Computer-aided programming using formally specificed design templates

This paper describes a formal component language, used to support automated component-based program development. The components, referred to as templates, are machine processable, meaning that appropriate tool support, such as retrieval support, can be developed. The templates are highly adaptable, meaning that they can be applied to a wide range of problems. Some of the main features of the language are described, including: higher-order parameters; state variable declarations; specification statements and conditionals; applicability conditions and theories; meta-level place holders; and abstract data structures.

Computer aided selection of candidate vaccine antigens

Immunoinformatics is an emergent branch of informatics science that long ago pullulated from the tree of knowledge that is bioinformatics. It is a discipline which applies informatic techniques to problems of the immune system. To a great extent, immunoinformatics is typified by epitope prediction methods. It has found disappointingly limited use in the design and discovery of new vaccines, which is an area where proper computational support is generally lacking. Most extant vaccines are not based around isolated epitopes but rather correspond to chemically-treated or attenuated whole pathogens or correspond to individual proteins extract from whole pathogens or correspond to complex carbohydrate. In this chapter we attempt to review what progress there has been in an as-yet-underexplored area of immunoinformatics: the computational discovery of whole protein antigens. The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. We begin our review by placing antigen prediction firmly into context, exploring the role of reverse vaccinology in the design and discovery of vaccines. We also highlight several competing yet ultimately complementary methodological approaches: sub-cellular location prediction, identifying antigens using sequence similarity, and the use of sophisticated statistical approaches for predicting the probability of antigen characteristics. We end by exploring how a systems immunomics approach to the prediction of immunogenicity would prove helpful in the prediction of antigens.

Integrating security services into computer supported cooperative work

This research describes the development of a groupware system which adds security services to a Computer Supported Cooperative Work system operating over the Internet. The security services use cryptographic techniques to provide a secure access control service and an information protection service. These security services are implemented as a protection layer for the groupware system. These layers are called External Security Layer (ESL) and Internal Security Layer (ISL) respectively. The security services are sufficiently flexible to allow the groupware system to operate in both synchronous and asynchronous modes. The groupware system developed - known as Secure Software Inspection Groupware (SecureSIG) - provides security for a distributed group performing software inspection. SecureSIG extends previous work on developing flexible software inspection groupware (FlexSIG) Sahibuddin, 1999). The SecureSIG model extends the FlexSIG model, and the prototype system was added to the FlexSIG prototype. The prototype was built by integrating existing software, communication and cryptography tools and technology. Java Cryptography Extension (JCE) and Internet technology were used to build the prototype. To test the suitability and transparency of the system, an evaluation was conducted. A questionnaire was used to assess user acceptability.

Modelling tribology of slider and disk in a computer hard drive system

Issues of wear and tribology are increasingly important in computer hard drives as slider flying heights are becoming lower and disk protective coatings thinner to minimise spacing loss and allow higher areal density. Friction, stiction and wear between the slider and disk in a hard drive were studied using Accelerated Friction Test (AFT) apparatus. Contact Start Stop (CSS) and constant speed drag tests were performed using commercial rigid disks and two different air bearing slider types. Friction and stiction were captured during testing by a set of strain gauges. System parameters were varied to investigate their effect on tribology at the head/disk interface. Chosen parameters were disk spinning velocity, slider fly height, temperature, humidity and intercycle pause. The effect of different disk texturing methods was also studied. Models were proposed to explain the influence of these parameters on tribology. Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM) were used to study head and disk topography at various test stages and to provide physical parameters to verify the models. X-ray Photoelectron Spectroscopy (XPS) was employed to identify surface composition and determine if any chemical changes had occurred as a result of testing. The parameters most likely to influence the interface were identified for both CSS and drag testing. Neural Network modelling was used to substantiate results. Topographical AFM scans of disk and slider were exported numerically to file and explored extensively. Techniques were developed which improved line and area analysis. A method for detecting surface contacts was also deduced, results supported and explained observed AFT behaviour. Finally surfaces were computer generated to simulate real disk scans, this allowed contact analysis of many types of surface to be performed. Conclusions were drawn about what disk characteristics most affected contacts and hence friction, stiction and wear.

Analysis of computer communication systems by use of digital signal processing methods

Queueing theory is an effective tool in the analysis of canputer camrunication systems. Many results in queueing analysis have teen derived in the form of Laplace and z-transform expressions. Accurate inversion of these transforms is very important in the study of computer systems, but the inversion is very often difficult. In this thesis, methods for solving some of these queueing problems, by use of digital signal processing techniques, are presented. The z-transform of the queue length distribution for the Mj GY jl system is derived. Two numerical methods for the inversion of the transfom, together with the standard numerical technique for solving transforms with multiple queue-state dependence, are presented. Bilinear and Poisson transform sequences are presented as useful ways of representing continuous-time functions in numerical computations.

Development of real-time process control systems using formal techniques

A major application of computers has been to control physical processes in which the computer is embedded within some large physical process and is required to control concurrent physical processes. The main difficulty with these systems is their event-driven characteristics, which complicate their modelling and analysis. Although a number of researchers in the process system community have approached the problems of modelling and analysis of such systems, there is still a lack of standardised software development formalisms for the system (controller) development, particular at early stage of the system design cycle. This research forms part of a larger research programme which is concerned with the development of real-time process-control systems in which software is used to control concurrent physical processes. The general objective of the research in this thesis is to investigate the use of formal techniques in the analysis of such systems at their early stages of development, with a particular bias towards an application to high speed machinery. Specifically, the research aims to generate a standardised software development formalism for real-time process-control systems, particularly for software controller synthesis. In this research, a graphical modelling formalism called Sequential Function Chart (SFC), a variant of Grafcet, is examined. SFC, which is defined in the international standard IEC1131 as a graphical description language, has been used widely in industry and has achieved an acceptable level of maturity and acceptance. A comparative study between SFC and Petri nets is presented in this thesis. To overcome identified inaccuracies in the SFC, a formal definition of the firing rules for SFC is given. To provide a framework in which SFC models can be analysed formally, an extended time-related Petri net model for SFC is proposed and the transformation method is defined. The SFC notation lacks a systematic way of synthesising system models from the real world systems. Thus a standardised approach to the development of real-time process control systems is required such that the system (software) functional requirements can be identified, captured, analysed. A rule-based approach and a method called system behaviour driven method (SBDM) are proposed as a development formalism for real-time process-control systems.

Computer control of machines utilising independent drive mechanisms

The thesis describes an investigation into methods for the specification, design and implementation of computer control systems for flexible manufacturing machines comprising multiple, independent, electromechanically-driven mechanisms. An analysis is made of the elements of conventional mechanically-coupled machines in order that the operational functions of these elements may be identified. This analysis is used to define the scope of requirements necessary to specify the format, function and operation of a flexible, independently driven mechanism machine. A discussion of how this type of machine can accommodate modern manufacturing needs of high-speed and flexibility is presented. A sequential method of capturing requirements for such machines is detailed based on a hierarchical partitioning of machine requirements from product to independent drive mechanism. A classification of mechanisms using notations, including Data flow diagrams and Petri-nets, is described which supports capture and allows validation of requirements. A generic design for a modular, IDM machine controller is derived based upon hierarchy of control identified in these machines. A two mechanism experimental machine is detailed which is used to demonstrate the application of the specification, design and implementation techniques. A computer controller prototype and a fully flexible implementation for the IDM machine, based on Petri-net models described using the concurrent programming language Occam, is detailed. The ability of this modular computer controller to support flexible, safe and fault-tolerant operation of the two intermittent motion, discrete-synchronisation independent drive mechanisms is presented. The application of the machine development methodology to industrial projects is established.

CADS*: Computer-Aided Development of self-* systems

We present the prototype tool CADS* for the computer-aided development of an important class of self-* systems, namely systems whose components can be modelled as Markov chains. Given a Markov chain representation of the IT components to be included into a self-* system, CADS* automates or aids (a) the development of the artifacts necessary to build the self-* system; and (b) their integration into a fully-operational self-* solution. This is achieved through a combination of formal software development techniques including model transformation, model-driven code generation and dynamic software reconfiguration.