An Intuitive Automated Modelling Interface for Systems Biology

We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We demonstrate the language on a model of Fc-gamma receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic pi calculus language, Microsoft Research's SPiM

A formal support to business and architectural design for service-oriented systems

Architectural Design Rewriting (ADR) is an approach for the design of software architectures developed within Sensoria by reconciling graph transformation and process calculi techniques. The key feature that makes ADR a suitable and expressive framework is the algebraic handling of structured graphs, which improves the support for specification, analysis and verification of service-oriented architectures and applications. We show how ADR is used as a formal ground for high-level modelling languages and approaches developed within Sensoria

Object-oriented Programming Laws for Annotated Java Programs

Object-oriented programming laws have been proposed in the context of languages that are not combined with a behavioral interface specification language (BISL). The strong dependence between source-code and interface specifications may cause a number of difficulties when transforming programs. In this paper we introduce a set of programming laws for object-oriented languages like Java combined with the Java Modeling Language (JML). The set of laws deals with object-oriented features taking into account their specifications. Some laws deal only with features of the specification language. These laws constitute a set of small transformations for the development of more elaborate ones like refactorings

An Analysis of Aspect Composition Problems

The composition of multiple software units does not always yield the desired results. In particular, aspect-oriented composition mechanisms introduce new kinds of composition problems. These are caused by different characteristics as compared to object-oriented composition, such as inverse dependencies. The aim of this paper is to contribute to the understanding of aspect-oriented composition problems, and eventually composition problems in a more general context. To this extent we propose and illustrate a systematic approach to analyze composition problems in a precise and concrete manner. In this approach we represent aspect-based composition mechanisms as transformation rules on program graphs. We explicitly model and show where composition problems occur, in a way that can easily be fully automated. In this paper we focus on structural superimposition (cf. intertype declarations) to illustrate our approach; this results in the identification of three categories of causes of composition problems. \u

Specifying UML protocol state machines in Alloy

A UML Protocol State Machine (PSM) is a behavioral diagram for the specification of the external behavior of a class, interface or component. PSMs have been used in the software development process for different purposes, such as requirements analysis and testing. However, like other UML diagrams, they are often difficult to validate and verify, specially when combined with other artifacts, such as Object Constraint Language (OCL) specifications. This drawback can be overcome by application of an off-the-shelf formal method, namely one supporting automatic validation and verification. Among those, we have the increasingly popular Alloy, based on a simple relational flavor of first-order logic. This paper presents a model transformation from PSMs, optionally complemented with OCL specifications, to Alloy. Not only it enables automatic verification and validation of PSMs, but also a smooth integration of Alloy in current software development practices.Fundação para a Ciência e a Tecnologi

Specifications and Development of Interoperability Solution dedicated to Multiple Expertise Collaboration in a Design Framework

This paper describes the specifications of an interoperability platform based on the PPO (Product Process Organization) model developed by the French community IPPOP in the context of collaborative and innovative design. By using PPO model as a reference, this work aims to connect together heterogonous tools used by experts easing data and information exchanges. After underlining the growing needs of collaborative design process, this paper focuses on interoperability concept by describing current solutions and their limits. Then a solution based on the flexibility of the PPO model adapted to the philosophy of interoperability is proposed. To illustrate these concepts, several examples are more particularly described (robustness analysis, CAD and Product Lifecycle Management systems connections)

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

An overview of very high level software design methods

Very High Level design methods emphasize automatic transfer of requirements to formal design specifications, and/or may concentrate on automatic transformation of formal design specifications that include some semantic information of the system into machine executable form. Very high level design methods range from general domain independent methods to approaches implementable for specific applications or domains. Applying AI techniques, abstract programming methods, domain heuristics, software engineering tools, library-based programming and other methods different approaches for higher level software design are being developed. Though one finds that a given approach does not always fall exactly in any specific class, this paper provides a classification for very high level design methods including examples for each class. These methods are analyzed and compared based on their basic approaches, strengths and feasibility for future expansion toward automatic development of software systems