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

Towards Realizability Checking of Contracts using Theories

Virtual integration techniques focus on building architectural models of systems that can be analyzed early in the design cycle to try to lower cost, reduce risk, and improve quality of complex embedded systems. Given appropriate architectural descriptions and compositional reasoning rules, these techniques can be used to prove important safety properties about the architecture prior to system construction. Such proofs build from "leaf-level" assume/guarantee component contracts through architectural layers towards top-level safety properties. The proofs are built upon the premise that each leaf-level component contract is realizable; i.e., it is possible to construct a component such that for any input allowed by the contract assumptions, there is some output value that the component can produce that satisfies the contract guarantees. Without engineering support it is all too easy to write leaf-level components that can't be realized. Realizability checking for propositional contracts has been well-studied for many years, both for component synthesis and checking correctness of temporal logic requirements. However, checking realizability for contracts involving infinite theories is still an open problem. In this paper, we describe a new approach for checking realizability of contracts involving theories and demonstrate its usefulness on several examples.Comment: 15 pages, to appear in NASA Formal Methods (NFM) 201

A Model-Driven Engineering Approach for ROS using Ontological Semantics

This paper presents a novel ontology-driven software engineering approach for the development of industrial robotics control software. It introduces the ReApp architecture that synthesizes model-driven engineering with semantic technologies to facilitate the development and reuse of ROS-based components and applications. In ReApp, we show how different ontological classification systems for hardware, software, and capabilities help developers in discovering suitable software components for their tasks and in applying them correctly. The proposed model-driven tooling enables developers to work at higher abstraction levels and fosters automatic code generation. It is underpinned by ontologies to minimize discontinuities in the development workflow, with an integrated development environment presenting a seamless interface to the user. First results show the viability and synergy of the selected approach when searching for or developing software with reuse in mind.Comment: Presented at DSLRob 2015 (arXiv:1601.00877), Stefan Zander, Georg Heppner, Georg Neugschwandtner, Ramez Awad, Marc Essinger and Nadia Ahmed: A Model-Driven Engineering Approach for ROS using Ontological Semantic

Towards a Formal Framework for Mobile, Service-Oriented Sensor-Actuator Networks

Service-oriented sensor-actuator networks (SOSANETs) are deployed in health-critical applications like patient monitoring and have to fulfill strong safety requirements. However, a framework for the rigorous formal modeling and analysis of SOSANETs does not exist. In particular, there is currently no support for the verification of correct network behavior after node failure or loss/addition of communication links. To overcome this problem, we propose a formal framework for SOSANETs. The main idea is to base our framework on the \pi-calculus, a formally defined, compositional and well-established formalism. We choose KLAIM, an existing formal language based on the \pi-calculus as the foundation for our framework. With that, we are able to formally model SOSANETs with possible topology changes and network failures. This provides the basis for our future work on prediction, analysis and verification of the network behavior of these systems. Furthermore, we illustrate the real-life applicability of this approach by modeling and extending a use case scenario from the medical domain.Comment: In Proceedings FESCA 2013, arXiv:1302.478

DOOR: towards a formalization of ontology relations

In this paper, we describe our ongoing effort in describing and formalizing semantic relations that link ontolo- gies with each others on the Semantic Web in order to create an ontology, DOOR, to represent, manipulate and reason upon these relations. DOOR is a Descriptive Ontology of Ontology Relations which intends to define relations such as inclusion, versioning, similarity and agreement using ontological primitives as well as rules. Here, we provide a detailed description of the methodology used to design the DOOR ontology, as well as an overview of its content. We also describe how DOOR is used in a complete framework (called KANNEL) for detecting and managing semantic relations between ontologies in large ontology repositories. Applied in the context of a large collection of automatically crawled ontologies, DOOR and KANNEL provide a starting point for analyzing the underlying structure of the network of ontologies that is the Semantic Web

Can Component/Service-Based Systems Be Proved Correct?

Component-oriented and service-oriented approaches have gained a strong enthusiasm in industries and academia with a particular interest for service-oriented approaches. A component is a software entity with given functionalities, made available by a provider, and used to build other application within which it is integrated. The service concept and its use in web-based application development have a huge impact on reuse practices. Accordingly a considerable part of software architectures is influenced; these architectures are moving towards service-oriented architectures. Therefore applications (re)use services that are available elsewhere and many applications interact, without knowing each other, using services available via service servers and their published interfaces and functionalities. Industries propose, through various consortium, languages, technologies and standards. More academic works are also undertaken concerning semantics and formalisation of components and service-based systems. We consider here both streams of works in order to raise research concerns that will help in building quality software. Are there new challenging problems with respect to service-based software construction? Besides, what are the links and the advances compared to distributed systems?Comment: 16 page

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