A Process-Oriented Architecture for Complex System Modelling

A fine-grained massively-parallel process-oriented model of platelets (potentially artificial) within a blood vessel is presented. This is a CSP inspired design, expressed and implemented using the occam-pi language. It is part of the TUNA pilot study on nanite assemblers at the universities of York, Surrey and Kent. The aim for this model is to engineer emergent behaviour from the platelets, such that they respond to a wound in the blood vessel wall in a way similar to that found in the human body -- i.e. the formation of clots to stem blood flow from the wound and facilitate healing. An architecture for a three dimensional model (relying strongly on the dynamic and mobile capabilities of occam-pi) is given, along with mechanisms for visualisation and interaction. The biological accuracy of the current model is very approximate. However, its process-oriented nature enables simple refinement (through the addition of processes modelling different stimulants/inhibitors of the clotting reaction, different platelet types and other participating organelles) to greater and greater realism. Even with the current system, simple experiments are possible and have scientific interest (e.g. the effect of platelet density on the success of the clotting mechanism in stemming blood flow: too high or too low and the process fails). General principles for the design of large and complex system models are drawn. The described case study runs to millions of processes engaged in ever-changing communication topologies. It is free from deadlock, livelock, race hazards and starvation em by design, employing a small set of synchronisation patterns for which we have proven safety theorems

Tools and collaborative environments for bioinformatics research

Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies

A theoretical and practical approach to a persuasive agent model for change behaviour in oral care and hygiene

There is an increased use of the persuasive agent in behaviour change interventions due to the agent‘s features of sociable, reactive, autonomy, and proactive. However, many interventions have been unsuccessful, particularly in the domain of oral care. The psychological reactance has been identified as one of the major reasons for these unsuccessful behaviour change interventions. This study proposes a formal persuasive agent model that leads to psychological reactance reduction in order to achieve an improved behaviour change intervention in oral care and hygiene. Agent-based simulation methodology is adopted for the development of the proposed model. Evaluation of the model was conducted in two phases that include verification and validation. The verification process involves simulation trace and stability analysis. On the other hand, the validation was carried out using user-centred approach by developing an agent-based application based on belief-desire-intention architecture. This study contributes an agent model which is made up of interrelated cognitive and behavioural factors. Furthermore, the simulation traces provide some insights on the interactions among the identified factors in order to comprehend their roles in behaviour change intervention. The simulation result showed that as time increases, the psychological reactance decreases towards zero. Similarly, the model validation result showed that the percentage of respondents‘ who experienced psychological reactance towards behaviour change in oral care and hygiene was reduced from 100 percent to 3 percent. The contribution made in this thesis would enable agent application and behaviour change intervention designers to make scientific reasoning and predictions. Likewise, it provides a guideline for software designers on the development of agent-based applications that may not have psychological reactance

Engineering Self-Adaptive Collective Processes for Cyber-Physical Ecosystems

The pervasiveness of computing and networking is creating significant opportunities for building valuable socio-technical systems. However, the scale, density, heterogeneity, interdependence, and QoS constraints of many target systems pose severe operational and engineering challenges. Beyond individual smart devices, cyber-physical collectives can provide services or solve complex problems by leveraging a “system effect” while coordinating and adapting to context or environment change. Understanding and building systems exhibiting collective intelligence and autonomic capabilities represent a prominent research goal, partly covered, e.g., by the field of collective adaptive systems. Therefore, drawing inspiration from and building on the long-time research activity on coordination, multi-agent systems, autonomic/self-* systems, spatial computing, and especially on the recent aggregate computing paradigm, this thesis investigates concepts, methods, and tools for the engineering of possibly large-scale, heterogeneous ensembles of situated components that should be able to operate, adapt and self-organise in a decentralised fashion. The primary contribution of this thesis consists of four main parts. First, we define and implement an aggregate programming language (ScaFi), internal to the mainstream Scala programming language, for describing collective adaptive behaviour, based on field calculi. Second, we conceive of a “dynamic collective computation” abstraction, also called aggregate process, formalised by an extension to the field calculus, and implemented in ScaFi. Third, we characterise and provide a proof-of-concept implementation of a middleware for aggregate computing that enables the development of aggregate systems according to multiple architectural styles. Fourth, we apply and evaluate aggregate computing techniques to edge computing scenarios, and characterise a design pattern, called Self-organising Coordination Regions (SCR), that supports adjustable, decentralised decision-making and activity in dynamic environments.Con lo sviluppo di informatica e intelligenza artificiale, la diffusione pervasiva di device computazionali e la crescente interconnessione tra elementi fisici e digitali, emergono innumerevoli opportunità per la costruzione di sistemi socio-tecnici di nuova generazione. Tuttavia, l'ingegneria di tali sistemi presenta notevoli sfide, data la loro complessità—si pensi ai livelli, scale, eterogeneità, e interdipendenze coinvolti. Oltre a dispositivi smart individuali, collettivi cyber-fisici possono fornire servizi o risolvere problemi complessi con un “effetto sistema” che emerge dalla coordinazione e l'adattamento di componenti fra loro, l'ambiente e il contesto. Comprendere e costruire sistemi in grado di esibire intelligenza collettiva e capacità autonomiche è un importante problema di ricerca studiato, ad esempio, nel campo dei sistemi collettivi adattativi. Perciò, traendo ispirazione e partendo dall'attività di ricerca su coordinazione, sistemi multiagente e self-*, modelli di computazione spazio-temporali e, specialmente, sul recente paradigma di programmazione aggregata, questa tesi tratta concetti, metodi, e strumenti per l'ingegneria di ensemble di elementi situati eterogenei che devono essere in grado di lavorare, adattarsi, e auto-organizzarsi in modo decentralizzato. Il contributo di questa tesi consiste in quattro parti principali. In primo luogo, viene definito e implementato un linguaggio di programmazione aggregata (ScaFi), interno al linguaggio Scala, per descrivere comportamenti collettivi e adattativi secondo l'approccio dei campi computazionali. In secondo luogo, si propone e caratterizza l'astrazione di processo aggregato per rappresentare computazioni collettive dinamiche concorrenti, formalizzata come estensione al field calculus e implementata in ScaFi. Inoltre, si analizza e implementa un prototipo di middleware per sistemi aggregati, in grado di supportare più stili architetturali. Infine, si applicano e valutano tecniche di programmazione aggregata in scenari di edge computing, e si propone un pattern, Self-Organising Coordination Regions, per supportare, in modo decentralizzato, attività decisionali e di regolazione in ambienti dinamici

A Taxonomy for and Analysis of Anonymous Communications Networks

Any entity operating in cyberspace is susceptible to debilitating attacks. With cyber attacks intended to gather intelligence and disrupt communications rapidly replacing the threat of conventional and nuclear attacks, a new age of warfare is at hand. In 2003, the United States acknowledged that the speed and anonymity of cyber attacks makes distinguishing among the actions of terrorists, criminals, and nation states difficult. Even President Obama’s Cybersecurity Chief-elect recognizes the challenge of increasingly sophisticated cyber attacks. Now through April 2009, the White House is reviewing federal cyber initiatives to protect US citizen privacy rights. Indeed, the rising quantity and ubiquity of new surveillance technologies in cyberspace enables instant, undetectable, and unsolicited information collection about entities. Hence, anonymity and privacy are becoming increasingly important issues. Anonymization enables entities to protect their data and systems from a diverse set of cyber attacks and preserves privacy. This research provides a systematic analysis of anonymity degradation, preservation and elimination in cyberspace to enhance the security of information assets. This includes discovery/obfuscation of identities and actions of/from potential adversaries. First, novel taxonomies are developed for classifying and comparing well-established anonymous networking protocols. These expand the classical definition of anonymity and capture the peer-to-peer and mobile ad hoc anonymous protocol family relationships. Second, a unique synthesis of state-of-the-art anonymity metrics is provided. This significantly aids an entity’s ability to reliably measure changing anonymity levels; thereby, increasing their ability to defend against cyber attacks. Finally, a novel epistemic-based mathematical model is created to characterize how an adversary reasons with knowledge to degrade anonymity. This offers multiple anonymity property representations and well-defined logical proofs to ensure the accuracy and correctness of current and future anonymous network protocol design

Engineering Language-Parametric End-User Programming Environments for DSLs

Human-computer communication can be achieved through different interfaces such as Graphical User Interfaces (GUIs), Tangible User Interfaces (TUIs), command-line interfaces, and programming languages. In this thesis, we used some of these inter- faces; however, we focused on programming languages which are artificial languages consisting of instructions written by humans and executed by computers. In order to create these programs, humans use specialized tools called programming environments that offer a set of utilities that ease human-computer communication. When creating programs, users must learn the language’s syntax and get acquainted with the pro- gramming environment. Unfortunately, programming languages usually offer a single user interface or syntax, which is not ideal considering different types of users with varied backgrounds and expertise will use it. Given the increasing number of people performing any kind of programming activity, it is important to offer different inter- faces depending on the programming task and the background of the users. However, from the language engineering point of view, offering multiple user interfaces for the same language is expensive, and if we specifically consider Domain-Specific Languages (DSLs), it is even more expensive given their audience and development teams’ size. Therefore, we study how to engineer different user interfaces for DSLs in a practical way.This thesis presents different mechanisms to engineer different language-parametric programming environments for end-users. These mechanisms rely heavily on reusing existing language components for existing languages or helping language engineers define these interfaces for new languages. We mainly studied four technological spaces, namely, Grammarware, Computational Notebooks, Block-based environments, and Projec- tional editors. We present three different language-parametric interfaces for interacting with DSLs, namely computational notebooks, projectional editors, and block-based editors. These interfaces offer different user experiences and rely upon different technological spaces. Different notations are associated with different technological spaces; for in- stance, grammarware is associated with text files, while block-based environments are associated with Blockly and JavaScript files. Therefore, to provide different notations for their languages, we have to "space travel" so that language engineers can select the most appropriate technological space and interface for their target audience. To support this, we defined grammarware as a common starting point to allow traveling to different technological spaces (e.g., computational notebooks space, projectional editors space, or block-based space). Based on this idea, we developed three tools that allowed language engineers to generate different interfaces for their DSLs based on a grammar definition of the language. Our results show that it is possible to generate these different user interfaces and decrease the effort required to create these. However, additional research is required to improve the usability of the generated interfaces and make the generation of these interfaces more flexible so that users’ data can be used as part of the generated interfaces