Implementing in Prolog an Effective Cellular Solution to the Knapsack Problem

In this paper we present an implementation in Prolog of an effective solution to the Knapsack problem via a family of deterministic P systems with active membranes using 2-division.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

A Simulator for Confluent P Systems

Software simulators for P system are nowadays the main tool to carry out experiments in the field of Membrane Computing. Although the simulation of a P system is a quite complex task, current simulators have been successfully used for pedagogical purposes and also as assistant tools for researchers. Up to now, simulators have always been designed to deal with a specific model of P systems. In this paper we present a new simulator which is not oriented to only one model of systems, but it allows the researcher to experiment with many existing models or even to create new ones.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Available Membrane Computing Software

The simulation of a P system with current computers is a quite com-plex task. P systems are intrinsically nondeterministic computational devices and therefore their computation trees are di±cult to store and handle with computers with one processor (or a bounded number of processors). Nevertheless, there exists a ¯rst generation of simulators which can be successfully used for pedagogical pur-poses and as assistant tools for researchers. This chapter summarizes some of these simulators, presenting the state of the art of the available software for simulating (di®erent variants of) cell-like membrane systems.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

A Programming Perspective of the Membrane Systems

We present an operational semantics of the membrane systems, using an appropriate notion of configurations and sets of inference rules corresponding to the three stages of an evolution step in membrane systems: maximal parallel rewriting step, parallel communication of objects through membranes, and parallel membrane dissolving. We define various arithmetical operations over multisets in the framework of membrane systems, indicating their complexity and presenting the membrane systems which implement the arithmetic operations. Finally we discuss and compare various sequential and parallel software simulators of the membrane systems, emphasizing their specific feature

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Evolutionary computation applied to combinatorial optimisation problems

This thesis addresses the issues associated with conventional genetic algorithms (GA) when applied to hard optimisation problems. In particular it examines the problem of selecting and implementing appropriate genetic operators in order to meet the validity constraints for constrained optimisation problems. The problem selected is the travelling salesman problem (TSP), a well known NP-hard problem. Following a review of conventional genetic algorithms, this thesis advocates the use of a repair technique for genetic algorithms: GeneRepair. We evaluate the effectiveness of this operator against a wide range of benchmark problems and compare these results with conventional genetic algorithm approaches. A comparison between GeneRepair and the conventional GA approaches is made in two forms: firstly a handcrafted approach compares GAs without repair against those using GeneRepair. A second automated approach is then presented. This meta-genetic algorithm examines different configurations of operators and parameters. Through the use of a cost/benefit (Quality-Time Tradeoff) function, the user can balance the computational effort against the quality of the solution and thus allow the user to specify exactly what the cost benefit point should be for the search. Results have identified the optimal configuration settings for solving selected TSP problems. These results show that GeneRepair when used consistently generates very good TSP solutions for 50, 70 and 100 city problems. GeneRepair assists in finding TSP solutions in an extremely efficient manner, in both time and number of evaluations required

Dynamics in Logistics

This open access book highlights the interdisciplinary aspects of logistics research. Featuring empirical, methodological, and practice-oriented articles, it addresses the modelling, planning, optimization and control of processes. Chiefly focusing on supply chains, logistics networks, production systems, and systems and facilities for material flows, the respective contributions combine research on classical supply chain management, digitalized business processes, production engineering, electrical engineering, computer science and mathematical optimization. To celebrate 25 years of interdisciplinary and collaborative research conducted at the Bremen Research Cluster for Dynamics in Logistics (LogDynamics), in this book hand-picked experts currently or formerly affiliated with the Cluster provide retrospectives, present cutting-edge research, and outline future research directions

Security Configuration Management in Intrusion Detection and Prevention Systems

Intrusion Detection and/or Prevention Systems (IDPS) represent an important line of defense against a variety of attacks that can compromise the security and proper functioning of an enterprise information system. IDPSs can be network or host-based and can collaborate in order to provide better detection of malicious traffic. Although several IDPS systems have been proposed, their appropriate con figuration and control for e effective detection/ prevention of attacks and efficient resource consumption is still far from trivial. Another concern is related to the slowing down of system performance when maximum security is applied, hence the need to trade o between security enforcement levels and the performance and usability of an enterprise information system. In this dissertation, we present a security management framework for the configuration and control of the security enforcement mechanisms of an enterprise information system. The approach leverages the dynamic adaptation of security measures based on the assessment of system vulnerability and threat prediction, and provides several levels of attack containment. Furthermore, we study the impact of security enforcement levels on the performance and usability of an enterprise information system. In particular, we analyze the impact of an IDPS con figuration on the resulting security of the network, and on the network performance. We also analyze the performance of the IDPS for different con figurations and under different traffic characteristics. The analysis can then be used to predict the impact of a given security con figuration on the prediction of the impact on network performance