Graphical application for the statistical analysis of copy number variations in aCGH data

This document is the final report describing the development process of a graphical, statistical analysis application of copy number variations in aCGH data. The document is intended to provide an insight in the development process used to produce the final prototype delivered by the project. The project entailed the design and implementation of a graphical, statistical analysis applica- tion for aCGH data. The applications main functionality is the displaying of the corresponding aCGH profile, as well as the analysis of this profile in order to determine any significant copy number variations in the analysed genome. The application also identifies genes located in these significant regions and provides annotation data about these genes, which are retrieved from a variety of external databases. Other functionality included by the product are the export of the displayed data as well as the displaying of relations between the identified gene in a circular plot using the Circos application. The above listed functionality was derived from the extensive list of requirements created during the requirements phase of the development. The creation of this list was supported well by the basic knowledge acquired during the orientation phase, which proved invaluable in the interviews with the clients. The design of the system divides the system into a set of six subsystems, in which the database component is divided into a client-server component. The Ibidas system forms the server-side element of this component. The subsystem division is designed to keep the different compo- nents of the application compartmentalised and well-defined. The application also incorporates a multi-threaded design in order to keep the application responsive when performing lengthy tasks. The main problems encountered during the implementation of the application was the size of the data, which required a number of optimisations even though the data structures were de- signed accordingly. The main performance problems were encountered in the visualisation of data, which were solved by the implementation of a customised and optimised view to draw the data efficiently. The product has been subjected to a number of automated and manual tests to verify it meets the set requirements of functionality and the expectance of the clients. The product produced in this project meets the set requirements and has therefore been suc- cessful. The developed prototype is still a prototype demonstrating its possibilities however and leaves much room for improvement before it should be applied in actual use cases.BioinformaticsElectrical Engineering, Mathematics and Computer Scienc

Unreal Goal Bots

It remains a challenge with current state of the art technology to use BDI agents to control real-time, dynamic and complex environments. We report on our effort to connect the GOAL agent programming language to the real-time game UNREAL TOURNAMENT 2004. We focus in particular on the design of a suitable interface to manage agent-bot interaction and argue that the use of a recent toolkit for developing an agent-environment interface provides many advantages.Intelligent SystemsElectrical Engineering, Mathematics and Computer Scienc