Logic-Based Specification Languages for Intelligent Software Agents

The research field of Agent-Oriented Software Engineering (AOSE) aims to find abstractions, languages, methodologies and toolkits for modeling, verifying, validating and prototyping complex applications conceptualized as Multiagent Systems (MASs). A very lively research sub-field studies how formal methods can be used for AOSE. This paper presents a detailed survey of six logic-based executable agent specification languages that have been chosen for their potential to be integrated in our ARPEGGIO project, an open framework for specifying and prototyping a MAS. The six languages are ConGoLog, Agent-0, the IMPACT agent programming language, DyLog, Concurrent METATEM and Ehhf. For each executable language, the logic foundations are described and an example of use is shown. A comparison of the six languages and a survey of similar approaches complete the paper, together with considerations of the advantages of using logic-based languages in MAS modeling and prototyping.Comment: 67 pages, 1 table, 1 figure. Accepted for publication by the Journal "Theory and Practice of Logic Programming", volume 4, Maurice Bruynooghe Editor-in-Chie

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

The CIAO multiparadigm compiler and system: A progress report

Abstract is not available

Logic programming in the context of multiparadigm programming: the Oz experience

Oz is a multiparadigm language that supports logic programming as one of its major paradigms. A multiparadigm language is designed to support different programming paradigms (logic, functional, constraint, object-oriented, sequential, concurrent, etc.) with equal ease. This article has two goals: to give a tutorial of logic programming in Oz and to show how logic programming fits naturally into the wider context of multiparadigm programming. Our experience shows that there are two classes of problems, which we call algorithmic and search problems, for which logic programming can help formulate practical solutions. Algorithmic problems have known efficient algorithms. Search problems do not have known efficient algorithms but can be solved with search. The Oz support for logic programming targets these two problem classes specifically, using the concepts needed for each. This is in contrast to the Prolog approach, which targets both classes with one set of concepts, which results in less than optimal support for each class. To explain the essential difference between algorithmic and search programs, we define the Oz execution model. This model subsumes both concurrent logic programming (committed-choice-style) and search-based logic programming (Prolog-style). Instead of Horn clause syntax, Oz has a simple, fully compositional, higher-order syntax that accommodates the abilities of the language. We conclude with lessons learned from this work, a brief history of Oz, and many entry points into the Oz literature.Comment: 48 pages, to appear in the journal "Theory and Practice of Logic Programming

The role of concurrency in an evolutionary view of programming abstractions

In this paper we examine how concurrency has been embodied in mainstream programming languages. In particular, we rely on the evolutionary talking borrowed from biology to discuss major historical landmarks and crucial concepts that shaped the development of programming languages. We examine the general development process, occasionally deepening into some language, trying to uncover evolutionary lineages related to specific programming traits. We mainly focus on concurrency, discussing the different abstraction levels involved in present-day concurrent programming and emphasizing the fact that they correspond to different levels of explanation. We then comment on the role of theoretical research on the quest for suitable programming abstractions, recalling the importance of changing the working framework and the way of looking every so often. This paper is not meant to be a survey of modern mainstream programming languages: it would be very incomplete in that sense. It aims instead at pointing out a number of remarks and connect them under an evolutionary perspective, in order to grasp a unifying, but not simplistic, view of the programming languages development process

A distributed Real-Time Java system based on CSP

CSP is a fundamental concept for developing software for distributed real time systems. The CSP paradigm constitutes a natural addition to object orientation and offers higher order multithreading constructs. The CSP channel concept that has been implemented in Java deals with single- and multi-processor environments and also takes care of the real time priority scheduling requirements. For this, the notion of priority and scheduling has been carefully examined and as a result it was reasoned that priority scheduling should be attached to the communicating channels rather than to the processes. In association with channels, a priority based parallel construct is developed for composing processes: hiding threads and priority indexing from the user. This approach simplifies the use of priorities for the object oriented paradigm. Moreover, in the proposed system, the notion of scheduling is no longer connected to the operating system but has become part of the application instead