DVMS 1.5: A user manual (the data visualization and modeling system)

The data available during the drug discovery process is vast in amount and diverse in nature. To gain useful information from such data, an effective visualisation tool is required. To provide better visualisation facilities to the domain experts (screening scientist, biologist, chemist, etc.),we developed a software which is based on recently developed principled visualisation algorithms such as Generative Topographic Mapping (GTM) and Hierarchical Generative Topographic Mapping (HGTM). The software also supports conventional visualisation techniques such as Principal Component Analysis, NeuroScale, PhiVis, and Locally Linear Embedding (LLE). The software also provides global and local regression facilities . It supports regression algorithms such as Multilayer Perceptron (MLP), Radial Basis Functions network (RBF), Generalised Linear Models (GLM), Mixture of Experts (MoE), and newly developed Guided Mixture of Experts (GME). This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install & use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

miniDVMS v1.8 : A user manual(The data visualization and modeling system)

Today, the data available to tackle many scientific challenges is vast in quantity and diverse in nature. The exploration of heterogeneous information spaces requires suitable mining algorithms as well as effective visual interfaces. miniDVMS v1.8 provides a flexible visual data mining framework which combines advanced projection algorithms developed in the machine learning domain and visual techniques developed in the information visualisation domain. The advantage of this interface is that the user is directly involved in the data mining process. Principled projection methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), are integrated with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates, and user interaction facilities, to provide this integrated visual data mining framework. The software also supports conventional visualisation techniques such as principal component analysis (PCA), Neuroscale, and PhiVis. This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install and use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

Linking the witness simulation software to an expert system to represent a decision-making process

Expert systems, and artificial intelligence more generally, can provide a useful means for representing decision-making processes. By linking expert systems software to simulation software an effective means of including these decision-making processes in a simulation model can be achieved. This paper demonstrates how a commercial-off-the-shelf simulation package (Witness) can be linked to an expert systems package (XpertRule) through a Visual Basic interface. The methodology adopted could be used for models, and possibly software, other than those presented here.

The design of a real-time nowcasting system for localised weather

National meteorological offices are largely concerned with synoptic-scale forecasting where weather predictions are produced for a whole country for 24 hours ahead. In practice, many local organisations (such as emergency services, construction industries, forestry, farming, and sports) require only local short-term, bespoke, weather predictions and warnings. This thesis shows that the less-demanding requirements do not require exceptional computing power and can be met by a modern, desk-top system which monitors site-specific ground conditions (such as temperature, pressure, wind speed and direction, etc) augmented with above ground information from satellite images to produce `nowcasts'. The emphasis in this thesis has been towards the design of such a real-time system for nowcasting. Local site-specific conditions are monitored using a custom-built, stand alone, Motorola 6809 based sub-system. Above ground information is received from the METEOSAT 4 geo-stationary satellite using a sub-system based on a commercially available equipment. The information is ephemeral and must be captured in real-time. The real-time nowcasting system for localised weather handles the data as a transparent task using the limited capabilities of the PC system. Ground data produces a time series of measurements at a specific location which represents the past-to-present atmospheric conditions of the particular site from which much information can be extracted. The novel approach adopted in this thesis is one of constructing stochastic models based on the AutoRegressive Integrated Moving Average (ARIMA) technique. The satellite images contain features (such as cloud formations) which evolve dynamically and may be subject to movement, growth, distortion, bifurcation, superposition, or elimination between images. The process of extracting a weather feature, following its motion and predicting its future evolution involves algorithms for normalisation, partitioning, filtering, image enhancement, and correlation of multi-dimensional signals in different domains. To limit the processing requirements, the analysis in this thesis concentrates on an `area of interest'. By this rationale, only a small fraction of the total image needs to be processed, leading to a major saving in time. The thesis also proposes an extention to an existing manual cloud classification technique for its implementation in automatically classifying a cloud feature over the `area of interest' for nowcasting using the multi-dimensional signals.

Mathematical methods in power system stability studies

In this thesis various mathematical methods of studying the transient and dynamic stabiIity of practical power systems are presented. Certain long established methods are reviewed and refinements of some proposed. New methods are presented which remove some of the difficulties encountered in applying the powerful stability theories based on the concepts of Liapunov. Chapter 1 is concerned with numerical solution of the transient stability problem. Following a review and comparison of synchronous machine models the superiority of a particular model from the point of view of combined computing time and accuracy is demonstrated. A digital computer program incorporating all the synchronous machine models discussed, and an induction machine model, is described and results of a practical multi-machine transient stability study are presented. Chapter 2 reviews certain concepts and theorems due to Liapunov. In Chapter 3 transient stability regions of single, two and multi~machine systems are investigated through the use of energy type Liapunov functions. The treatment removes several mathematical difficulties encountered in earlier applications of the method. In Chapter 4 a simple criterion for the steady state stability of a multi-machine system is developed and compared with established criteria and a state space approach. In Chapters 5, 6 and 7 dynamic stability and small signal dynamic response are studied through a state space representation of the system. In Chapter 5 the state space equations are derived for single machine systems. An example is provided in which the dynamic stability limit curves are plotted for various synchronous machine representations. In Chapter 6 the state space approach is extended to multi~machine systems. To draw conclusions concerning dynamic stability or dynamic response the system eigenvalues must be properly interpreted, and a discussion concerning correct interpretation is included. Chapter 7 presents a discussion of the optimisation of power system small sjgnal performance through the use of Liapunov functions.

Reconfigurable service-oriented architecture for autonomic computing

Almost a decade has passed since the objectives and benefits of autonomic computing were stated, yet even the latest system designs and deployments exhibit only limited and isolated elements of autonomic functionality. In previous work, we identified several of the key challenges behind this delay in the adoption of autonomic solutions, and proposed a generic framework for the development of autonomic computing systems that overcomes these challenges. In this article, we describe how existing technologies and standards can be used to realise our autonomic computing framework, and present its implementation as a service-oriented architecture. We show how this implementation employs a combination of automated code generation, model-based and object-oriented development techniques to ensure that the framework can be used to add autonomic capabilities to systems whose characteristics are unknown until runtime. We then use our framework to develop two autonomic solutions for the allocation of server capacity to services of different priorities and variable workloads, thus illustrating its application in the context of a typical data-centre resource management problem.

Resource-definition policies for autonomic computing

The paper introduces a framework for the formal specification of autonomic computing policies, and uses it to define a new type of autonomic computing policy termed a resource-definition policy. We describe the semantics of resource-definition policies, explain how they can be used as a basis for the development of autonomic system of systems, and present a sample data-centre application built using the new policy type.

An architecture for a collaborative authoring system

Collaborative working with the aid of computers is increasing rapidly due to the widespread use of computer networks, geographic mobility of people, and small powerful personal computers. For the past ten years research has been conducted into this use of computing technology from a wide variety of perspectives and for a wide range of uses. This thesis adds to that previous work by examining the area of collaborative writing amongst groups of people. The research brings together a number of disciplines, namely sociology for examining group dynamics, psychology for understanding individual writing and learning processes, and computer science for database, networking, and programming theory. The project initially looks at groups and how they form, communicate, and work together, progressing on to look at writing and the cognitive processes it entails for both composition and retrieval. The thesis then details a set of issues which need to be addressed in a collaborative writing system. These issues are then followed by developing a model for collaborative writing, detailing an iterative process of co-ordination, writing and annotation, consolidation, and negotiation, based on a structured but extensible document model. Implementation issues for a collaborative application are then described, along with various methods of overcoming them. Finally the design and implementation of a collaborative writing system, named Collaborwriter, is described in detail, which concludes with some preliminary results from initial user trials and testing.

Factors affecting end-user computing sophistication in small business

This thesis describes research on End-User Computing (EUC) in small business in an environment where no Information System (IS) support and expertise are available. The research aims to identify the factors that contribute to EUC Sophistication and understand the extent small firms are capable of developing their own applications. The intention is to assist small firms to adopt EUC, encourage better utilisation of their IT resources and gain the benefits associated with computerisation. The factors examined are derived inductively from previous studies where a model is developed to map these factors with the degree of sophistication associated with IT and EUC. This study attempts to combine the predictive power of quantitative research through surveys with the explanatory power of qualitative research through action-oriented case study. Following critical examination of the literature, a survey of IT Adoption and EUC was conducted. Instruments were then developed to measure EUC and IT Sophistication indexes based on sophistication constructs adapted from previous studies using data from the survey. This is followed by an in-depth action case study involving two small firms to investigate the EUC phenomenon in its real life context. The accumulated findings from these mixed research strategies are used to form the final model of EUC Sophistication in small business. Results of the study suggest both EUC Sophistication and the Presence of EUC in small business are affected by Management Support and Behaviour towards EUC. Additionally EUC Sophistication is also affected by the presence of an EUC Champion. Results are also consistent with respect to the independence between IT Sophistication and EUC Sophistication. The main research contributions include an accumulated knowledge of EUC in small business, the Model of EUC Sophistication, an instrument to measure EUC Sophistication Index for small firms, and a contribution to research methods in IS.

The development of a multi-function computer-assisted instruction system using a hierarchical database structure as the lesson compendium.

Computer-Based Learning systems of one sort or another have been in existence for almost 20 years, but they have yet to achieve real credibility within Commerce, Industry or Education. A variety of reasons could be postulated for this, typically: - cost - complexity - inefficiency - inflexibility - tedium Obviously different systems deserve different levels and types of criticism, but it still remains true that Computer-Based Learning (CBL) is falling significantly short of its potential. Experience of a small, but highly successful CBL system within a large, geographically distributed industry (the National Coal Board) prompted an investigation into currently available packages, the original intention being to purchase the most suitable software and run it on existing computer hardware, alongside existing software systems. It became apparent that none of the available CBL packages were suitable, and a decision was taken to develop an in-house Computer-Assisted Instruction system according to the following criteria: - cheap to run; - easy to author course material; - easy to use; - requires no computing knowledge to use (as either an author or student) ; - efficient in the use of computer resources; - has a comprehensive range of facilities at all levels. This thesis describes the initial investigation, resultant observations and the design, development and implementation of the SCHOOL system. One of the principal characteristics c£ SCHOOL is that it uses a hierarchical database structure for the storage of course material - thereby providing inherently a great deal of the power, flexibility and efficiency originally required. Trials using the SCHOOL system on IBM 303X series equipment are also detailed, along with proposed and current development work on what is essentially an operational CBL system within a large-scale Industrial environment.

A knowledge-based system for process planning in a seamless steel tube plant

The thesis describes the work carried out to develop a prototype knowledge-based system 'KBS-SETUPP' to generate process plans for the manufacture of seamless tubes. The work is specifically related to a plant in which hollows are made from solid billets using a rotary piercing process and then reduced to required size and finished properties using the fixed plug cold drawing process. The thesis first discusses various methods of tube production in order to give a general background of tube manufacture. Then a review of the automation of the process planning function is presented in terms of its basic sub-tasks and the techniques and suitability of a knowledge-based system is established. In the light of such a review and a case study, the process planning problem is formulated in the domain of seamless tube manufacture, its basic sub-tasks are identified and capabilities and constraints of the available equipment in the specific plant are established. The task of collecting and collating the process planning knowledge in seamless tube manufacture is discussed and is mostly fulfilled from domain experts, analysing of existing manufacturing records specific to plant, textbooks and applicable Standards. For the cold drawing mill, tube-drawing schedules have been rationalised to correspond with practice. The validation of such schedules has been achieved by computing the process parameters and then comparing these with the drawbench capacity to avoid over-loading. The existing models cannot be simulated in the computer program as such, therefore a mathematical model has been proposed which estimates the process parameters which are in close agreement with experimental values established by other researchers. To implement the concepts, a Knowledge-Based System 'KBS- SETUPP' has been developed on Personal Computer using Turbo- Prolog. The system is capable of generating process plans, production schedules and some additional capabilities to supplement process planning. The system generated process plans have been compared with the actual plans of the company and it has been shown that the results are satisfactory and encouraging and that the system has the capabilities which are useful.

Meta level component-based framework for distributed computing applications

Adaptability for distributed object-oriented enterprise frameworks is a critical mission for system evolution. Today, building adaptive services is a complex task due to lack of adequate framework support in the distributed computing environment. In this thesis, we propose a Meta Level Component-Based Framework (MELC) which uses distributed computing design patterns as components to develop an adaptable pattern-oriented framework for distributed computing applications. We describe our novel approach of combining a meta architecture with a pattern-oriented framework, resulting in an adaptable framework which provides a mechanism to facilitate system evolution. The critical nature of distributed technologies requires frameworks to be adaptable. Our framework employs a meta architecture. It supports dynamic adaptation of feasible design decisions in the framework design space by specifying and coordinating meta-objects that represent various aspects within the distributed environment. The meta architecture in MELC framework can provide the adaptability for system evolution. This approach resolves the problem of dynamic adaptation in the framework, which is encountered in most distributed applications. The concept of using a meta architecture to produce an adaptable pattern-oriented framework for distributed computing applications is new and has not previously been explored in research. As the framework is adaptable, the proposed architecture of the pattern-oriented framework has the abilities to dynamically adapt new design patterns to address technical system issues in the domain of distributed computing and they can be woven together to shape the framework in future. We show how MELC can be used effectively to enable dynamic component integration and to separate system functionality from business functionality. We demonstrate how MELC provides an adaptable and dynamic run time environment using our system configuration and management utility. We also highlight how MELC will impose significant adaptability in system evolution through a prototype E-Bookshop application to assemble its business functions with distributed computing components at the meta level in MELC architecture. Our performance tests show that MELC does not entail prohibitive performance tradeoffs. The work to develop the MELC framework for distributed computing applications has emerged as a promising way to meet current and future challenges in the distributed environment.

Clinical decision support system for point of care use: ontology driven design and software implementation

OBJECTIVES: The objective of this research was to design a clinical decision support system (CDSS) that supports heterogeneous clinical decision problems and runs on multiple computing platforms. Meeting this objective required a novel design to create an extendable and easy to maintain clinical CDSS for point of care support. The proposed solution was evaluated in a proof of concept implementation. METHODS: Based on our earlier research with the design of a mobile CDSS for emergency triage we used ontology-driven design to represent essential components of a CDSS. Models of clinical decision problems were derived from the ontology and they were processed into executable applications during runtime. This allowed scaling applications' functionality to the capabilities of computing platforms. A prototype of the system was implemented using the extended client-server architecture and Web services to distribute the functions of the system and to make it operational in limited connectivity conditions. RESULTS: The proposed design provided a common framework that facilitated development of diversified clinical applications running seamlessly on a variety of computing platforms. It was prototyped for two clinical decision problems and settings (triage of acute pain in the emergency department and postoperative management of radical prostatectomy on the hospital ward) and implemented on two computing platforms-desktop and handheld computers. CONCLUSIONS: The requirement of the CDSS heterogeneity was satisfied with ontology-driven design. Processing of application models described with the help of ontological models allowed having a complex system running on multiple computing platforms with different capabilities. Finally, separation of models and runtime components contributed to improved extensibility and maintainability of the system.

A language for self-adaptive system requirements

Self-adaptive systems have the capability to autonomously modify their behaviour at run-time in response to changes in their environment. Such systems are now commonly built in domains as diverse as enterprise computing, automotive control systems, and environmental monitoring systems. To date, however, there has been limited attention paid to how to engineer requirements for such systems. As a result, selfadaptivity is often constructed in an ad-hoc manner. In this paper, we argue that a more rigorous treatment of requirements relating to self-adaptivity is needed and that, in particular, requirements languages for self-adaptive systems should include explicit constructs for specifying and dealing with the uncertainty inherent in self-adaptive systems. We present some initial thoughts on a new requirements language for selfadaptive systems and illustrate it using examples from the services domain. © 2008 IEEE.

EPiCS:engineering proprioception in computing systems

Modern compute systems continue to evolve towards increasingly complex, heterogeneous and distributed architectures. At the same time, functionality and performance are no longer the only aspects when developing applications for such systems, and additional concerns such as flexibility, power efficiency, resource usage, reliability and cost are becoming increasingly important. This does not only raise the question of how to efficiently develop applications for such systems, but also how to cope with dynamic changes in the application behaviour or the system environment. The EPiCS Project aims to address these aspects through exploring self-awareness and self-expression. Self-awareness allows systems and applications to gather and maintain information about their current state and environment, and reason about their behaviour. Self-expression enables systems to adapt their behaviour autonomously to changing conditions. Innovations in EPiCS are based on systematic integration of research in concepts and foundations, customisable hardware/software platforms and operating systems, and self-aware networking and middleware infrastructure. The developed technologies are validated in three application domains: computational finance, distributed smart cameras and interactive mobile media systems. © 2012 IEEE.