Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-

Towards the Formal Verification of Model Transformations: An Application to Kermeta

Model-Driven Engineering (MDE) is becoming a popular engineering methodology for developing large-scale software applications, using models and transformations as primary principles. MDE is now being successfully applied to domain-specific languages (DSLs), which target a narrow subject domain like process management, telecommunication, product lines, smartphone applications among others, providing experts high-level and intuitive notations very close to their problem domain. More recently, MDE has been applied to safety-critical applications, where failure may have dramatic consequences, either in terms of economic, ecologic or human losses. These recent application domains call for more robust and more practical approaches for ensuring the correctness of models and model transformations. Testing is the most common technique used in MDE for ensuring the correctness of model transformations, a recurrent, yet unsolved problem in MDE. But testing suffers from the so-called coverage problem, which is unacceptable when safety is at stake. Rather, exhaustive coverage is required in this application domain, which means that transformation designers need to use formal analysis methods and tools to meet this requirement. Unfortunately, two factors seem to limit the use of such methods in an engineer’s daily life. First, a methodological factor, because MDE engineers rarely possess the effective knowledge for deploying formal analysis techniques in their daily life developments. Second, a practical factor, because DSLs do not necessarily have a formal explicit semantics, which is a necessary enabler for exhaustive analysis. In this thesis, we contribute to the problem of formal analysis of model transformations regarding each perspective. On the conceptual side, we propose a methodological framework for engineering verified model transformations based on current best practices. For that purpose, we identify three important dimensions: (i) the transformation being built; (ii) the properties of interest ensuring the transformation’s correctness; and finally, (iii) the verification technique that allows proving these properties with minimal effort. Finding which techniques are better suited for which kind of properties is the concern of the Computer-Aided Verification community. Consequently in this thesis, we focus on studying the relationship between transformations and properties. Our methodological framework introduces two novel notions. A transformation intent gathers all transformations sharing the same purpose, abstracting from the way the transformation is expressed. A property class captures under the same denomination all properties sharing the same form, abstracting away from their underlying property languages. The framework consists of mapping each intent with its characteristic set of property classes, meaning that for proving the correctness of a particular transformation obeying this intent, one has to prove properties of these specific classes. We illustrate the use and utility of our framework through the detailed description of five common intents in MDE, and their application to a case study drawn from the automative software domain, consisting of a chain of more than thirty transformations. On a more practical side, we study the problem of verifying DSLs whose behaviour is expressed with Kermeta. Kermeta is an object-oriented transformation framework aligned with Object Management Group standard specification MOF (Meta-Object Facility). It can be used for defining metamodels and models, as well as their behaviour. Kermeta lacks a formal semantics: we first specify such a semantics, and then choose an appropriate verification domain for handling the analysis one is interested in. Since the semantics is defined at the level of Kermeta’s transformation language itself, our work presents two interesting features: first, any DSL whose behaviour is defined using Kermeta (more precisely, any transformation defined with Kermeta) enjoys a de facto formal underground for free; second, it is easier to define appropriate abstractions for targeting specific analysis for this full-fledged semantics than defining specific semantics for each possible kind of analysis. To illustrate this point, we have selected Maude, a powerful rewriting system based on algebraic specifications equipped with model-checking and theorem-proving capabilities. Maude was chosen because its underlying formalism is close to the mathematical tools we use for specifying the formal semantics, reducing the implementation gap and consequently limiting the possible implementation mistakes. We validate our approach by illustrating behavioural properties of small, yet representative DSLs from the literature

A logic-based approach for the verification of UML timed models

This article presents a novel technique to formally verify models of real-time systems captured through a set of heterogeneous UML diagrams. The technique is based on the following key elements: (i) a subset of Unified Modeling Language (UML) diagrams, called Coretto UML (C-UML), which allows designers to describe the components of the system and their behavior through several kinds of diagrams (e.g., state machine diagrams, sequence diagrams, activity diagrams, interaction overview diagrams), and stereotypes taken from the UML Profile for Modeling and Analysis of Real-Time and Embedded Systems; (ii) a formal semantics of C-UML diagrams, defined through formulae of the metric temporal logic Tempo Reale ImplicitO (TRIO); and (iii) a tool, called Corretto, which implements the aforementioned semantics and allows users to carry out formal verification tasks on modeled systems. We validate the feasibility of our approach through a set of different case studies, taken from both the academic and the industrial domain

Highly-cited papers in software engineering: The top 100

Context: According to the search reported in this paper, as of this writing (May 2015), a very large number of papers (more than 70,000) have been published in the area of Software Engineering (SE) since its inception in 1968. Citations are crucial in any research area to position the work and to build on the work of others. Identification and characterization of highly-cited papers are common and are regularly reported in various disciplines. Objective: The objective of this study is to identify the papers in the area of SE that have influenced others the most as measured by citation count. Studying highly-cited SE papers helps researchers to see the type of approaches and research methods presented and applied in such papers, so as to be able to learn from them to write higher quality papers which will likely receive high citations. Method: To achieve the above objective, we conducted a study, comprised of five research questions, to identify and classify the top-100 highly-cited SE papers in terms of two metrics: total number of citations and average annual number of citations. Results: By total number of citations, the top paper is "A metrics suite for object-oriented design", cited 1,817 times and published in 1994. By average annual number of citations, the top paper is "QoS-aware middleware for Web services composition", cited 154.2 times on average annually and published in 2004. Conclusion: It is concluded that it is important to identify the highly-cited SE papers and also to characterize the overall citation landscape in the SE field. We hope that this paper will encourage further discussions in the SE community towards further analysis and formal characterization of the highly-cited SE papers.Vahid Garousi was partially supported by several internal grants provided by the Hacettepe University. The authors would like to thank the anonymous reviewers for their insightful comments

Towards Language-Oriented Modeling

In this habilitation à diriger des recherches (HDR), I review a decade of research work in the fields of Model-Driven Engineering (MDE) and Software Language Engineering (SLE). I propose contributions to support a language-oriented modeling, with the particular focus on enabling early validation & verification (V&V) of software-intensive systems. I first present foundational concepts and engineering facilities which help to capture the core domain knowledge into the various heterogeneous concerns of DSMLs (aka. metamodeling in the small), with a particular focus on executable DSMLs to automate the development of dynamic V&V tools. Then, I propose structural and behavioral DSML interfaces, and associated composition operators to reuse and integrate multiple DSMLs (aka. metamodeling in the large).In these research activities I explore various breakthroughs in terms of modularity and reusability of DSMLs. I also propose an original approach which bridges the gap between the concurrency theory and the algorithm theory, to integrate a formal concurrency model into the execution semantics of DSMLs. All the contributions have been implemented in software platforms — the language workbench Melange and the GEMOC studio – and experienced in real-world case studies to assess their validity. In this context, I also founded the GEMOC initiative, an attempt to federate the community on the grand challenge of the globalization of modeling languages

Model Transformation Testing and Debugging: A Survey

Model transformations are the key technique in Model-Driven Engineering (MDE) to manipulate and construct models. As a consequence, the correctness of software systems built with MDE approaches relies mainly on the correctness of model transformations, and thus, detecting and locating bugs in model transformations have been popular research topics in recent years. This surge of work has led to a vast literature on model transformation testing and debugging, which makes it challenging to gain a comprehensive view of the current state of the art. This is an obstacle for newcomers to this topic and MDE practitioners to apply these approaches. This paper presents a survey on testing and debugging model transformations based on the analysis of \nPapers~papers on the topics. We explore the trends, advances, and evolution over the years, bringing together previously disparate streams of work and providing a comprehensive view of these thriving areas. In addition, we present a conceptual framework to understand and categorise the different proposals. Finally, we identify several open research challenges and propose specific action points for the model transformation community.This work is partially supported by the European Commission (FEDER) and Junta de Andalucia under projects APOLO (US-1264651) and EKIPMENT-PLUS (P18-FR-2895), by the Spanish Government (FEDER/Ministerio de Ciencia e Innovación – Agencia Estatal de Investigación) under projects HORATIO (RTI2018-101204-B-C21), COSCA (PGC2018-094905-B-I00) and LOCOSS (PID2020-114615RB-I00), by the Austrian Science Fund (P 28519-N31, P 30525-N31), and by the Austrian Federal Ministry for Digital and Economic Affairs and the National Foundation for Research, Technology and Development (CDG

Designing precise and flexible graphical modelling languages for software development

Model-driven approaches to software development involve building computerized models of software and the environment in which it is intended to operate. This thesis offers a selection of the author’s work over the last three decades that addresses the design of precise and flexible graphical modelling languages for use in model-driven software development. The primary contributions of this work are: • Syntropy: the first published object-oriented analysis and design (OOAD) method to fully integrate formal and graphical modelling techniques. • The creation of the Object Constraint Language (OCL) and its integration into the Unified Modeling Language (UML) specification. • The identification of requirements and mechanisms for increasing the flexibility of the UML specification. • The design and implementation of tools for implementing graphical Domain Specific Languages (DSLs). The starting point was the author’s experience with formal specification techniques contrasted with the lack of precision of published object-oriented analysis and design methods. This led to a desire to fully integrate these two topics – formal specification and object-orientation - into a coherent discipline. The Syntropy approach, created in 1994 by this author and John Daniels, was the first published complete attempt to do this. Much of the author’s subsequent published work concerns the Unified Modeling Language (UML). UML represented a welcome unification of earlier OOAD approaches, but suffered badly from inflexibility and lack of precision. A significant part of the work included in this thesis addresses the drawbacks of the UML and proposes improvements to the precision of its definition, including through the invention of Object Constraint Language (OCL) and its incorporation into the UML specification, and the consideration of UML as source material for the definition of Domain Specific Languages (DSLs). Several of the author’s published works in this thesis concern mechanisms for the creation of DSLs, both within a UML framework and separately

Transformation by example

La transformation de modèles consiste à transformer un modèle source en un modèle cible conformément à des méta-modèles source et cible. Nous distinguons deux types de transformations. La première est exogène où les méta-modèles source et cible représentent des formalismes différents et où tous les éléments du modèle source sont transformés. Quand elle concerne un même formalisme, la transformation est endogène. Ce type de transformation nécessite généralement deux étapes : l’identification des éléments du modèle source à transformer, puis la transformation de ces éléments. Dans le cadre de cette thèse, nous proposons trois principales contributions liées à ces problèmes de transformation. La première contribution est l’automatisation des transformations des modèles. Nous proposons de considérer le problème de transformation comme un problème d'optimisation combinatoire où un modèle cible peut être automatiquement généré à partir d'un nombre réduit d'exemples de transformations. Cette première contribution peut être appliquée aux transformations exogènes ou endogènes (après la détection des éléments à transformer). La deuxième contribution est liée à la transformation endogène où les éléments à transformer du modèle source doivent être détectés. Nous proposons une approche pour la détection des défauts de conception comme étape préalable au refactoring. Cette approche est inspirée du principe de la détection des virus par le système immunitaire humain, appelée sélection négative. L’idée consiste à utiliser de bonnes pratiques d’implémentation pour détecter les parties du code à risque. La troisième contribution vise à tester un mécanisme de transformation en utilisant une fonction oracle pour détecter les erreurs. Nous avons adapté le mécanisme de sélection négative qui consiste à considérer comme une erreur toute déviation entre les traces de transformation à évaluer et une base d’exemples contenant des traces de transformation de bonne qualité. La fonction oracle calcule cette dissimilarité et les erreurs sont ordonnées selon ce score. Les différentes contributions ont été évaluées sur d’importants projets et les résultats obtenus montrent leurs efficacités.Model transformations take as input a source model and generate as output a target model. The source and target models conform to given meta-models. We distinguish between two transformation categories. Exogenous transformations are transformations between models expressed using different languages, and the whole source model is transformed. Endogenous transformations are transformations between models expressed in the same language. For endogenous transformations, two steps are needed: identifying the source model elements to transform and then applying the transformation on them. In this thesis, we propose three principal contributions. The first contribution aims to automate model transformations. The process is seen as an optimization problem where different transformation possibilities are evaluated and, for each possibility, a quality is associated depending on its conformity with a reference set of examples. This first contribution can be applied to exogenous as well as endogenous transformation (after determining the source model elements to transform). The second contribution is related precisely to the detection of elements concerned with endogenous transformations. In this context, we present a new technique for design defect detection. The detection is based on the notion that the more a code deviates from good practice, the more likely it is bad. Taking inspiration from artificial immune systems, we generate a set of detectors that characterize the ways in which a code can diverge from good practices. We then use these detectors to determine how far the code in the assessed systems deviates from normality. The third contribution concerns transformation mechanism testing. The proposed oracle function compares target test cases with a base of examples containing good quality transformation traces, and assigns a risk level based on the dissimilarity between the two. The traces help the tester understand the origin of an error. The three contributions are evaluated with real software projects and the obtained results confirm their efficiencies

Survey of Template-Based Code Generation

L'automatisation de la génération des artefacts textuels à partir des modèles est une étape critique dans l'Ingénierie Dirigée par les Modèles (IDM). C'est une transformation de modèles utile pour générer le code source, sérialiser les modèles dans de stockages persistents, générer les rapports ou encore la documentation. Parmi les différents paradigmes de transformation de modèle-au-texte, la génération de code basée sur les templates (TBCG) est la plus utilisée en IDM. La TBCG est une technique de génération qui produit du code à partir des spécifications de haut niveau appelées templates. Compte tenu de la diversité des outils et des approches, il est nécessaire de classifier et de comparer les techniques de TBCG existantes afin d'apporter un soutien approprié aux développeurs. L'objectif de ce mémoire est de mieux comprendre les caractéristiques des techniques de TBCG, identifier les tendances dans la recherche, et éxaminer l'importance du rôle de l'IDM par rapport à cette approche. J'évalue également l'expressivité, la performance et la mise à l'échelle des outils associés selon une série de modèles. Je propose une étude systématique de cartographie de la littérature qui décrit une intéressante vue d'ensemble de la TBCG et une étude comparitive des outils de la TBCG pour mieux guider les dévloppeurs dans leur choix. Cette étude montre que les outils basés sur les modèles offrent plus d'expressivité tandis que les outils basés sur le code sont les plus performants. Enfin, Xtend2 offre le meilleur compromis entre l'expressivité et la performance.A critical step in model-driven engineering (MDE) is the automatic synthesis of a textual artifact from models. This is a very useful model transformation to generate application code, to serialize the model in persistent storage, generate documentation or reports. Among the various model-to-text transformation paradigms, Template-Based Code Generation (TBCG) is the most popular in MDE. TBCG is a synthesis technique that produces code from high-level specifications, called templates. It is a popular technique in MDE given that they both emphasize abstraction and automation. Given the diversity of tools and approaches, it is necessary to classify and compare existing TBCG techniques to provide appropriate support to developers. The goal of this thesis is to better understand the characteristics of TBCG techniques, identify research trends, and assess the importance of the role of MDE in this code synthesis approach. We also evaluate the expressiveness, performance and scalability of the associated tools based on a range of models that implement critical patterns. To this end, we conduct a systematic mapping study of the literature that paints an interesting overview of TBCG and a comparative study on TBCG tools to better guide developers in their choices. This study shows that model-based tools offer more expressiveness whereas code-based tools performed much faster. Xtend2 offers the best compromise between the expressiveness and the performance