The Multiscale Systems Immunology project: software for cell-based immunological simulation.

BACKGROUND: Computer simulations are of increasing importance in modeling biological phenomena. Their purpose is to predict behavior and guide future experiments. The aim of this project is to model the early immune response to vaccination by an agent based immune response simulation that incorporates realistic biophysics and intracellular dynamics, and which is sufficiently flexible to accurately model the multi-scale nature and complexity of the immune system, while maintaining the high performance critical to scientific computing. RESULTS: The Multiscale Systems Immunology (MSI) simulation framework is an object-oriented, modular simulation framework written in C++ and Python. The software implements a modular design that allows for flexible configuration of components and initialization of parameters, thus allowing simulations to be run that model processes occurring over different temporal and spatial scales. CONCLUSION: MSI addresses the need for a flexible and high-performing agent based model of the immune system.

Distributed digital post-production

It is now possible to use powerful general purpose computer architectures to support post-production of both video and multimedia projects. By devising a suitable portable software architecture and using high-speed networking in an appropriate manner, a system has been constructed where editors are no longer tied to a specific location. New types of production, such as multi-threaded interactive video, are supported. Editors may also work remotely where very high speed network connection is not currently provided. An object-oriented database is used for the comprehensive cataloging of material and to support automatic audio/video object migration and replication. Copyright © 1997 by the Society of Motion Picture and Television Engineers, Inc.

A design pattern approach to bitemporal data modeling

The importance of patterns in constructing complex systems has long been recognised in other disciplines. In software engineering, for example, well-crafted object-oriented architectures contain several design patterns. Focusing on mechanisms of constructing software during system development can yield an architecture that is simpler, clearer and more understandable than if design patterns were ignored or not properly applied. In this paper, we propose a model that uses object-oriented design patterns to develop a core bitemporal conceptual model. We define three core design patterns that form a core bitemporal conceptual model of a typical bitemporal object. Our framework is known as the Bitemporal Object, State and Event Modelling Approach (BOSEMA) and the resulting core model is known as a Bitemporal Object, State and Event (BOSE) model. Using this approach, we demonstrate that we can enrich data modelling by using well known design patterns which can help designers to build complex models of bitemporal databases.

Implications for the scheduling of theory versus application in learning

This paper presents the findings of an experiment which looked at the effects of performing applied tasks (action learning) prior to the completion of the theoretical learning of these tasks (explanation-based learning), and vice-versa. The applied tasks took the form of laboratories for the Object-Oriented Analysis and Design (OOAD) course, theoretical learning was via lectures.

The Agent-Rule-Class Framework for Multi-Agent Systems

Multi-agent systems have become increasingly mature, but their appearance does not make the traditional OO approach obsolete. On the contrary, OO methodologies can benefit from the principles and tools designed for agent systems. The Agent-Rule-Class (ARC) framework is proposed as an approach that builds agents upon traditional OO system components and makes use of business rules to dictate agent behaviour with the aid of OO components. By modelling agent knowledge in business rules, the proposed paradigm provides a straightforward means to develop agent-oriented systems based on the existing object-oriented systems and offers features that are otherwise difficult to achieve in the original OO systems. The main outcome of using ARC is the achievement of adaptivity. The framework is supported by a tool that ensures agents implement up-to-date requirements from business people, reflecting desired current behaviour, without the need for frequent system rebuilds. ARC is illustrated with a rail track example.

Numerical simulation of the charge balance in an EBIT

The electron beam ions traps (EBITs) are widely used to study highly charged ions (HCIs). In an EBIT, a high energy electron beam collides with atoms and ions to generate HCIs in the trap region. It is important to study the physics in the trap. The atomic processes, such as electron impact ionisation (EI), radiative recombination (RR), dielectronic recombination (DR) and charge exchange (CX), occur in the trap and numerical simulation can give some parameters for design, predict the composition and describe charge state evolution in an EBIT [Phys. Rev. A 43 (199 1) 4861]. We are presently developing a new code, which additionally includes a description of the overlaps between the ion clouds of the various charge-states. It has been written so that it can simulate experiments where various machine parameters (e.g. beam energy and current) can vary throughout the simulation and will be able to use cross- sections either based on scaling laws or derived from atomic structure calculations. An object-oriented method is used in developing the new software, which is an efficient way to organize and write code. (C) 2003 Elsevier Science B.V. All rights reserved.

An automated machine vision system for the histological grading of cervical intraepithelial neoplasia (CIN)

The histological grading of cervical intraepithelial neoplasia (CIN) remains subjective, resulting in inter- and intra-observer variation and poor reproducibility in the grading of cervical lesions. This study has attempted to develop an objective grading system using automated machine vision. The architectural features of cervical squamous epithelium are quantitatively analysed using a combination of computerized digital image processing and Delaunay triangulation analysis; 230 images digitally captured from cases previously classified by a gynaecological pathologist included normal cervical squamous epithelium (n = 30), koilocytosis (n = 46), CIN 1 (n = 52), CIN 2 (n = 56), and CIN 3 (n=46). Intra- and inter-observer variation had kappa values of 0.502 and 0.415, respectively. A machine vision system was developed in KS400 macro programming language to segment and mark the centres of all nuclei within the epithelium. By object-oriented analysis of image components, the positional information of nuclei was used to construct a Delaunay triangulation mesh. Each mesh was analysed to compute triangle dimensions including the mean triangle area, the mean triangle edge length, and the number of triangles per unit area, giving an individual quantitative profile of measurements for each case. Discriminant analysis of the geometric data revealed the significant discriminatory variables from which a classification score was derived. The scoring system distinguished between normal and CIN 3 in 98.7% of cases and between koilocytosis and CIN 1 in 76.5% of cases, but only 62.3% of the CIN cases were classified into the correct group, with the CIN 2 group showing the highest rate of misclassification. Graphical plots of triangulation data demonstrated the continuum of morphological change from normal squamous epithelium to the highest grade of CIN, with overlapping of the groups originally defined by the pathologists. This study shows that automated location of nuclei in cervical biopsies using computerized image analysis is possible. Analysis of positional information enables quantitative evaluation of architectural features in CIN using Delaunay triangulation meshes, which is effective in the objective classification of CIN. This demonstrates the future potential of automated machine vision systems in diagnostic histopathology. Copyright (C) 2000 John Wiley and Sons, Ltd.

Numerical simulation of the charge balance and temperature evolution in an electron beam ion trap

A computer code has been developed to simulate and study the evolution of ion charge states inside the trap region of an electron beam ion trap. In addition to atomic physics phenomena previously included in similar codes such as electron impact ionization, radiative recombination, and charge exchange, several aspects of the relevant physics such as dielectronic recombination, ionization heating, and ion cloud expansion have been included for the first time in the model. The code was developed using object oriented concepts with database support, making it readable, accurate, and well organized. The simulation results show a good agreement with various experiments, and give useful information for selection of operating conditions and experiment design.

Soundweaving: Writings on Improvisation

This book consists of eight chapters with writings on improvisation and an introduction by one of the most intriguing improvisers of our generation – Evan Parker.
The initial discussions for this book were carried out during the “Two Thousand + TEN” symposium, which took place on the 6th of November 2010 at the Sonic Arts Research Centre in Belfast. The symposium’s theme was ‘improvisation’. Georgina Born and David Borgo gave keynote addresses, alongside many other excellent speakers, several of who are included in this book.
My contribution is a novel way of editing texts, as I have woven all chapters into an overall piece of writing, interlaced with my own contribution of around 40 pages.

MALTS: A Tool to Simulate Lorentz Transmission Electron Microscopy From Micromagnetic Simulations

Here we describe the development of the MALTS software which is a generalized tool that simulates Lorentz Transmission Electron Microscopy (LTEM) contrast of magnetic nanostructures. Complex magnetic nanostructures typically have multiple stable domain structures. MALTS works in conjunction with the open access micromagnetic software Object Oriented Micromagnetic Framework or MuMax. Magnetically stable trial magnetization states of the object of interest are input into MALTS and simulated LTEM images are output. MALTS computes the magnetic and electric phases accrued by the transmitted electrons via the Aharonov-Bohm expressions. Transfer and envelope functions are used to simulate the progression of the electron wave through the microscope lenses. The final contrast image due to these effects is determined by Fourier Optics. Similar approaches have been used previously for simulations of specific cases of LTEM contrast. The novelty here is the integration with micromagnetic codes via a simple user interface enabling the computation of the contrast from any structure. The output from MALTS is in good agreement with both experimental data and published LTEM simulations. A widely-available generalized code for the analysis of Lorentz contrast is a much needed step towards the use of LTEM as a standardized laboratory technique.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Class Responsibility Assignment (CRA) for Use Case Specification to Sequence Diagrams (UC2SD)

Identifying responsibility for classes in object oriented software design phase is a crucial task. This paper proposes an approach for producing high quality and robust behavioural diagrams (e.g. Sequence Diagrams) through Class Responsibility Assignment (CRA). GRASP or General Responsibility Assignment Software Pattern (or Principle) was used to direct the CRA process when deriving behavioural diagrams. A set of tools to support CRA was developed to provide designers and developers with a cognitive toolkit that can be used when analysing and designing object-oriented software. The tool developed is called Use Case Specification to Sequence Diagrams (UC2SD). UC2SD uses a new approach for developing Unified Modelling Language (UML) software designs from Natural Language, making use of a meta-domain oriented ontology, well established software design principles and established Natural Language Processing (NLP) tools. UC2SD generates a well-formed UML sequence diagrams as output.

Exploiting Human Resource Requirements to Infer Human Movement Patterns for Use in Modelling Disease Transmission Systems: An Example from Eastern Province, Zambia

In this research, an agent-based model (ABM) was developed to generate human movement routes between homes and water resources in a rural setting, given commonly available geospatial datasets on population distribution, land cover and landscape resources. ABMs are an object-oriented computational approach to modelling a system, focusing on the interactions of autonomous agents, and aiming to assess the impact of these agents and their interactions on the system as a whole. An A* pathfinding algorithm was implemented to produce walking routes, given data on the terrain in the area. A* is an extension of Dijkstra's algorithm with an enhanced time performance through the use of heuristics. In this example, it was possible to impute daily activity movement patterns to the water resource for all villages in a 75 km long study transect across the Luangwa Valley, Zambia, and the simulated human movements were statistically similar to empirical observations on travel times to the water resource (Chi-squared, 95% confidence interval). This indicates that it is possible to produce realistic data regarding human movements without costly measurement as is commonly achieved, for example, through GPS, or retrospective or real-time diaries. The approach is transferable between different geographical locations, and the product can be useful in providing an insight into human movement patterns, and therefore has use in many human exposure-related applications, specifically epidemiological research in rural areas, where spatial heterogeneity in the disease landscape, and space-time proximity of individuals, can play a crucial role in disease spread.

Gestão de informação académica com base na Web: um sistema de apoio a programas de pós-graduação

Esta dissertação descreve o processo de desenvolvimento de um sistema de informação para a gestão da informação académica de programas de pósgraduação - Sistema WebMaster - que tem como objectivo tornar aquela informação acessível aos utilizadores através da World Wide Web (WWW). Começa-se por apresentar alguns conceitos que se julgam relevantes para a compreensão da problemática dos sistemas de informação em toda a sua abrangência numa determinada organização, particularizando alguns conceitos para o caso das universidades. De seguida reflecte-se sobre os sistemas de informação com base na Web, confrontando-se os conceitos de Web Site (tradicional) e aplicação Web, a nível de arquitectura tecnológica, principais vantagens e desvantagens, fazendo-se, ainda, uma breve referência às principais tecnologias para a construção de soluções com geração dinâmica de conteúdos. Por último representa-se o sistema WebMaster ao longo das suas diferentes etapas de desenvolvimento, desde a análise de requisitos, projecto do sistema, até à fase da implementação. A fase análise de requisitos foi levada a cabo através de um inquérito realizado aos potenciais utilizadores no sentido de identificar as suas necessidades de informação. Com base nos resultados desta fase apresenta-se o projecto do sistema numa perspectiva conceptual, navegacional e de interface de utilizador, fazendo uso da metodologia OOHDM - Object-Oriented Hypermedia Design Method. Finalmente, passa-se à fase da implementação que, com base nas etapas anteriores e nas tecnologias seleccionadas na fase do planeamento, proporciona um espaço interactivo e de troca de informação a todos os interessados da comunidade académica envolvidos em cursos de pós-graduação.