A framework for efficient model transformations

The reported productivity gains while using models and model transformations to develop entire systems, after almost a decade of experience applying model-driven approaches for system development, are already undeniable benefits of this approach. However, the slowness of higher-level, rule based model transformation languages hinders the applicability of this approach to industrial scales. Lower-level, and efficient, languages can be used but productivity and easy maintenance seize to exist. The abstraction penalty problem is not new, it also exists for high-level, object oriented languages but everyone is using them now. Why is not everyone using rule based model transformation languages then? In this thesis, we propose a framework, comprised of a language and its respective environment, designed to tackle the most performance critical operation of high-level model transformation languages: the pattern matching. This framework shows that it is possible to mitigate the performance penalty while still using high-level model transformation languages.

Développement logiciel par transformation de modèles

La recherche en génie logiciel a depuis longtemps tenté de mieux comprendre le processus de développement logiciel, minimalement, pour en reproduire les bonnes pratiques, et idéalement, pour pouvoir le mécaniser. On peut identifier deux approches majeures pour caractériser le processus. La première approche, dite transformationnelle, perçoit le processus comme une séquence de transformations préservant certaines propriétés des données à l’entrée. Cette idée a été récemment reprise par l’architecture dirigée par les modèles de l’OMG. La deuxième approche consiste à répertorier et à codifier des solutions éprouvées à des problèmes récurrents. Les recherches sur les styles architecturaux, les patrons de conception, ou les cadres d’applications s’inscrivent dans cette approche. Notre travail de recherche reconnaît la complémentarité des deux approches, notamment pour l’étape de conception: dans le cadre du développement dirigé par les modèles, nous percevons l’étape de conception comme l’application de patrons de solutions aux modèles reçus en entrée. Il est coutume de définir l’étape de conception en termes de conception architecturale, et conception détaillée. La conception architecturale se préoccupe d’organiser un logiciel en composants répondant à un ensemble d’exigences non-fonctionnelles, alors que la conception détaillée se préoccupe, en quelque sorte, du contenu de ces composants. La conception architecturale s’appuie sur des styles architecturaux qui sont des principes d’organisation permettant d’optimiser certaines qualités, alors que la conception détaillée s’appuie sur des patrons de conception pour attribuer les responsabilités aux classes. Les styles architecturaux et les patrons de conception sont des artefacts qui codifient des solutions éprouvées à des problèmes récurrents de conception. Alors que ces artefacts sont bien documentés, la décision de les appliquer reste essentiellement manuelle. De plus, les outils proposés n’offrent pas un support adéquat pour les appliquer à des modèles existants. Dans cette thèse, nous nous attaquons à la conception détaillée, et plus particulièrement, à la transformation de modèles par application de patrons de conception, en partie parce que les patrons de conception sont moins complexes, et en partie parce que l’implémentation des styles architecturaux passe souvent par les patrons de conception. Ainsi, nous proposons une approche pour représenter et appliquer les patrons de conception. Notre approche se base sur la représentation explicite des problèmes résolus par ces patrons. En effet, la représentation explicite du problème résolu par un patron permet : (1) de mieux comprendre le patron, (2) de reconnaître l’opportunité d’appliquer le patron en détectant une instance de la représentation du problème dans les modèles du système considéré, et (3) d’automatiser l’application du patron en la représentant, de façon déclarative, par une transformation d’une instance du problème en une instance de la solution. Pour vérifier et valider notre approche, nous l’avons utilisée pour représenter et appliquer différents patrons de conception et nous avons effectué des tests pratiques sur des modèles générés à partir de logiciels libres.

Fujaba Days 2011

Fujaba is an Open Source UML CASE tool project started at the software engineering group of Paderborn University in 1997. In 2002 Fujaba has been redesigned and became the Fujaba Tool Suite with a plug-in architecture allowing developers to add functionality easily while retaining full control over their contributions. Multiple Application Domains Fujaba followed the model-driven development philosophy right from its beginning in 1997. At the early days, Fujaba had a special focus on code generation from UML diagrams resulting in a visual programming language with a special emphasis on object structure manipulating rules. Today, at least six rather independent tool versions are under development in Paderborn, Kassel, and Darmstadt for supporting (1) reengineering, (2) embedded real-time systems, (3) education, (4) specification of distributed control systems, (5) integration with the ECLIPSE platform, and (6) MOF-based integration of system (re-) engineering tools. International Community According to our knowledge, quite a number of research groups have also chosen Fujaba as a platform for UML and MDA related research activities. In addition, quite a number of Fujaba users send requests for more functionality and extensions. Therefore, the 8th International Fujaba Days aimed at bringing together Fujaba develop- ers and Fujaba users from all over the world to present their ideas and projects and to discuss them with each other and with the Fujaba core development team.

The Joint UK Land Environment Simulator (JULES), model description – part 1: energy and water fluxes

This manuscript describes the energy and water components of a new community land surface model called the Joint UK Land Environment Simulator (JULES). This is developed from the Met Office Surface Exchange Scheme (MOSES). It can be used as a stand alone land surface model driven by observed forcing data, or coupled to an atmospheric global circulation model. The JULES model has been coupled to the Met Office Unified Model (UM) and as such provides a unique opportunity for the research community to contribute their research to improve both world-leading operational weather forecasting and climate change prediction systems. In addition JULES, and its forerunner MOSES, have been the basis for a number of very high-profile papers concerning the land-surface and climate over the last decade. JULES has a modular structure aligned to physical processes, providing the basis for a flexible modelling platform.

The synergies between goal sketching and enterprise architecture

This paper introduces a pragmatic and practical method for requirements modeling. The method is built using the concepts of our goal sketching technique together with techniques from an enterprise architecture modeling language. Our claim is that our method will help project managers who want to establish early control of their projects and will also give managers confidence in the scope of their project. In particular we propose the inclusion of assumptions as first class entities in the ArchiMate enterprise architecture modeling language and an extension of the ArchiMate Motivation Model principle to allow radical as well as normative analyses. We demonstrate the usefulness of this method using a simple university library system as an example.

Touch ‘n’ sketch: pen and fingers on a multi-touch sketch application for tablet PC’s

In many creative and technical areas, professionals make use of paper sketches for developing and expressing concepts and models. Paper offers an almost constraint free environment where they have as much freedom to express themselves as they need. However, paper does have some disadvantages, such as size and not being able to manipulate the content (other than remove it or scratch it), which can be overcome by creating systems that can offer the same freedom people have from paper but none of the disadvantages and limitations. Only in recent years has the technology become massively available that allows doing precisely that, with the development in touch‐sensitive screens that also have the ability to interact with a stylus. In this project a prototype was created with the objective of finding a set of the most useful and usable interactions, which are composed of combinations of multi‐touch and pen. The project selected Computer Aided Software Engineering (CASE) tools as its application domain, because it addresses a solid and well‐defined discipline with still sufficient room for new developments. This was the result from the area research conducted to find an application domain, which involved analyzing sketching tools from several possible areas and domains. User studies were conducted using Model Driven Inquiry (MDI) to have a better understanding of the human sketch creation activities and concepts devised. Then the prototype was implemented, through which it was possible to execute user evaluations of the interaction concepts created. Results validated most interactions, in the face of limited testing only being possible at the time. Users had more problems using the pen, however handwriting and ink recognition were very effective, and users quickly learned the manipulations and gestures from the Natural User Interface (NUI).

Integrating eye tracking in virtual reality for stroke rehabilitation

This thesis reports on research done for the integration of eye tracking technology into virtual reality environments, with the goal of using it in rehabilitation of patients who suffered from stroke. For the last few years, eye tracking has been a focus on medical research, used as an assistive tool  to help people with disabilities interact with new technologies  and as an assessment tool  to track the eye gaze during computer interactions. However, tracking more complex gaze behaviors and relating them to motor deficits in people with disabilities is an area that has not been fully explored, therefore it became the focal point of this research. During the research, two exploratory studies were performed in which eye tracking technology was integrated in the context of a newly created virtual reality task to assess the impact of stroke. Using an eye tracking device and a custom virtual task, the system developed is able to monitor the eye gaze pattern changes over time in patients with stroke, as well as allowing their eye gaze to function as an input for the task. Based on neuroscientific hypotheses of upper limb motor control, the studies aimed at verifying the differences in gaze patterns during the observation and execution of the virtual goal-oriented task in stroke patients (N=10), and also to assess normal gaze behavior in healthy participants (N=20). Results were found consistent and supported the hypotheses formulated, showing that eye gaze could be used as a valid assessment tool on these patients. However, the findings of this first exploratory approach are limited in order to fully understand the effect of stroke on eye gaze behavior. Therefore, a novel model-driven paradigm is proposed to further understand the relation between the neuronal mechanisms underlying goal-oriented actions and eye gaze behavior.

CrossMDA-SPL: uma abordagem para gerência de variabilidades dirigida por modelos e aspectos

This paper proposes a systematic approach to management of variability modelsdriven and aspects using the mechanisms of approaches Aspect-Oriented Software Development (AOSD) and Model-Driven Development (MDD). The main goal of the approach, named CrossMDA-SPL, is to improve the management(gerência), modularization and isolation ou separation of the variability of the LPSs of architecture in a high level of abstraction (model) at the design and implementing phases of development Software Product Lines (SPLs), exploiting the synergy between AOSD and MDD. The CrossMDA-SPL approach defines some artifacts basis for advance the separation clear in between the mandatory (bounden) and optional features in the architecture of SPL. The artifacts are represented by two models named: (i) core model (base domain) - responsible for specify the common features the all members of the SPL, and (ii) variability model - responsible for represent the variables features of SPL. In addition, the CrossMDA-SPL approach is composed of: (i) guidelines for modeling and representation of variability, (ii) CrossMDA-SPL services and process, and (iii) models of the architecture of SPL or product instance of SPL. The guidelines use the advantages of AOSD and MDD to promote a better modularization of the variable features of the architecture of SPL during the creation of core and variability models of the approach. The services and sub-processes are responsible for combination automatically, through of process of transformation between the core and variability models, and the generation of new models that represent the implementation of the architecture of SPL or a instance model of SPL. Mechanisms for effective modularization of variability for architectures of SPL at model level. The concepts are described and measured with the execution of a case study of an SPL for management systems of transport electronic tickets

Um método para desenvolvimento de abordagens generativas com composição de linguagens específicas de domínio

The software systems development with domain-specific languages has become increasingly common. Domain-specific languages (DSLs) provide increased of the domain expressiveness, raising the abstraction level by facilitating the generation of models or low-level source code, thus increasing the productivity of systems development. Consequently, methods for the development of software product lines and software system families have also proposed the adoption of domain-specific languages. Recent studies have investigated the limitations of feature model expressiveness and proposing the use of DSLs as a complement or substitute for feature model. However, in complex projects, a single DSL is often insufficient to represent the different views and perspectives of development, being necessary to work with multiple DSLs. In order to address new challenges in this context, such as the management of consistency between DSLs, and the need to methods and tools that support the development with multiple DSLs, over the past years, several approaches have been proposed for the development of generative approaches. However, none of them considers matters relating to the composition of DSLs. Thus, with the aim to address this problem, the main objectives of this dissertation are: (i) to investigate the adoption of the integrated use of feature models and DSLs during the domain and application engineering of the development of generative approaches; (ii) to propose a method for the development of generative approaches with composition DSLs; and (iii) to investigate and evaluate the usage of modern technology based on models driven engineering to implement strategies of integration between feature models and composition of DSLs

A contribuição de modelos utilizando uma abordagem modelo - código

In a world that is increasingly working with software, the need arises for effective approaches that encourage software reuse. The reuse practice must be aligned to a set of practices, procedures and methodologies that create a stable and high quality product. These questions produce new styles and approaches in the software engineering. In this way, this thesis aims to address concepts related to development and model-driven architecture. The model-driven approach provides significant aspects of the automated development, which helps it with produced models built in the specification phase. The definition of terms such as model, architecture and platform makes the focus becomes clearer, because for MDA and MDD is important to split between technical and business issues. Important processes are covered, so you can highlight the artifacts that are built into each stage of model-driven development. The stages of development: CSM, PIM, PSM and ISM, detailing the purpose of each phase in oriented models, making the end of each stage are gradually produced artifacts that may be specialized. The models are handled by different prospects for modeling, abstracting the concepts and building a set of details that portrays a specific scenario. This retraction can be a graphical or textual representation, however, in most cases is chosen a language modeling, for example, UML. In order to provide a practical view, this dissertation shows some tools that improve the construction of models and the code generate that assists in the development, keeping the documentation systemic. Finally, the paper presents a case study that refers to the theoretical aspects discussed throughout the dissertation, therefore it is expected that the architecture and the model-driven development may be able to explain important features to consider in software engineering

Desenvolvimento de sistemas orientado a modelos

The Software Engineering originated with the motivation to mass produce components for increased productivity in production systems. Since its origins, numerous studies have been proposed on the subject as new features in the creation of systems, like the Object- Oriented Programming and Aspect-Oriented Programming, have been established and methodologies have been developed to control them efficiently. However, years of studies in the area were not sufficient to create a methodology for reusing software artifacts really efficient and easy enough to be widespread. Given this, the Model-Driven Development (MDD) is trying to promote it using the modeling of systems as a reference, becoming part of it and establishing a huge productivity gain. One of his approaches is called Model-Driven Software Development (MDSD), which focuses on improving the practices and systems development using Domain-Specific Languages (DSL) for this purpose. In this Final Paper, Xtext is used as a tool to prove the productivity and efficiency of this approach, and for that bibliographic studies were made on the approach and the tool, and show the methodology and a case study to demonstrate results and conclusions regarding this work

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide election

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an impor-tant reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macro-scopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabili-ties. Proc. Natl. Acad. Sci. U.S.A. 84, 663–667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, in-cluding the actual time to insert a nucleotide plus delays due to polymerase detachment from ei-ther the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are ex-pressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the in-fluence of G+C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a compe-tition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.

Tokamak TCABR: Acquisition system, data analysis, and remote participation using MDSplus

Each plasma physics laboratory has a proprietary scheme to control and data acquisition system. Usually, it is different from one laboratory to another. It means that each laboratory has its own way to control the experiment and retrieving data from the database. Fusion research relies to a great extent on international collaboration and this private system makes it difficult to follow the work remotely. The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The choice of MDSplus (Model Driven System plus) is proved by the fact that it is widely utilized, and the scientists from different institutions may use the same system in different experiments in different tokamaks without the need to know how each system treats its acquisition system and data analysis. Another important point is the fact that the MDSplus has a library system that allows communication between different types of language (JAVA, Fortran, C, C++, Python) and programs such as MATLAB, IDL, OCTAVE. In the case of tokamak TCABR interfaces (object of this paper) between the system already in use and MDSplus were developed, instead of using the MDSplus at all stages, from the control, and data acquisition to the data analysis. This was done in the way to preserve a complex system already in operation and otherwise it would take a long time to migrate. This implementation also allows add new components using the MDSplus fully at all stages. (c) 2012 Elsevier B.V. All rights reserved.

Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.

Hemodynamic Performance of Edwards Intuity Valve in a Compliant Aortic Root Model

Numerous designs of bioprosthetic valves exist. The sutureless surgical valve is a newer design concept which combines elements of the transcatheter valve technology with surgical valves. This design aims at shorter and easier implantation. It was the aim of this study to perform hemodynamic and kinematic measurements for this type of valves to serve as a baseline for following studies which investigate the effect of the aortic root on the valve performance. To this end, the Edwards Intuity aortic valve was investigated in a new in vitro flow loop mimicking the left heart. The valve was implanted in a transparent, compliant aortic root model, and the valve kinematics was investigated using a high speed camera together with synchronized hemodynamic measurements of pressures and flows. The valve closure was asynchronous (one by one leaflet), and the valve started to close before the deceleration of the fluid. The aortic root model showed a dilation of the sinuses which was different to the ascending aorta, and the annulus was found to move towards the left ventricle during diastole and towards the aorta during systole.