SimuMap: a computational system for spatial modelling

The paper presents a computational system based upon formal principles to run spatial models for environmental processes. The simulator is named SimuMap because it is typically used to simulate spatial processes over a mapped representation of terrain. A model is formally represented in SimuMap as a set of coupled sub-models. The paper considers the situation where spatial processes operate at different time levels, but are still integrated. An example of such a situation commonly occurs in watershed hydrology where overland flow and stream channel flow have very different flow rates but are highly related as they are subject to the same terrain runoff processes. SimuMap is able to run a network of sub-models that express different time-space derivatives for water flow processes. Sub-models may be coded generically with a map algebra programming language that uses a surface data model. To address the problem of differing time levels in simulation, the paper: (i) reviews general approaches for numerical solvers, (ii) considers the constraints that need to be enforced to use more adaptive time steps in discrete time specified simulations, and (iii) scaling transfer rates in equations that use different time bases for time-space derivatives. A multistep scheme is proposed for SimuMap. This is presented along with a description of its visual programming interface, its modelling formalisms and future plans. (C) 2003 Elsevier Ltd. All rights reserved.

Producing computer-generated tailored written information for stroke patients and their carers: System development and preliminary evaluation

Purpose: The aim of this project was to design and evaluate a system that would produce tailored information for stroke patients and their carers, customised according to their informational needs, and facilitate communication between the patient and, health professional. Method: A human factors development approach was used to develop a computer system, which dynamically compiles stroke education booklets for patients and carers. Patients and carers are able to select the topics about which they wish to receive information, the amount of information they want, and the font size of the printed booklet. The system is designed so that the health professional interacts with it, thereby providing opportunities for communication between the health professional and patient/carer at a number of points in time. Results: Preliminary evaluation of the system by health professionals, patients and carers was positive. A randomised controlled trial that examines the effect of the system on patient and carer outcomes is underway. (C) 2004 Elsevier Ireland Ltd. All rights reserved.

Hybrid knowledge representation in a blackboard KBS for liquid retaining structure design

This paper highlights the importance of design expertise, for designing liquid retaining structures, including subjective judgments and professional experience. Design of liquid retaining structures has special features different from the others. Being more vulnerable to corrosion problem, they have stringent requirements against serviceability limit state of crack. It is the premise of the study to transferring expert knowledge in a computerized blackboard system. Hybrid knowledge representation schemes, including production rules, object-oriented programming, and procedural methods, are employed to express engineering heuristics and standard design knowledge during the development of the knowledge-based system (KBS) for design of liquid retaining structures. This approach renders it possible to take advantages of the characteristics of each method. The system can provide the user with advice on preliminary design, loading specification, optimized configuration selection and detailed design analysis of liquid retaining structure. It would be beneficial to the field of retaining structure design by focusing on the acquisition and organization of expert knowledge through the development of recent artificial intelligence technology. (C) 2003 Elsevier Ltd. All rights reserved.

An expert system on design of liquid-retaining structures with blackboard architecture

The design of liquid-retaining structures involves many decisions to be made by the designer based on rules of thumb, heuristics, judgement, codes of practice and previous experience. Structural design problems are often ill structured and there is a need to develop programming environments that can incorporate engineering judgement along with algorithmic tools. Recent developments in artificial intelligence have made it possible to develop an expert system that can provide expert advice to the user in the selection of design criteria and design parameters. This paper introduces the development of an expert system in the design of liquid-retaining structures using blackboard architecture. An expert system shell, Visual Rule Studio, is employed to facilitate the development of this prototype system. It is a coupled system combining symbolic processing with traditional numerical processing. The expert system developed is based on British Standards Code of Practice BS8007. Explanations are made to assist inexperienced designers or civil engineering students to learn how to design liquid-retaining structures effectively and sustainably in their design practices. The use of this expert system in disseminating heuristic knowledge and experience to practitioners and engineering students is discussed.

Tool support for executable documentation of Java class hierarchies

While object-oriented programming offers great solutions for today's software developers, this success has created difficult problems in class documentation and testing. In Java, two tools provide assistance: Javadoc allows class interface documentation to be embedded as code comments and JUnit supports unit testing by providing assert constructs and a test framework. This paper describes JUnitDoc, an integration of Javadoc and JUnit, which provides better support for class documentation and testing. With JUnitDoc, test cases are embedded in Javadoc comments and used as both examples for documentation and test cases for quality assurance. JUnitDoc extracts the test cases for use in HTML files serving as class documentation and in JUnit drivers for class testing. To address the difficult problem of testing inheritance hierarchies, JUnitDoc provides a novel solution in the form of a parallel test hierarchy. A small controlled experiment compares the readability of JUnitDoc documentation to formal documentation written in Object-Z. Copyright (c) 2005 John Wiley & Sons, Ltd.

A theory for execution-time derivation in real-time programs

We provide an abstract command language for real-time programs and outline how a partial correctness semantics can be used to compute execution times. The notions of a timed command, refinement of a timed command, the command traversal condition, and the worst-case and best-case execution time of a command are formally introduced and investigated with the help of an underlying weakest liberal precondition semantics. The central result is a theory for the computation of worst-case and best-case execution times from the underlying semantics based on supremum and infimum calculations. The framework is applied to the analysis of a message transmitter program and its implementation. (c) 2005 Elsevier B.V. All rights reserved.

Specification and validation of process constraints for flexible workflows

Workflow systems have traditionally focused on the so-called production processes which are characterized by pre-definition, high volume, and repetitiveness. Recently, the deployment of workflow systems in non-traditional domains such as collaborative applications, e-learning and cross-organizational process integration, have put forth new requirements for flexible and dynamic specification. However, this flexibility cannot be offered at the expense of control, a critical requirement of business processes. In this paper, we will present a foundation set of constraints for flexible workflow specification. These constraints are intended to provide an appropriate balance between flexibility and control. The constraint specification framework is based on the concept of pockets of flexibility which allows ad hoc changes and/or building of workflows for highly flexible processes. Basically, our approach is to provide the ability to execute on the basis of a partially specified model, where the full specification of the model is made at runtime, and may be unique to each instance. The verification of dynamically built models is essential. Where as ensuring that the model conforms to specified constraints does not pose great difficulty, ensuring that the constraint set itself does not carry conflicts and redundancy is an interesting and challenging problem. In this paper, we will provide a discussion on both the static and dynamic verification aspects. We will also briefly present Chameleon, a prototype workflow engine that implements these concepts. (c) 2004 Elsevier Ltd. All rights reserved.

Procedures and parameters in the real-time program refinement calculus

The real-time refinement calculus is a formal method for the systematic derivation of real-time programs from real-time specifications in a style similar to the non-real-time refinement calculi of Back and Morgan. In this paper we extend the real-time refinement calculus with procedures and provide refinement rules for refining real-time specifications to procedure calls. A real-time specification can include constraints on, not only what outputs are produced, but also when they are produced. The derived programs can also include time constraints oil when certain points in the program must be reached; these are expressed in the form of deadline commands. Such programs are machine independent. An important consequence of the approach taken is that, not only are the specifications machine independent, but the whole refinement process is machine independent. To implement the machine independent code on a target machine one has a separate task of showing that the compiled machine code will reach all its deadlines before they expire. For real-time programs, externally observable input and output variables are essential. These differ from local variables in that their values are observable over the duration of the execution of the program. Hence procedures require input and output parameter mechanisms that are references to the actual parameters so that changes to external inputs are observable within the procedure and changes to output parameters are externally observable. In addition, we allow value and result parameters. These may be auxiliary parameters, which are used for reasoning about the correctness of real-time programs as well as in the expression of timing deadlines, but do not lead to any code being generated for them by a compiler. (c) 2006 Elsevier B.V. All rights reserved.

Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

Multi-threaded Communicating Agents in Qu-Prolog

In this tutorial paper we summarise the key features of the multi-threaded Qu-Prolog language for implementing multi-threaded communicating agent applications. Internal threads of an agent communicate using the shared dynamic database used as a generalisation of Linda tuple store. Threads in different agents, perhaps on different hosts, communicate using either a thread-to-thread store and forward communication system, or by a publish and subscribe mechanism in which messages are routed to their destinations based on content test subscriptions. We illustrate the features using an auction house application. This is fully distributed with multiple auctioneers and bidders which participate in simultaneous auctions. The application makes essential use of the three forms of inter-thread communication of Qu-Prolog. The agent bidding behaviour is specified graphically as a finite state automaton and its implementation is essentially the execution of its state transition function. The paper assumes familiarity with Prolog and the basic concepts of multi-agent systems.

Compact tiled display with uniform illumination

The demand for more pixels is beginning to be met as manufacturers increase the native resolution of projector chips. Tiling several projectors still offers a solution to augment the pixel capacity of a display. However, problems of color and illumination uniformity across projectors need to be addressed as well as the computer software required to drive such devices. We present the results obtained on a desktop-size tiled projector array of three D-ILA projectors sharing a common illumination source. A short throw lens (0.8:1) on each projector yields a 21-in. diagonal for each image tile; the composite image on a 3×1 array is 3840×1024 pixels with a resolution of about 80 dpi. The system preserves desktop resolution, is compact, and can fit in a normal room or laboratory. The projectors are mounted on precision six-axis positioners, which allow pixel level alignment. A fiber optic beamsplitting system and a single set of red, green, and blue dichroic filters are the key to color and illumination uniformity. The D-ILA chips inside each projector can be adjusted separately to set or change characteristics such as contrast, brightness, or gamma curves. The projectors were then matched carefully: photometric variations were corrected, leading to a seamless image. Photometric measurements were performed to characterize the display and are reported here. This system is driven by a small PC cluster fitted with graphics cards and running Linux. It can be scaled to accommodate an array of 2×3 or 3×3 projectors, thus increasing the number of pixels of the final image. Finally, we present current uses of the display in fields such as astrophysics and archaeology (remote sensing).

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

Fast evolution strategies

Evolution strategies are a class of general optimisation algorithms which are applicable to functions that are multimodal, nondifferentiable, or even discontinuous. Although recombination operators have been introduced into evolution strategies, the primary search operator is still mutation. Classical evolution strategies rely on Gaussian mutations. A new mutation operator based on the Cauchy distribution is proposed in this paper. It is shown empirically that the new evolution strategy based on Cauchy mutation outperforms the classical evolution strategy on most of the 23 benchmark problems tested in this paper. The paper also shows empirically that changing the order of mutating the objective variables and mutating the strategy parameters does not alter the previous conclusion significantly, and that Cauchy mutations with different scaling parameters still outperform the Gaussian mutation with self-adaptation. However, the advantage of Cauchy mutations disappears when recombination is used in evolution strategies. It is argued that the search step size plays an important role in determining evolution strategies' performance. The large step size of recombination plays a similar role as Cauchy mutation.

An improved seeded region growing algorithm

Recently Adams and Bischof (1994) proposed a novel region growing algorithm for segmenting intensity images. The inputs to the algorithm are the intensity image and a set of seeds - individual points or connected components - that identify the individual regions to be segmented. The algorithm grows these seed regions until all of the image pixels have been assimilated. Unfortunately the algorithm is inherently dependent on the order of pixel processing. This means, for example, that raster order processing and anti-raster order processing do not, in general, lead to the same tessellation. In this paper we propose an improved seeded region growing algorithm that retains the advantages of the Adams and Bischof algorithm fast execution, robust segmentation, and no tuning parameters - but is pixel order independent. (C) 1997 Elsevier Science B.V.