Life of occam-Pi

This paper considers some questions prompted by a brief review of the history of computing. Why is programming so hard? Why is concurrency considered an “advanced” subject? What’s the matter with Objects? Where did all the Maths go? In searching for answers, the paper looks at some concerns over fundamental ideas within object orientation (as represented by modern programming languages), before focussing on the concurrency model of communicating processes and its particular expression in the occam family of languages. In that focus, it looks at the history of occam, its underlying philosophy (Ockham’s Razor), its semantic foundation on Hoare’s CSP, its principles of process oriented design and its development over almost three decades into occam-? (which blends in the concurrency dynamics of Milner’s ?-calculus). Also presented will be an urgent need for rationalisation – occam-? is an experiment that has demonstrated significant results, but now needs time to be spent on careful review and implementing the conclusions of that review. Finally, the future is considered. In particular, is there a future

Development and Specification of Virtual Environments

This thesis concerns the issues involved in the development of virtual environments (VEs). VEs are more than virtual reality. We identify four main characteristics of them: graphical interaction, multimodality, interface agents, and multi-user. These characteristics are illustrated with an overview of different classes of VE-like applications, and a number of state-of-the-art VEs. To further define the topic of research, we propose a general framework for VE systems development, in which we identify five major classes of development tools: methodology, guidelines, design specification, analysis, and development environments. Of each, we give an overview of existing best practices

A Service-Oriented Approach for Sensing in the Internet of Things: Intelligent Transportation Systems and Privacy Use Cases

This paper presents a Sensing-as-a-Service run-time Service Oriented Architecture (SOA), called 3SOA, for the development of Internet of Things (IoT) applications. 3SOA aims to allow interoperability among various IoT platforms and support service-oriented modelling at high levels of abstraction where fundamental SOA theories and techniques are fully integrated into a practical software engineering approach. 3SOA abstracts the dependencies of the middleware programming model from the application logic. This abstraction allows the development efforts to focus on writing the application logic independently from hardware platforms, middleware, and languages in which applications are programmed. To achieve this result, IoT objects are treated as independent entities that may interact with each other using a well-defined message exchange sequence. Each object is defined by the services it provides and the coordination protocol it supports. Objects are then able to coordinate their resources to address the global objectives of the system. To practically validate our proposals, we demonstrate an intelligent transportation system and data privacy functional prototypes as proof of concepts. The use cases show that 3SOA and the presented abstraction language allow the amalgamation of macroprogramming and node-centric programming to develop real-time and efficient applications over IoT

How the Common Component Architecture Advances Compuational Science

Computational chemists are using Common Component Architecture (CCA) technology to increase the parallel scalability of their application ten-fold. Combustion researchers are publishing science faster because the CCA manages software complexity for them. Both the solver and meshing communities in SciDAC are converging on community interface standards as a direct response to the novel level of interoperability that CCA presents. Yet, there is much more to do before component technology becomes mainstream computational science. This paper highlights the impact that the CCA has made on scientific applications, conveys some lessons learned from five years of the SciDAC program, and previews where applications could go with the additional capabilities that the CCA has planned for SciDAC 2

A Language-Independent Static Checking System for Coding Conventions

A thesis submitted in partial fulfilment of the requirements of the University of Wolverhampton for the degree of Doctor of Philosophy.Despite decades of research aiming to ameliorate the difficulties of creating software, programming still remains an error-prone task. Much work in Computer Science deals with the problem of specification, or writing the right program, rather than the complementary problem of implementation, or writing the program right. However, many desirable software properties (such as portability) are obtained via adherence to coding standards, and therefore fall outside the remit of formal specification and automatic verification. Moreover, code inspections and manual detection of standards violations are time consuming. To address these issues, this thesis describes Exstatic, a novel framework for the static detection of coding standards violations. Unlike many other static checkers Exstatic can be used to examine code in a variety of languages, including program code, in-line documentation, markup languages and so on. This means that checkable coding standards adhered to by a particular project or institution can be handled by a single tool. Consequently, a major challenge in the design of Exstatic has been to invent a way of representing code from a variety of source languages. Therefore, this thesis describes ICODE, which is an intermediate language suitable for representing code from a number of different programming paradigms. To substantiate the claim that ICODE is a universal intermediate language, a proof strategy has been developed: for a number of different programming paradigms (imperative, declarative, etc.), a proof is constructed to show that semantics-preserving translation exists from an exemplar language (such as IMP or PCF) to ICODE. The usefulness of Exstatic has been demonstrated by the implementation of a number of static analysers for different languages. This includes a checker for technical documentation written in Javadoc which validates documents against the Sun Microsystems (now Oracle) Coding Conventions and a checker for HTML pages against a site-specifc standard. A third system is targeted at a variant of the Python language, written by the author, called python-csp, based on Hoare's Communicating Sequential Processes

ProcessJ: A process-oriented programming language

Java is a general purpose object-oriented programming language that has been widely adopted. Because of its high adoption rate and its lineage as a C-style language, its syntax is familiar to many programmers. The downside is that Java is not natively concurrent. Volumes have been written about concurrent programming in Java; however, concurrent programming is difficult to reason about within an object-oriented paradigm and so is difficult to get right. occam -π is a general purpose process-oriented programming language. Concurrency is part of the theoretical underpinnings of the language. Concurrency is simple to reason about within an occam -π application because there is never any shared state; also occam -π is based on a process calculus, with algebraic laws for composing processes. It has well-defined semantics regarding how processes interact. The downside is that the syntax is foreign and even archaic to programmers who are used to the Java syntax. This thesis presents a new language, ProcessJ, which is a general purpose, process-oriented programming language meant to bridge the gap between Java and occam -π. ProcessJ does this by combining the familiar syntax of Java with the process semantics of occam -π. This allows for a familiar-looking language that is easy to reason about in concurrent programs. This thesis describes the ProcessJ language, as well as the implementation of a compiler that translates ProcessJ source code to Java with Java Communicating Sequential Processes (JCSP), a library that provides CSP-style communication primitives

Systematic use of models of concurrency in executable domain-specific modelling languages

Language-Oriented Programming (LOP) advocates designing eXecutable Domain-Specific Modeling Languages (xDSMLs) to facilitate the design, development, verification and validation of modern softwareintensive and highly-concurrent systems. These systems place their needs of rich concurrency constructs at the heart of modern software engineering processes. To ease theirdevelopment, theoretical computer science has studied the use of dedicated paradigms for the specification of concurrent systems, called Models of Concurrency (MoCs). They enable the use of concurrencyaware analyses such as detecting deadlocks or starvation situations, but are complex to understand and master. In this thesis, we develop and extend an approach that aims at reconciling LOP and MoCs by designing so-called Concurrencyaware xDSMLs. In these languages, the systematic use of a MoC is specified at the language level, removing from the end-user the burden of understanding or using MoCs. It also allows the refinement of the language for specific execution platforms, and enables the use of concurrency-aware analyses on the systems

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward