Composite Modeling based on Distributed Graph Transformation and the Eclipse Modeling Framework

Model-driven development (MDD) has become a promising trend in software engineering for a number of reasons. Models as the key artifacts help the developers to abstract from irrelevant details, focus on important aspects of the underlying domain, and thus master complexity. As software systems grow, models may grow as well and finally become possibly too large to be developed and maintained in a comprehensible way. In traditional software development, the complexity of software systems is tackled by dividing the system into smaller cohesive parts, so-called components, and let distributed teams work on each concurrently. The question arises how this strategy can be applied to model-driven development. The overall aim of this thesis is to develop a formalized modularization concept to enable the structured and largely independent development of interrelated models in larger teams. To this end, this thesis proposes component models with explicit export and import interfaces where exports declare what is provided while imports declare what it needed. Then, composite model can be connected by connecting their compatible export and import interfaces yielding so-called composite models. Suitable to composite models, a transformation approach is developed which allows to describe changes over the whole composition structure. From the practical point of view, this concept especially targets models based on the Eclipse Modeling Framework (EMF). In the modeling community, EMF has evolved to a very popular framework which provides modeling and code generation facilities for Java applications based on structured data models. Since graphs are a natural way to represent the underlying structure of visual models, the formalization is based on graph transformation. Incorporated concepts according to distribution heavily rely on distributed graph transformation introduced by Taentzer. Typed graphs with inheritance and containment structures are well suited to describe the essentials of EMF models. However, they also induce a number of constraints like acyclic inheritance and containment which have to be taken into account. The category-theoretical foundation in this thesis allows for the precise definition of consistent composite graph transformations satisfying all inheritance and containment conditions. The composite modeling approach is shown to be coherent with the development of tool support for composite EMF models and composite EMF model transformation

Finite strain chemo-thermo-electro-mechanics with applications in mechanobiology

La tesi proposta nasce da ben definite motivazioni biologiche, con lo scopo di fornire una caratterizzazione del comportamento delle cellule endoteliali nel processo di angiogenesi tumorale. Diversi framework multi-fisici vengono introdotti per applicazioni nel campo della meccanobiologia, così come in altre aree di ricerca. L’angiogenesi è un noto processo progressivo, fisiologico o patologico, caratterizzato dalla formazione di nuovi vasi sanguigni che si originano da quelli pre-esistenti. Le cellule endoteliali, le quali rivestono le pareti interne dei vasi sanguigni, vengono influenzate da stimuli extra-cellulari rilasciati dalle cellule tumorali, e rispondono tramite rilocazione di recettori (proteine) sulla loro membrana, migrazione cellulare collettiva e riorganizzazione in nuovi vasi sanguigni. Il ruolo della dinamica recettoriale e della meccanica cellulare in risposta agli stimuli extra-cellulari è dunque oggetto di grande interesse, in quanto processi cruciali nelle fasi iniziali dell’angiogenesi. Le funzioni strutturali della cellula, le quali permettono l’avvenimento di processi ben noti come l’adesione e l’accasciamento cellulare, la motilità e la migrazione, sono attribuite alla generazione e la riorganizzazione della macchina contrattile citoscheletrica. Il citoscheletro è una rete interconnessa di proteine e polimeri filamentosi, soggetto ad un imponente riarrangiamento che permette la generazione di diverse strutture polimeriche, fornendo le forze e il supporto strutturale necessari per il movimento cellulare. Il ruolo della meccanica nei processi biologici è dunque di inconfutabile rilevanza, così come la responsabilità della meccanobiologia di fornire un supporto ad una caratterizzazione esaustiva dei sistemi viventi. Modell multi-fisici con applicazioni in meccanobiologia richiedono di tener conto degli svariati fenomeni coinvolti nel processo sotto investigazione. La teoria della meccanica del continuo in grandi deformazioni rappresenta certamente il miglior candidato per descrivere la risposta strutturale delle cellule soggette a massicce deformazioni durante i processi di adesione cellulare, accasciamento e migrazione. Ciononostante, la sola meccanica è evidentemente insufficiente. Nonostante l’accoppiamento tra la meccanica in grandi deformazioni e la termodinamica sia alla base di innumerevoli modelli multi-fisici, è indubbia la necessità di considerare altri processi quali il trasporto di massa con appropriate leggi di diffusione, e di tenere conto delle reazioni chimiche. L’accoppiamento tra termodinamica, meccanica e chemo-diffusione conduce alla realizzazione dei così definiti chemo-transport-mechanical frameworks. Inoltre, e così come ben noto nel campo della termodinamica, la necessità di fornire una caratterizzazione statisticamente basata di alcuni fenomeni è frequente. È il caso della modellazione dei reticoli polimerici nel campo della fisica dei polimeri. Si presentano di conseguenza sfide aggiuntive nel tener conto di eventi multi-fisici a differenti scale spazio-temporali. In questa tesi, i modelli teorici multi-fisici proposti trovano applicazioni che non sono puramente ristrette al campo della meccanobiologia. Termodinamica e meccanica in grandi deformazioni, meccanica dei continui statisticamente basata, e la teoria dell’elettromagnetismo Galileiano, rappresentano i principali temi investigati nella tesi e adottati per la realizzazione di diverse formulazioni multi-fisiche.The proposed thesis comes from well-defined biological motivations, aiming at providing a characterization of endothelial cell behavior in tumor angiogenesis. Several multi-physics frameworks are introduced for applications in the realm of mechanobiology, as well as in many other research areas. Angiogenesis is a well known physiological or pathological multistep process that consists in the formation of new blood vessels from preexisting ones. Covering the inner walls of blood vessels, endothelial cells are affected by extracellular stimuli released by tumor cells, and respond via relocation of receptor proteins along their membrane, collective migration and reorganization in novel vessels. The role of receptor dynamics and cell mechanics in response to extracellular stimuli is therefore object of great interest, as they are pivotal processes at the early stages of angiogenesis. Cell structural functions, allowing the occurrence of well known processes such as cell adhesion and spreading, motility and migration, are ascribed to the generation and reorganization of the cytoskeletal contractile machinery. The cytoskeleton is an interconnected network of regulatory proteins and filamentous polymers that undergoes massive rearrangements to generate different biopolymer structures, providing the necessary forces and structural support for cell movements. It is therefore of unquestionable relevance the role of mechanics in biological processes, as well as the responsibility of mechanobiology to provide a support for an exhaustive characterization of alive systems. Multi-physics models with applications in mechanobiology require to account for several phenomena involved in the process under investigation. The finite strain theory in continuum mechanics certainly represents the best candidate to describe the structural response of cells undergoing massive deformations during cell adhesion, spreading, and migration. However, mechanics itself is evidently not sufficient. Despite the coupling between finite strain mechanics and thermodynamics stands for the basis of a countless amount of multi-physics models, the necessity to consider other processes such as mass transport with proper diffusion laws, and to account for chemical reactions, is beyond doubt. The coupling between thermo-mechanics and chemo-transport phenomena leads thus to design the so-termed chemo-transport-mechanical frameworks. Furthermore, and as well known in the realm of thermodynamics, insightful models often need to provide a statistically-based characterization of phenomena. It is the case of cross-linked polymer networks modeling in the field of polymer physics. Additional challenges therefore arise in accounting for multi-physics events that occur at different space-time scales. In this thesis, general and theoretical multi-physics models are proposed for applications that are not only restricted to the realm of mechanobiology. Finite strain continuum thermo-mechanics, diffusion laws and phase segregation, chemical reactions with trapping, statistically-based continuum mechanics, and the Galilean electromagnetic theory, represent the main topics investigated in this thesis and adopted for designing several multi-physics formulations

Towards Partial Composition of Components: Formal Foundation for Component Verification

The intention of this paper is to extend the generic component framework to partial composition. Basic Ideas of partial composition were introduced in [EM90] but we additionally want to allow component verification based on export-import implications. Import-Export implications relate sentences of the import stating what the component requires to sentences of the export stating what the component guarantees. The main result of this paper is the compatibility of import-export implications are compatible with the partial composition. The second part illustrates how this abstract concept can be instantiated to Petri net systems

Formal Foundations for Information-Preserving Model Synchronization Processes Based on Triple Graph Grammars

Zwischen verschiedenen Artefakten, die Informationen teilen, wieder Konsistenz herzustellen, nachdem eines von ihnen geändert wurde, ist ein wichtiges Problem, das in verschiedenen Bereichen der Informatik auftaucht. Mit dieser Dissertation legen wir eine Lösung für das grundlegende Modellsynchronisationsproblem vor. Bei diesem Problem ist ein Paar solcher Artefakte (Modelle) gegeben, von denen eines geändert wurde; Aufgabe ist die Wiederherstellung der Konsistenz. Tripelgraphgrammatiken (TGGs) sind ein etablierter und geeigneter Formalismus, um dieses und verwandte Probleme anzugehen. Da sie auf der algebraischen Theorie der Graphtransformation und dem (Double-)Pushout Zugang zu Ersetzungssystemen basieren, sind sie besonders geeignet, um Lösungen zu entwickeln, deren Eigenschaften formal bewiesen werden können. Doch obwohl TGG-basierte Ansätze etabliert sind, leiden viele von ihnen unter dem Problem des Informationsverlustes. Wenn ein Modell geändert wurde, können während eines Synchronisationsprozesses Informationen verloren gehen, die nur im zweiten Modell vorliegen. Das liegt daran, dass solche Synchronisationsprozesse darauf zurückfallen Konsistenz dadurch wiederherzustellen, dass sie das geänderte Modell (bzw. große Teile von ihm) neu übersetzen. Wir schlagen einen TGG-basierten Ansatz vor, der fortgeschrittene Features von TGGs unterstützt (Attribute und negative Constraints), durchgängig formalisiert ist, implementiert und inkrementell in dem Sinne ist, dass er den Informationsverlust im Vergleich mit vorherigen Ansätzen drastisch reduziert. Bisher gibt es keinen TGG-basierten Ansatz mit vergleichbaren Eigenschaften. Zentraler Beitrag dieser Dissertation ist es, diesen Ansatz formal auszuarbeiten und seine wesentlichen Eigenschaften, nämlich Korrektheit, Vollständigkeit und Termination, zu beweisen. Die entscheidende neue Idee unseres Ansatzes ist es, Reparaturregeln anzuwenden. Dies sind spezielle Regeln, die es erlauben, Änderungen an einem Modell direkt zu propagieren anstatt auf Neuübersetzung zurückzugreifen. Um diese Reparaturregeln erstellen und anwenden zu können, entwickeln wir grundlegende Beiträge zur Theorie der algebraischen Graphtransformation. Zunächst entwickeln wir eine neue Art der sequentiellen Komposition von Regeln. Im Gegensatz zur gewöhnlichen Komposition, die zu Regeln führt, die Elemente löschen und dann wieder neu erzeugen, können wir Regeln herleiten, die solche Elemente stattdessen bewahren. Technisch gesehen findet der Synchronisationsprozess, den wir entwickeln, außerdem in der Kategorie der partiellen Tripelgraphen statt und nicht in der der normalen Tripelgraphen. Daher müssen wir sicherstellen, dass die für Double-Pushout-Ersetzungssysteme ausgearbeitete Theorie immer noch gültig ist. Dazu entwickeln wir eine (kategorientheoretische) Konstruktion neuer Kategorien aus gegebenen und zeigen, dass (i) diese Konstruktion die Axiome erhält, die nötig sind, um die Theorie für Double-Pushout-Ersetzungssysteme zu entwickeln, und (ii) partielle Tripelgraphen als eine solche Kategorie konstruiert werden können. Zusammen ermöglichen diese beiden grundsätzlichen Beiträge es uns, unsere Lösung für das grundlegende Modellsynchronisationsproblem vollständig formal auszuarbeiten und ihre zentralen Eigenschaften zu beweisen.Restoring consistency between different information-sharing artifacts after one of them has been changed is an important problem that arises in several areas of computer science. In this thesis, we provide a solution to the basic model synchronization problem. There, a pair of such artifacts (models), one of which has been changed, is given and consistency shall be restored. Triple graph grammars (TGGs) are an established and suitable formalism to address this and related problems. Being based on the algebraic theory of graph transformation and (double-)pushout rewriting, they are especially suited to develop solutions whose properties can be formally proven. Despite being established, many TGG-based solutions do not satisfactorily deal with the problem of information loss. When one model is changed, in the process of restoring consistency such solutions may lose information that is only present in the second model because the synchronization process resorts to restoring consistency by re-translating (large parts of) the updated model. We introduce a TGG-based approach that supports advanced features of TGGs (attributes and negative constraints), is comprehensively formalized, implemented, and is incremental in the sense that it drastically reduces the amount of information loss compared to former approaches. Up to now, a TGG-based approach with these characteristics is not available. The central contribution of this thesis is to formally develop that approach and to prove its essential properties, namely correctness, completeness, and termination. The crucial new idea in our approach is the use of repair rules, which are special rules that allow one to directly propagate changes from one model to the other instead of resorting to re-translation. To be able to construct and apply these repair rules, we contribute more fundamentally to the theory of algebraic graph transformation. First, we develop a new kind of sequential rule composition. Whereas the conventional composition of rules leads to rules that delete and re-create elements, we can compute rules that preserve such elements instead. Furthermore, technically the setting in which the synchronization process we develop takes place is the category of partial triple graphs and not the one of ordinary triple graphs. Hence, we have to ensure that the elaborate theory of double-pushout rewriting still applies. Therefore, we develop a (category-theoretic) construction of new categories from given ones and show that (i) this construction preserves the axioms that are necessary to develop the theory of double-pushout rewriting and (ii) partial triple graphs can be constructed as such a category. Together, those two more fundamental contributions enable us to develop our solution to the basic model synchronization problem in a fully formal manner and to prove its central properties

Modelling Constrained Dynamic Software Architecture with Attributed Graph Rewriting Systems

Dynamic software architectures are studied for handling adap- tation in distributed systems, coping with new requirements, new envi- ronments, and failures. Graph rewriting systems have shown their ap- propriateness to model such architectures, particularly while considering the consistency of theirs reconfigurations. They provide generic formal means to specify structural properties, but imply a poor description of specific issues like behavioural properties. This paper lifts this limita- tion by proposing a formal approach for integrating the consideration of constraints, non-trivial attributes, and their propagation within the framework of graph rewriting systems

Towards the flexible reuse of model transformations: A formal approach based on Graph Transformation

This is the author’s version of a work that was accepted for publication in Journal of Logical and Algebraic Methods in Programming. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Logical and Algebraic Methods in Programming 83.5-6 (2014) , DOI:10.1016/j.jlamp.2014.08.005This special issue of the Journal of Logic and Algebraic Methods in Programming (JLAMP) includes full revised versions of selected papers that were presented at the 24th Nordic Workshop on Programming Theory (NWPT 2012). The workshop took place in Bergen, Norway, during 31 October–2 November 2012 and was organized by the Department of Informatics, University of Bergen, and the Bergen University College.Model transformations are the heart and soul of Model Driven Engineering (MDE). However, in order to increase the adoption of MDE by industry, techniques for developing model transformations in the large and raising the quality and productivity in their construction, like reusability, are still needed. In previous works, we developed a reutilization approach for graph transformations based on the definition of concepts, which gather the structural requirements needed by meta-models to qualify for the transformations. Reusable transformations are typed by concepts, becoming transformation templates. Transformation templates are instantiated by binding the concept to a concrete meta-model, inducing a retyping of the transformation for the given meta-model. This paper extends the approach allowing heterogeneities between the concept and the metamodel, thus increasing the reuse opportunities of transformation templates. Heterogeneities are resolved by using algebraic adapters which induce both a retyping and an adaptation of the transformation. As an alternative, the adapters can also be employed to induce an adaptation of the meta-model, and in this work we show the conditions for equivalence of both approaches to transformation reuse.We thank the referees for their detailed comments, which helped to greatly improve the paper. This work has been supported by the Spanish Ministry of Economy and Competitivity with project Go-Lite (TIN2011-24139)

Enhanced Graph Rewriting Systems for Complex Software Domain

International audienceMethodologies for correct by construction reconfigurations can efficiently solve consistency issues in dynamic software architecture. Graph-based models are appropriate for designing such architectures and methods. At the same time, they may be unfit to characterize a system from a non functional perspective. This stems from efficiency and applicability limitations in handling time-varying characteristics and their related dependencies. In order to lift these restrictions, an extension to graph rewriting systems is proposed herein. The suitability of this approach, as well as the restraints of currently available ones, are illustrated, analysed and experimentally evaluated with reference to a concrete example. This investigation demonstrates that the conceived solution can: (i) express any kind of algebraic dependencies between evolving requirements and properties; (ii) significantly ameliorate the efficiency and scalability of system modifications with respect to classic methodologies; (iii) provide an efficient access to attribute values; (iv) be fruitfully exploited in software management systems; (v) guarantee theoretical properties of a grammar, like its termination