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.

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.

Computer-aided biotechnology:from immuno-informatics to reverse vaccinology

Genome sequences from many organisms, including humans, have been completed, and high-throughput analyses have produced burgeoning volumes of 'omics' data. Bioinformatics is crucial for the management and analysis of such data and is increasingly used to accelerate progress in a wide variety of large-scale and object-specific functional analyses. Refined algorithms enable biotechnologists to follow 'computer-aided strategies' based on experiments driven by high-confidence predictions. In order to address compound problems, current efforts in immuno-informatics and reverse vaccinology are aimed at developing and tuning integrative approaches and user-friendly, automated bioinformatics environments. This will herald a move to 'computer-aided biotechnology': smart projects in which time-consuming and expensive large-scale experimental approaches are progressively replaced by prediction-driven investigations.

Computer-aided categorisation and quantification of connectives in English and Arabic (based on newspaper text corpora).

This study presents a detailed contrastive description of the textual functioning of connectives in English and Arabic. Particular emphasis is placed on the organisational force of connectives and their role in sustaining cohesion. The description is intended as a contribution for a better understanding of the variations in the dominant tendencies for text organisation in each language. The findings are expected to be utilised for pedagogical purposes, particularly in improving EFL teaching of writing at the undergraduate level. The study is based on an empirical investigation of the phenomenon of connectivity and, for optimal efficiency, employs computer-aided procedures, particularly those adopted in corpus linguistics, for investigatory purposes. One important methodological requirement is the establishment of two comparable and statistically adequate corpora, also the design of software and the use of existing packages and to achieve the basic analysis. Each corpus comprises ca 250,000 words of newspaper material sampled in accordance to a specific set of criteria and assembled in machine readable form prior to the computer-assisted analysis. A suite of programmes have been written in SPITBOL to accomplish a variety of analytical tasks, and in particular to perform a battery of measurements intended to quantify the textual functioning of connectives in each corpus. Concordances and some word lists are produced by using OCP. Results of these researches confirm the existence of fundamental differences in text organisation in Arabic in comparison to English. This manifests itself in the way textual operations of grouping and sequencing are performed and in the intensity of the textual role of connectives in imposing linearity and continuity and in maintaining overall stability. Furthermore, computation of connective functionality and range of operationality has identified fundamental differences in the way favourable choices for text organisation are made and implemented.

Computer-aided-design of saturated magnetic lenses for electron microscopes

In the last few years, there has been considerable interest in using saturated magnetic objective lenses in high resolution electron microscopes. Such lenses, in present commercial electron microscopes, are energized either by conventional or superconducting coils. Very little work, however, has been reported on the use of conventional coils in saturated magnetic electron lenses. The present investigation has been concerned with the design of high flux density saturated objective lenses of both single and double polepiece types which may be energized by conventional coils and in some cases by superconducting coils. Such coils have the advantage of being small and capable of carrying high current densities. The present work has been carried out with the aid of several computer programs based on the finite element method. The effect of the shape and position of the energizing coil on the electron optical parameter has been investigated. Electron optical properties such as chromatic and spherical aberration have been studies in detail for saturated single and double polepiece lenses. Several high flux density coils of different shapes have been investigated. The choice of the most favourable coil shape and position subject to the operational requirements, has been studied in some detail. The focal properties of such optimised lenses have been computed and compared.

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.

An Investigation into the adoption and implementation of computer aided production management systems:using the Rogers model of adoption and implementation and a social constuctionist account of technology

The research investigates the processes of adoption and implementation, by organisations, of computer aided production management systems (CAPM). It is organised around two different theoretical perspectives. The first part is informed by the Rogers model of the diffusion, adoption and implementation of innovations, and the second part by a social constructionist approach to technology. Rogers' work is critically evaluated and a model of adoption and implementation is distilled from it and applied to a set of empirical case studies. In the light of the case study data, strengths and weaknesses of the model are identified. It is argued that the model is too rational and linear to provide an adequate explanation of adoption processes. It is useful for understanding processes of implementation but requires further development. The model is not able to adequately encompass complex computer based technologies. However, the idea of 'reinvention' is identified as Roger's key concept but it needs to be conceptually extended. Both Roger's model and definition of CAPM found in the literature from production engineering tend to treat CAPM in objectivist terms. The problems with this view are addressed through a review of the literature on the sociology of technology, and it is argued that a social constructionist approach offers a more useful framework for understanding CAPM, its nature, adoption, implementation, and use. CAPM it is argued, must be understood on terms of the ways in which it is constituted in discourse, as part of a 'struggle for meaning' on the part of academics, professional engineers, suppliers, and users.

Computer aided design and manufacture for three dimensional milling

Advances in both computer technology and the necessary mathematical models capable of capturing the geometry of arbitarily shaped objects has led to the development in this thesis of a surface generation package called 'IBSCURF' aimed at providing a more economically viable solution to free-form surface manufacture. A suit of computer programs written in FORTRAN 77 has been developed to provide computer aids for every aspect of work in designing and machining free-form surfaces. A vector-valued parametric method was used for shape description and a lofting technique employed for the construction of the surface. The development of the package 'IBSCURF' consists of two phases. The first deals with CAD. The design process commences in defining the cross-sections which are represented by uniform B-spline curves as approximations to give polygons. The order of the curve and the position and number of the polygon vertices can be used as parameters for the modification to achieve the required curves. When the definitions of the sectional curves is complete, the surface is interpolated over them by cubic cardinal splines. To use the CAD function of the package to design a mould for a plastic handle, a mathematical model was developed. To facilitate the integration of design and machining using the mathematical representation of the surface, the second phase of the package is concerned with CAM which enables the generation of tool offset positions for ball-nosed cutters and a general post-processor has been developed which automatically generates NC tape programs for any CNC milling machine. The two phases of these programs have been successfully implemented, as a CAD/CAM package for free-form surfaces on the VAX 11/750 super-minicomputer with graphics facilities for displaying drawings interactively on the terminal screen. The development of this package has been beneficial in all aspects of design and machining of free form surfaces.

Computer aided manufacturing of geometric models

As systems for computer-aided-design and production of mechanical parts have developed, there has arisen a need for techniques for the comprehensive description of the desired part, including its 3-D shape. The creation and manipulation of shapes is generally known as geometric modelling. It is desirable that links be established between geometric modellers and machining programs. Currently, unbounded APT and some bounded geometry systems are being widely used in manufacturing industry for machining operations such as: milling, drilling, boring and turning, applied mainly to engineering parts. APT systems, however, are presently only linked to wire-frame drafting systems. The combination of a geometric modeller and APT will provide a powerful manufacturing system for industry from the initial design right through part manufacture using NC machines. This thesis describes a recently developed interface (ROMAPT) between a bounded geometry modeller (ROMULUS) and an unbounded NC processor (APT). A new set of theoretical functions and practical algorithms for the computer aided manufacturing of 3D solid geometric model has been investigated. This work has led to the development of a sophisticated computer program, ROMAPT, which provides a new link between CAD (in form of a goemetric modeller ROMULUS) and CAM (in form of the APT NC system). ROMAPT has been used to machine some engineering prototypes successfully both in soft foam material and aluminium. It has been demonstrated above that the theory and algorithms developed by the author for the development of computer aided manufacturing of 3D solid modelling are both valid and applicable. ROMAPT allows the full potential of a solid geometric modeller (ROMULUS) to be further exploited for NC applications without requiring major investment in new NC processor. ROMAPT supports output in APT-AC, APT4 and the CAM-I SSRI NC languages.

Computer aided process planning (CAPP) for flat rolling of copper alloys

The manufacture of copper alloy flat rolled metals involves hot and cold rolling operations, together with annealing and other secondary processes, to transform castings (mainly slabs and cakes) into such shapes as strip, plate, sheet, etc. Production is mainly to customer orders in a wide range of specifications for dimensions and properties. However, order quantities are often small and so process planning plays an important role in this industry. Much research work has been done in the past in relation to the technology of flat rolling and the details of the operations, however, there is little or no evidence of any research in the planning of processes for this type of manufacture. Practical observation in a number of rolling mills has established the type of manual process planning traditionally used in this industry. This manual approach, however, has inherent drawbacks, being particularly dependent on the individual planners who gain their knowledge over a long span of practical experience. The introduction of the retrieval CAPP approach to this industry was a first step to reduce these problems. But this could not provide a long-term answer because of the need for an experienced planner to supervise generation of any plan. It also fails to take account of the dynamic nature of the parameters involved in the planning, such as the availability of resources, operation conditions and variations in the costs. The other alternative is the use of a generative approach to planning in the rolling mill context. In this thesis, generative methods are developed for the selection of optimal routes for single orders and then for batches of orders, bearing in mind equipment restrictions, production costs and material yield. The batch order process planning involves the use of a special cluster analysis algorithm for optimal grouping of the orders. This research concentrates on cold-rolling operations. A prototype model of the proposed CAPP system, including both single order and batch order planning options, has been developed and tested on real order data in the industry. The results were satisfactory and compared very favourably with the existing manual and retrieval methods.

Computer aided design and analysis of cold formed sections

The work reported in this thesis is concerned with the improvement and expansion of the assistance given to the designer by the computer in the design of cold formed sections. The main contributions have been in four areas, which have consequently led to the fifth, the development of a methodology to optimise designs. This methodology can be considered an `Expert Design System' for cold formed sections. A different method of determining section properties of profiles was introduced, using the properties of line and circular elements. Graphics were introduced to show the outline of the profile on screen. The analysis of beam loading has been expanded to beam loading conditions where the number of supports, point loads, and uniform distributive loads can be specified by the designer. The profile can then be checked for suitability for the specified type of loading. Artificial Intelligence concepts have been introduced to give the designer decision support from the computer, in combination with the computer aided design facilities. The more complex decision support was adopted through the use of production rules. All the support was based on the British standards. A method has been introduced, by which the appropriate use of stiffeners can be determined and consequently designed by the designer. Finally, the methodology by which the designer is given assistance from the computer, without constraining the designer, was developed. This methodology gives advice to the designer on possible methods of improving the design, but allows the designer to reject that option, and analyse the profile accordingly. The methodology enables optimisation to be achieved by the designer, designing variety of profiles for a particular loading, and determining which one is best suited.

Linking finite-element analysis and computer-aided drafting processes

The aim of this research was to investigate the integration of computer-aided drafting and finite-element analysis in a linked computer-aided design procedure and to develop the necessary software. The Be'zier surface patch for surface representation was used to bridge the gap between the rather separate fields of drafting and finite-element analysis because the surfaces are defined by analytical functions which allow systematic and controlled variation of the shape and provide continuous derivatives up to any required degree. The objectives of this research were achieved by establishing : (i) A package which interpretes the engineering drawings of plate and shell structures and prepares the Be'zier net necessary for surface representation. (ii) A general purpose stand-alone meshed-surface modelling package for surface representation of plates and shells using the Be'zier surface patch technique. (iii) A translator which adapts the geometric description of plate and shell structures as given by the meshed-surface modeller to the form needed by the finite-element analysis package. The translator was extended to suit fan impellers by taking advantage of their sectorial symmetry. The linking processes were carried out for simple test structures, simplified and actual fan impellers to verify the flexibility and usefulness of the linking technique adopted. Finite-element results for thin plate and shell structures showed excellent agreement with those obtained by other investigators while results for the simplified and actual fan impellers also showed good agreement with those obtained in an earlier investigation where finite-element analysis input data were manually prepared. Some extensions of this work have also been discussed.