Our growing dependence on increasingly complex computer and software systems necessitates the development of formalisms, techniques, and tools for assessing functional properties of these systems. One such technique that has emerged in the last twenty years is model checking, which systematically (and automatically) checks whether a model of a given system satisfies a desired property such as deadlock freedom, invariants, and request-response properties. This automated technique for verification and debugging has developed into a mature and widely used approach with many applications. Principles of Model Checking offers a comprehensive introduction to model checking that is not only a text suitable for classroom use but also a valuable reference for researchers and practitioners in the field. The book begins with the basic principles for modeling concurrent and communicating systems, introduces different classes of properties (including safety and liveness), presents the notion of fairness, and provides automata-based algorithms for these properties. It introduces the temporal logics LTL and CTL, compares them, and covers algorithms for verifying these logics, discussing real-time systems as well as systems subject to random phenomena. Separate chapters treat such efficiency-improving techniques as abstraction and symbolic manipulation. The book includes an extensive set of examples (most of which run through several chapters) and a complete set of basic results accompanied by detailed proofs. Each chapter concludes with a summary, bibliographic notes, and an extensive list of exercises of both practical and theoretical nature.

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Principles of Model Checking

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Economic Control of Quality of Manufactured Product.

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A Break in the Clouds: Towards a Cloud Definition

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.

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Agents in bioinformatics, computational and systems biology

We address the problem of specifying and detecting emergent behavior in networks of cardiac myocytes, spiral electric waves in particular, a precursor to atrial and ventricular fibrillation. To solve this problem we: (1) apply discrete mode abstraction to the cycle-linear hybrid automata (CLHA) we have recently developed for modeling the behavior of myocyte networks; (2) introduce the new concept of spatial superposition of CLHA modes; (3) develop a new spatial logic, based on spatial superposition, for specifying emergent behavior; (4) devise a new method for learning the formulae of this logic from the spatial patterns under investigation; and (5) apply bounded model checking to detect the onset of spiral waves. We have implemented our methodology as the EMERALD tool suite, a component of our EHA framework for specification, simulation, analysis, and control of excitable hybrid automata. We illustrate the effectiveness of our approach by applying EMERALD to the scalar electrical fields produced by our CELLEXCITE simulation environment for excitable-cell networks.

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Learning and detecting emergent behavior in networks of cardiac myocytes

Inthe?eldofformalmethodsincomputerscience,concurrencytheoryisreceivinga constantlyincreasinginterest.Thisisespeciallytrueforprocessalgebra.Althoughit had been originally conceived as a means for reasoning about the semantics of c- current programs, process algebraic formalisms like CCS, CSP, ACP, ?-calculus, and their extensions (see, e.g., [154,119,112,22,155,181,30]) were soon used also for comprehendingfunctionaland nonfunctionalaspects of the behaviorof com- nicating concurrent systems. The scienti?c impact of process calculi and behavioral equivalences at the base of process algebra is witnessed not only by a very rich literature. It is in fact worth mentioningthe standardizationprocedurethat led to the developmentof the process algebraic language LOTOS [49], as well as the implementation of several modeling and analysis tools based on process algebra, like CWB [70] and CADP [93], some of which have been used in industrial case studies. Furthermore, process calculi and behavioral equivalencesare by now adopted in university-levelcourses to teach the foundations of concurrent programming as well as the model-driven design of concurrent, distributed, and mobile systems. Nevertheless, after 30 years since its introduction, process algebra is rarely adopted in the practice of software development. On the one hand, its technica- ties often obfuscate the way in which systems are modeled. As an example, if a process term comprises numerous occurrences of the parallel composition operator, it is hard to understand the communicationscheme among the varioussubterms. On the other hand, process algebra is perceived as being dif?cult to learn and use by practitioners, as it is not close enough to the way they think of software systems.

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A Process Algebraic Approach to Software Architecture Design

The paper presents an approach for deriving test plans for the conformance testing of a system implementation with respect to the formal description of its software architecture (SA). The SA describes a system in terms of its components and connections, therefore the derived test plans address the integration testing phase. We base our approach on a labelled transition system (LTS) modeling the SA dynamics, and on suitable abstractions of it, the Abstract Labelled Transition Systems (ALTSs). ALTSs offer specific views of the SA dynamics by concentrating on relevant features and abstracting away from uninteresting ones. ALTS is a tool we provide to the software architect that lets him/her focus on relevant behavioral patterns and more easily identify those that are meaningful for validation purposes. Intuitively, deriving an adequate set of functional test classes means deriving a set of paths appropriately covering the ALTS. We describe our approach in the scope of a real world case study and discuss in detail all the steps of our methodology, from ALTS identification to test plan generation.

Deriving test plans from architectural descriptions

Business process modeling allows abstracting and reasoning on how work is structured within complex organizations. Business process models represent blueprints that can serve different purposes for a variety of stakeholders. For example, business analysts can use these models to better understand how the organization works; employees playing a role in the process can use them to learn the tasks that they are supposed to perform; software analysts/developers can refer to the models to understand the system-as-is before designing the system-to-be. Given the variety of stakeholders that need to interpret these models, and considering the pivotal function that models play within organizations, understandability becomes a fundamental quality that need to be taken into particular account by modelers. In this paper we provide a set of fifty guidelines that can help modelers to improve the understandability of their models. The work focuses on the Business Process Modelling Notation 2.0 standard published by the Object Management Group, which has acquired a clear predominance among the modeling notations for business processes. Guidelines were derived by means of a thoughtful literature review – which allowed identifying around one hundred guidelines – and through successive activities of synthesis and homogenization. In addition, we implemented a freely available open source tool, named B EBoP (understandaBility vErifier for Business Process models), to check the adherence of a model to the guidelines. Finally, guidelines violation has been checked with B EBoP on a dataset of 11,294 models available in a publicly accessible repository. Our tests show that, although the majority of the guidelines are respected by the models, some guidelines, which are recognized as fundamental by the literature, are frequently violated.

Flavio Corradini

Papers

Agents in bioinformatics, computational and systems biology

Learning and detecting emergent behavior in networks of cardiac myocytes

A Process Algebraic Approach to Software Architecture Design

Deriving test plans from architectural descriptions

A Guidelines framework for understandable BPMN models