Rosen's (M,R) system in Unified Modelling Language

Robert Rosen's (M,R) system is an abstract biological network architecture that is allegedly non-computable on a Turing machine. If (M,R) is truly non-computable, there are serious implications for the modelling of large biological networks in computer software. A body of work has now accumulated addressing Rosen's claim concerning (M,R) by attempting to instantiate it in various software systems. However, a conclusive refutation has remained elusive, principally since none of the attempts to date have unambiguously avoided the critique that they have altered the properties of (M,R) in the coding process, producing merely approximate simulations of (M,R) rather than true computational models. In this paper, we use the Unified Modelling Language (UML), a diagrammatic notation standard, to express (M,R) as a system of objects having attributes, functions and relations. We believe that this instantiates (M,R) in such a way than none of the original properties of the system are corrupted in the process. Crucially, we demonstrate that (M,R) as classically represented in the relational biology literature is implicitly a UML communication diagram. Furthermore, since UML is formally compatible with object-oriented computing languages, instantiation of (M,R) in UML strongly implies its computability in object-oriented coding languages

Reusability in software engineering

This paper surveys recent work concerning reusability in software engineering. The current directions in software reusability are discussed, and the two major approaches of reusable building blocks and reusable patterns studied. An extensive bibliography, parts of which are annotated, is included

Towards a Java Subtyping Operad

The subtyping relation in Java exhibits self-similarity. The self-similarity in Java subtyping is interesting and intricate due to the existence of wildcard types and, accordingly, the existence of three subtyping rules for generic types: covariant subtyping, contravariant subtyping and invariant subtyping. Supporting bounded type variables also adds to the complexity of the subtyping relation in Java and in other generic nominally-typed OO languages such as C# and Scala. In this paper we explore defining an operad to model the construction of the subtyping relation in Java and in similar generic nominally-typed OO programming languages. Operads, from category theory, are frequently used to model self-similar phenomena. The Java subtyping operad, we hope, will shed more light on understanding the type systems of generic nominally-typed OO languages.Comment: 13 page

Iterative criteria-based approach to engineering the requirements of software development methodologies

Software engineering endeavours are typically based on and governed by the requirements of the target software; requirements identification is therefore an integral part of software development methodologies. Similarly, engineering a software development methodology (SDM) involves the identification of the requirements of the target methodology. Methodology engineering approaches pay special attention to this issue; however, they make little use of existing methodologies as sources of insight into methodology requirements. The authors propose an iterative method for eliciting and specifying the requirements of a SDM using existing methodologies as supplementary resources. The method is performed as the analysis phase of a methodology engineering process aimed at the ultimate design and implementation of a target methodology. An initial set of requirements is first identified through analysing the characteristics of the development situation at hand and/or via delineating the general features desirable in the target methodology. These initial requirements are used as evaluation criteria; refined through iterative application to a select set of relevant methodologies. The finalised criteria highlight the qualities that the target methodology is expected to possess, and are therefore used as a basis for de. ning the final set of requirements. In an example, the authors demonstrate how the proposed elicitation process can be used for identifying the requirements of a general object-oriented SDM. Owing to its basis in knowledge gained from existing methodologies and practices, the proposed method can help methodology engineers produce a set of requirements that is not only more complete in span, but also more concrete and rigorous

Frameworks: the future of formal software development?

It could be argued that the primary issue to be dealt with in software engineering today is re-use of software. Current software development rarely, if ever, starts from nothing. Unfortunately, the same cannot be said for the development of specifications. To overcome this problem, various works have attempted to show how specifications can be built using architectural principles. We discuss one such approach in particular, the Architectural Semantics of Open Distributed Processing. We show the limitations of this work with regard to the architecting of specifications and propose a new approach, based on frameworks. To highlight the approach we use the work currently being done in the TOSCA project in its development of a service creation and validation environment for telecommunication services

Automated Verification of Design Patterns with LePUS3

Specification and [visual] modelling languages are expected to combine strong abstraction mechanisms with rigour, scalability, and parsimony. LePUS3 is a visual, object-oriented design description language axiomatized in a decidable subset of the first-order predicate logic. We demonstrate how LePUS3 is used to formally specify a structural design pattern and prove (‗verify‘) whether any JavaTM 1.4 program satisfies that specification. We also show how LePUS3 specifications (charts) are composed and how they are verified fully automatically in the Two-Tier Programming Toolkit