Leila Ribeiro

Verification of Distributed Object-Based Systems

Distributed systems for open environments, like the Internet, are becoming more frequent and important. However, it is difficult to assure that such systems have the required functional properties. In this paper we use a visual formal specification language, called Object-Based Graph Grammars (OBGG), to specify asynchronous distributed systems. After discussing the main concepts of OBGG, we propose an approach for the verification of OBGG specifications using model checking. This approach consists on the translation of OBGG specifications into PROMELA (PROcess/PROtocol MEta LAnguage), which is the input language of the SPIN model checker. The approach we use for verification allows one to write properties based on the OBGG specification instead of on the generated PROMELA model.

Translating Java Code to Graph Transformation Systems

We propose a faithful encoding of Java programs (written in a suitable fragment of the language) to Graph Transformation Systems. Every program is translated to a set of rules including some basic rules, common to all programs and providing the operational semantics of Java (data and control) operators, and the program specific rules, namely one rule for each method or constructor declared in the program.

Specification of mobile code system using graph grammars

In this paper we introduce a formal approach for the specification of mobile code systems. This approach is based on graph grammars, that is a formal description technique that is suitable for the description of highly parallel systems, and is intuitive even for non-theoreticians We define a special class of graph grammars using the concepts of object-based systems and include location information explicitly. Aspects of modularity and execution in an open environment are discussed.

Unfolding semantics of graph transformation

Several attempts have been made of extending to graph grammars the unfolding semantics originally developed by Winskel for (safe) Petri nets, but only partial results were obtained. In this paper, we fully extend Winskels approach to single-pushout grammars providing them with a categorical concurrent semantics expressed as a coreflection between the category of (semi-weighted) graph grammars and the category of prime algebraic domains, which factorises through the category of occurrence grammars and the category of asymmetric event structures. For general, possibly nonsemi-weighted single-pushout grammars, we define an analogous functorial concurrent semantics, which, however, is not characterised as an adjunction. Similar results can be obtained for double-pushout graph grammars, under the assumptions that nodes are never deleted.

Verifying Object-Based Graph Grammars

Object-Based Graph Grammars (OBGG) is a formal language suitable for the specification of distributed systems. On previous work, a translation from OBGG models to PROMELA (the input language of the SPIN model checker) was defined, enabling the verification of OBGG models using SPIN. This paper builds on these results, where we extend the approach for property specification and define an approach to interpret PROMELA traces as OBGG derivations, generating graphical counter-examples for properties that are not true for an OBGG model.

Verification of graph grammars using a logical approach

Graph grammars may be used as specification technique for different kinds of systems, specially in situations in which states are complex structures that can be adequately modeled as graphs (possibly with an attribute data part) and in which the behavior involves a large amount of parallelism and can be described as reactions to stimuli that can be observed in the state of the system. The verification of properties of such systems is a difficult task due to many aspects: the systems in many situations involve an infinite number of states; states themselves are complex and large; there are a number of different computation possibilities due to the fact that rule applications may occur in parallel. There are already some approaches to verification of graph grammars based on model checking, but in these cases only finite state systems can be analyzed. Other approaches propose over- and/or under-approximations of the state space, but in this case it is not possible to check arbitrary properties. This work proposes a relational and logical approach to graph grammars that allows formal verification of systems using mathematical induction. We use relational structures to define graph grammars and first-order logic to model graph transformations. This approach allows proving properties of systems with infinite state spaces. In this paper we first consider the case of simple (typed) graphs, and then we extend the approach to the non-trivial case of attributed graphs, that are graphs in which values are associated to vertices. Attributed graph grammars are very interesting from a practical point of view, since it is possible to use variables and terms when specifying the behavior expressed by rules. These values (or terms) come from algebras specified as abstract data types. The use of attributed graphs gives the specifier a language that is more suitable for specification, merging the advantages of the graphical representation with the standard representation of classical data types. We show that attributes can be smoothly integrated in our representation of graph grammars, giving rise to a framework to reason about attributed graph grammars.

Formal Verification of Object-Oriented Graph Grammars Specifications

Concurrent object-oriented systems are ubiquitous due to the importance of networks and the current demands for modular, reusable, and easy to develop software. However, checking the correctness of such systems is a hard task, mainly due to concurrency and inheritance aspects. In this paper we present an approach to the verification of concurrent object-oriented systems. We use graph grammars equipped with object oriented features (including inheritance and polymorphism) as the specification formalism, and define a translation from such specifications to Promela, the input language of the SPIN model checker.

Verifying Object-based Graph Grammars

The development of concurrent and reactive systems is gaining importance since they are well-suited to modern computing platforms, such as the Internet. However, the development of correct concurrent and reactive systems is a non-trivial task. Object-based graph grammar (OBGG) is a visual formal language suitable for the specification of this class of systems. In previous work, a translation from OBGG to PROMELA (the input language of the SPIN model checker) was defined, enabling the verification of OBGG models using SPIN. In this paper we extend this approach in two different ways: (1) the approach for property specification is improved, enabling to prove properties not only about possible OBGG derivations, but also about the internal state of involved objects; (2) an approach is defined to interpret PROMELA races as OBGG derivations, generating graphical counter-examples for properties that are not true for a given OBGG model. Another contribution of this paper is (3) the definition of a method for model checking partial systems (isolated objects or a set of objects) using an assume-guarantee approach. A gas station system modeled with OBGGs is used to illustrate the contributions.

Modal Systems: Specification, Refinement and Realisation

Operation modes are useful structuring units that facilitate design of several safety-critical systems such as such as avionic, transportation and space systems. Although some support to the construction of modal systems can be found in the literature, modelling abstractions for the formal specification, analysis and correct construction of modal systems are still lacking. This paper discusses existing support for the construction of modal systems and proposes both a formalisation and a refinement notion for modal systems. A modal system, specified using the proposed abstractions, can be realised using different specification languages. Complementing the contribution, we define the requirements for an Event-B model to realise a modal system specification. A case study illustrates the proposed approach.

Gene Expression Profile of NF-κB, Nrf2, Glycolytic, and p53 Pathways During the SH-SY5Y Neuronal Differentiation Mediated by Retinoic Acid

SH-SY5Y cells, a neuroblastoma cell line that is a well-established model system to study the initial phases of neuronal differentiation, have been used in studies to elucidate the mechanisms of neuronal differentiation. In the present study, we investigated alterations of gene expression in SH-SY5Y cells during neuronal differentiation mediated by retinoic acid (RA) treatment. We evaluated important pathways involving nuclear factor kappa B (NF-κB), nuclear E2-related factor 2 (Nrf2), glycolytic, and p53 during neuronal differentiation. We also investigated the involvement of reactive oxygen species (ROS) in modulating the gene expression profile of those pathways by antioxidant co-treatment with Trolox®, a hydrophilic analogue of α-tocopherol. We found that RA treatment increases levels of gene expression of NF-κB, glycolytic, and antioxidant pathway genes during neuronal differentiation of SH-SY5Y cells. We also found that ROS production induced by RA treatment in SH-SY5Y cells is involved in gene expression profile alterations, chiefly in NF-κB, and glycolytic pathways. Antioxidant co-treatment with Trolox® reversed the effects mediated by RA NF-κB, and glycolytic pathways gene expression. Interestingly, co-treatment with Trolox® did not reverse the effects in antioxidant gene expression mediated by RA in SH-SY5Y. To confirm neuronal differentiation, we quantified endogenous levels of tyrosine hydroxylase, a recognized marker of neuronal differentiation. Our data suggest that during neuronal differentiation mediated by RA, changes in profile gene expression of important pathways occur. These alterations are in part mediated by ROS production. Therefore, our results reinforce the importance in understanding the mechanism by which RA induces neuronal differentiation in SH-SY5Y cells, principally due this model being commonly used as a neuronal cell model in studies of neuronal pathologies.