GUBS, a Behavior-based Language for Open System Dedicated to Synthetic Biology

In this article, we propose a domain specific language, GUBS (Genomic Unified Behavior Specification), dedicated to the behavioral specification of synthetic biological devices, viewed as discrete open dynamical systems. GUBS is a rule-based declarative language. By contrast to a closed system, a program is always a partial description of the behavior of the system. The semantics of the language accounts the existence of some hidden non-specified actions possibly altering the behavior of the programmed device. The compilation framework follows a scheme similar to automatic theorem proving, aiming at improving synthetic biological design safety.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347

Formal Object Interaction Language: Modeling and Verification of Sequential and Concurrent Object-Oriented Software

As software systems become larger and more complex, developers require the ability to model abstract concepts while ensuring consistency across the entire project. The internet has changed the nature of software by increasing the desire for software deployment across multiple distributed platforms. Finally, increased dependence on technology requires assurance that designed software will perform its intended function. This thesis introduces the Formal Object Interaction Language (FOIL). FOIL is a new object-oriented modeling language specifically designed to address the cumulative shortcomings of existing modeling techniques. FOIL graphically displays software structure, sequential and concurrent behavior, process, and interaction in a simple unified notation, and has an algebraic representation based on a derivative of the π-calculus. The thesis documents the technique in which FOIL software models can be mathematically verified to anticipate deadlocks, ensure consistency, and determine object state reachability. Scalability is offered through the concept of behavioral inheritance; and, FOIL’s inherent support for modeling concurrent behavior and all known workflow patterns is demonstrated. The concepts of process achievability, process complete achievability, and process determinism are introduced with an algorithm for simulating the execution of a FOIL object model using a FOIL process model. Finally, a technique for using a FOIL process model as a constraint on FOIL object system execution is offered as a method to ensure that object-oriented systems modeled in FOIL will complete their processes based activities. FOIL’s capabilities are compared and contrasted with an extensive array of current software modeling techniques. FOIL is ideally suited for data-aware, behavior based systems such as interactive or process management software

Web Services Compositions Modelling and Choreographies Analysis

International audienceIn (Rouached, Godart and al. 2006; Rouached, Godart 2007), we have described the semantics of WSBPEL by way of mapping each of the WSBPEL (Arkin, Askary and al. 2004) constructs to the EC algebra and building a model of the process behaviour. With these mapping rules, we have described a modelling approach of a process defined for a single Web service composition. However, this modelling is limited to a local view and can only be used to model the behaviour of a single process. A series of compositions in Web service choreography need specific modelling activities that are not explicitly derived from an implementation. An elaboration of modelling is then required to represent the behaviour of interacting compositions across partnered processes. This elaboration provides a representation that enables us to perform analysis of service interaction for behaviour properties. The ability to perform verification and validation between execution and design, and within the process compositions themselves, is a key requirement of the Web services architecture specification. In this paper, we further the semantic mapping to include Web service composition interactions through modelling Web service conversations and their choreography. We describe this elaboration of models to support a view of interacting Web service compositions extending the mapping from WSBPEL to EC, and including Web service interfaces (WSDL) for use in modelling between services. The verification and validation techniques are also exposed. An automated induction-based theorem prover is used as verification back-end

Computer Modelling of Theory: Explanation for the 21st Century

Abstract not availabl

A method for rigorous design of reconfigurable systems

Reconfigurability, understood as the ability of a system to behave differently in different modes of operation and commute between them along its lifetime, is a cross-cutting concern in modern Software Engineering. This paper introduces a specification method for reconfigurable software based on a global transition structure to capture the system's reconfiguration space, and a local specification of each operation mode in whatever logic (equational, first-order, partial, fuzzy, probabilistic, etc.) is found expressive enough for handling its requirements. In the method these two levels are not only made explicit and juxtaposed, but formally interrelated. The key to achieve such a goal is a systematic process of hybridisation of logics through which the relationship between the local and global levels of a specification becomes internalised in the logic itself.This work is financed by the ERDF – European Regional Development Fund through the Operational Programme for Competitiveness and Internationalisation – COMPETE 2020 Programme and by National Funds through the Portuguese funding agency, FCT – Fundação para a Ciência e a Tecnologia within projects POCI-01-0145-FEDER-016692 and UID/MAT/04106/2013. The first author is further supported by the BPD FCT Grant SFRH/BPD/103004/2014, and R. Neves is sponsored by FCT Grant SFRH/BD/52234/2013. M.A. Martins is also funded by the EU FP7 Marie Curie PIRSESGA-2012-318986 project GeTFun: Generalizing Truth-Functionality

Bridging formal models : an engineering perspective

The thesis presents different techniques that can be used to build formal behavioral models. If modal properties are formulated, the models can be subjected to verification techniques to determine whether a model possesses the desired properties. However many native environments do not facilitate tools or techniques to verify them. Hence, these models need to be transformed into other models that provide suitable techniques for a formal analysis. The transformations are classified into two engineering approaches, namely syntactically engineered models and semantically engineered models. Syntactically engineered models are constructed from input specifications without explicitly considering the semantics. Semantically engineered models are constructed from input specifications by explicitly considering the semantics. The syntactic engineering approach presents four dedicated modeling techniques that construct or disseminate verification results for formal models. The first modeling technique describes a way to create models from system descriptions that specify concurrent behavior. Here, we model three variations of a 2×2 switch, for which the models are subsequently compared to models created in the specification languages: TLA+, Bluespec, Statecharts, and ACP. The comparison validates that mCRL2 is a suitable specification language to model descriptions or specify the behavior for prototype systems. The second syntactic technique constructs an mCRL2 model from a software implementation that operates a printer for printing Printed Circuit Boards. The model is used to advise (other) software engineers on dangerous language constructs in the control software. Hence, the model is model checked for various safety properties. The implementation is modeled through an over-approximation on the behavior by abstracting from program variables, such that only interface calls between processes and non-deterministic choices in procedures remain. The third modeling technique describes a language transformation from the language Chi 2.0 language to the mCRL2 language. The purpose of the transformation is to facilitate model checking techniques to the discrete part of the Chi 2.0 language

Foundations of the B method

B is a method for specifying, designing and coding software systems. It is based on Zermelo-Fraenkel set theory with the axiom of choice, the concept of generalized substitution and on structuring mechanisms (machine, refinement, implementation). The concept of refinement is the key notion for developing B models of (software) systems in an incremental way. B models are accompanied by mathematical proofs that justify them. Proofs of B models convince the user (designer or specifier) that the (software) system is effectively correct. We provide a survey of the underlying logic of the B method and the semantic concepts related to the B method; we detail the B development process partially supported by the mechanical engine of the prover