delay Differential Equations, the deterministic framework for modeling of biological systems with delays. We end the paper with two example models of biological systems with delays to illustrate the approach.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Measurable Stochastics for Brane Calculus

We give a stochastic extension of the Brane Calculus, along the lines of recent work by Cardelli and Mardare. In this presentation, the semantics of a Brane process is a measure of the stochastic distribution of possible derivations. To this end, we first introduce a labelled transition system for Brane Calculus, proving its adequacy w.r.t. the usual reduction semantics. Then, brane systems are presented as Markov processes over the measurable space generated by terms up-to syntactic congruence, and where the measures are indexed by the actions of this new LTS. Finally, we provide a SOS presentation of this stochastic semantics, which is compositional and syntax-driven.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

An Abstraction Theory for Qualitative Models of Biological Systems

Multi-valued network models are an important qualitative modelling approach used widely by the biological community. In this paper we consider developing an abstraction theory for multi-valued network models that allows the state space of a model to be reduced while preserving key properties of the model. This is important as it aids the analysis and comparison of multi-valued networks and in particular, helps address the well-known problem of state space explosion associated with such analysis. We also consider developing techniques for efficiently identifying abstractions and so provide a basis for the automation of this task. We illustrate the theory and techniques developed by investigating the identification of abstractions for two published MVN models of the lysis-lysogeny switch in the bacteriophage lambda.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Novel detection schemes and automated image analysis algorithms for planar chromatography and gel electrophoresis

After a detailed introduction to Charge Coupled Devices (CCDs) and a discussion of personal computer capabilities, examples of their applications involving novel analytical techniques are presented;A new laser-based indirect fluorometric detection method for thin-layer chromatography is demonstrated with digitally controlled two-dimensional scanning and computer-aided image acquisition and vision. Utilizing this mode, universal detection is possible without derivatization, with a detection limit of 6 pg; 100 times lower than with human vision;A detection scheme for DNA in agarose slab gel electrophoresis based on ultraviolet absorption allows for convenient in situ monitoring of conventional gels via a CCD camera system, which greatly improves detectability compared to previous applications of this detection mode. With the use of the CCD system, low light level images can be acquired rapidly with minimal noise. Further on-line processing of the image allows one to correct for background and lighting variations and other non-random noise. The detection limit is about 5 ng of double-stranded DNA per band, which is at least 25 times lower than those obtained previously for UV absorption;The UV imaging method, along with a native fluorescence scheme, is demonstrated for detection of proteins in agarose slab gels. Detectability is comparable to traditional visualization schemes based on coomassie blue staining;A computerized method for correcting systematic signal distortions of images from slab gel electrophoresis is presented. The method is useful for interpretation of one-dimensional slab gel electrophoresis images where the information is manifested in rectangular shaped bands and the distortions can be described by low order polynomial functions. The purpose is to eliminate human judgement and interaction from the process, which is necessary for automated analysis of electrophoretic gels;A computerized expert system is introduced for the reduction of data acquisition in random access two-dimensional scanners or imaging devices where multiple scans are necessary to identify all features. The various areas of the image are probed to different extents based on the accumulated signal to noise ratio (SNR) of each area, resulting in a constant SNR throughout the final image. The method is applied to sequencing gel interpretation

Modelling and Analysis of Corporate Efficiency and Productivity Loss Associated with Enterprise Information Security Technologies

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.By providing effective access control mechanisms, enterprise information security technologies have been proven successful in protecting the sensitive information in business organizations. However, such security mechanisms typically reduce the work productivity of the staff, by making them spend time working on non-project related tasks. Therefore, organizations have to invest a signification amount of capital in the information security technologies, and then to continue incurring additional costs. In this study, we investigate the non-productive time (NPT) in an organization, resulting from the implementation of information security technologies. An approximate analytical solution is discussed first, and the loss of staff member productivity is quantified using non-productive time. Stochastic Petri nets are then used to provide simulation results. Moreover, sensitivity analysis is applied to develop a cost-effective strategy for mitigating the negative impact of implementing information security technologies. The presented study can help information security managers to make investment decisions, and to take actions toward reducing the cost of information security technologies, so that a balance is kept between information security expense, resource drain and effectiveness of security technologies