Heuristic algorithm for computing reversal distance with multigene families via binary integer programming

Hannenhalli and Pevzner developed the first polynomial-time algorithm for the combinatorial problem of sorting of signed genomic data. Their algorithm solves the minimum number of reversals required for rearranging a genome to another when gene duplication is nonexisting. In this paper, we show how to extend the Hannenhalli-Pevzner approach to genomes with multigene families. We propose a new heuristic algorithm to compute the reversal distance between two genomes with multigene families via the concept of binary integer programming without removing gene duplicates. The experimental results on simulated and real biological data demonstrate that the proposed algorithm is able to find the reversal distance accurately. ©2005 IEEE

The real-time refinement calculus: A foundation for machine-independent real-time programming

The real-time refinement calculus is an extension of the standard refinement calculus in which programs are developed from a precondition plus post-condition style of specification. In addition to adapting standard refinement rules to be valid in the real-time context, specific rules are required for the timing constructs such as delays and deadlines. Because many real-time programs may be nonterminating, a further extension is to allow nonterminating repetitions. A real-time specification constrains not only what values should be output, but when they should be output. Hence for a program to implement such a specification, it must guarantee to output values by the specified times. With standard programming languages such guarantees cannot be made without taking into account the timing characteristics of the implementation of the program on a particular machine. To avoid having to consider such details during the refinement process, we have extended our real-time programming language with a deadline command. The deadline command takes no time to execute and always guarantees to meet the specified time; if the deadline has already passed the deadline command is infeasible (miraculous in Dijkstra's terminology). When such a realtime program is compiled for a particular machine, one needs to ensure that all execution paths leading to a deadline are guaranteed to reach it by the specified time. We consider this checking as part of an extended compilation phase. The addition of the deadline command restores for the real-time language the advantage of machine independence enjoyed by non-real-time programming languages.

Combining data driven programming with component based software development:with applications in geovisualisation and dynamic data driven application systems

Software development methodologies are becoming increasingly abstract, progressing from low level assembly and implementation languages such as C and Ada, to component based approaches that can be used to assemble applications using technologies such as JavaBeans and the .NET framework. Meanwhile, model driven approaches emphasise the role of higher level models and notations, and embody a process of automatically deriving lower level representations and concrete software implementations. The relationship between data and software is also evolving. Modern data formats are becoming increasingly standardised, open and empowered in order to support a growing need to share data in both academia and industry. Many contemporary data formats, most notably those based on XML, are self-describing, able to specify valid data structure and content, and can also describe data manipulations and transformations. Furthermore, while applications of the past have made extensive use of data, the runtime behaviour of future applications may be driven by data, as demonstrated by the field of dynamic data driven application systems. The combination of empowered data formats and high level software development methodologies forms the basis of modern game development technologies, which drive software capabilities and runtime behaviour using empowered data formats describing game content. While low level libraries provide optimised runtime execution, content data is used to drive a wide variety of interactive and immersive experiences. This thesis describes the Fluid project, which combines component based software development and game development technologies in order to define novel component technologies for the description of data driven component based applications. The thesis makes explicit contributions to the fields of component based software development and visualisation of spatiotemporal scenes, and also describes potential implications for game development technologies. The thesis also proposes a number of developments in dynamic data driven application systems in order to further empower the role of data in this field.

Towards identifying salient patterns in genetic programming individuals

This thesis addresses the problem of offline identification of salient patterns in genetic programming individuals. It discusses the main issues related to automatic pattern identification systems, namely that these (a) should help in understanding the final solutions of the evolutionary run, (b) should give insight into the course of evolution and (c) should be helpful in optimizing future runs. Moreover, it proposes an algorithm, Extended Pattern Growing Algorithm ([E]PGA) to extract, filter and sort the identified patterns so that these fulfill as many as possible of the following criteria: (a) they are representative for the evolutionary run and/or search space, (b) they are human-friendly and (c) their numbers are within reasonable limits. The results are demonstrated on six problems from different domains.

Using Problems to Introduce some Tools and Technologies for Implementation of Graphics and Animation in C#

This paper is devoted to the learning of event programming by using Visual C# in specialized training in Informatics in high schools. Some basic tools and technologies for the implementation of graphics and animation in C# are discussed. Two example problems are proposed.

On the Equivalence between Assumption-Based Argumentation and Logic Programming

Postprint

Epigenetics and developmental programming of welfare and production traits in farm animals

Acknowledgements Financial support for composing this article was obtained from the Agriculture and Horticulture Development Board (AHDB, Beef and Lamb), UK. Concept of review was also initiated from discussions originating from EU COST Action FA1201, Epiconcept: Epigenetics and Periconception Environment