Toward composing variable structure models and their interfaces: a case of intensional coupling definitions

In this thesis, we investigate a combination of traditional component-based and variable structure modeling. The focus is on a structural consistent specification of couplings in modular, hierarchical models with a variable structure. For this, we exploitintensional definitions, as known from logic, and introduce a novel intensional coupling definition, which allows a concise yet expressive specification of complex communication and interaction patterns in static as well as variable structure models, without the need to worryabout structural consistency.In der Arbeit untersuchen wir ein Zusammenbringen von klassischer komponenten-basierter und variabler Strukturmodellierung. Der Fokus liegt dabei auf der Spezifikation von strukturkonsistenten Kopplungen in modular-hierarchischen Modellen mit einer variablen Struktur. Dafür nutzen wir intensionale Definitionen, wie sie aus der Logik bekannt sind, und führen ein neuartiges Konzept von intensionalen Kopplungen ein, welches kompakte gleichzeitig ausdrucksstarke Spezifikationen von komplexen Kommunikations- und Interaktionsmuster in statischen und variablen Strukturmodellen erlaubt

Ein verallgemeinerter Prozess zur Verifikation und Validerung von Modellen und Simulationsergebnissen

With technologies increasing rapidly, symbolic, quantitative modeling and computer-based simulation (M&S) have become affordable and easy-to-apply tools in numerous application areas as, e.g., supply chain management, pilot training, car safety improvement, design of industrial buildings, or theater-level war gaming. M&S help to reduce the resources required for many types of projects, accelerate the development of technical systems, and enable the control and management of systems of high complexity. However, as the impact of M&S on the real world grows, the danger of adverse effects of erroneous or unsuitable models or simu-lation results also increases. These effects may range from the delayed delivery of an item ordered by mail to hundreds of avoidable casualties caused by the simulation-based acquisi-tion (SBA) of a malfunctioning communication system for rescue teams. In order to benefit from advancing M&S, countermeasures against M&S disadvantages and drawbacks must be taken. Verification and Validation (V&V) of models and simulation results are intended to ensure that only correct and suitable models and simulation results are used. However, during the development of any technical system including models for simulation, numerous errors may occur. The later they are detected, and the further they have propagated through the model development process, the more resources they require to correct thus, their propaga-tion should be avoided. If the errors remain undetected, and major decisions are based on in-correct or unsuitable models or simulation results, no benefit is gained from M&S, but a dis-advantage. This thesis proposes a structured and rigorous approach to support the verification and valida-tion of models and simulation results by a) the identification of the most significant of the current deficiencies of model develop-ment (design and implementation) and use, including the need for more meaningful model documentation and the lack of quality assurance (QA) as an integral part of the model development process; b) giving an overview of current quality assurance measures in M&S and in related areas. The transferability of concepts like the capability maturity model for software (SW-CMM) and the ISO9000 standard is discussed, and potentials and limits of documents such as the VV&A Recommended Practices Guide of the US Defense Modeling and Simulation Office are identified; c) analysis of quality assurance measures and so called V&V techniques for similarities and differences, to amplify their strengths and to reduce their weaknesses. d) identification and discussion of influences that drive the required rigor and intensity of V&V measures (risk involved in using models and simulation results) on the one hand, and that limit the maximum reliability of V&V activities (knowledge about both the real system and the model) on the other. This finally leads to the specification of a generalized V&V process - the V&V Triangle. It illustrates the dependencies between numerous V&V objectives, which are derived from spe-cific potential errors that occur during model development, and provides guidance for achiev-ing these objectives by the association of V&V techniques, required input, and evidence made available. The V&V Triangle is applied to an M&S sample project, and the lessons learned from evaluating the results lead to the formulation of future research objectives in M&S V&V

ICSEA 2021: the sixteenth international conference on software engineering advances

The Sixteenth International Conference on Software Engineering Advances (ICSEA 2021), held on October 3 - 7, 2021 in Barcelona, Spain, continued a series of events covering a broad spectrum of software-related topics. The conference covered fundamentals on designing, implementing, testing, validating and maintaining various kinds of software. The tracks treated the topics from theory to practice, in terms of methodologies, design, implementation, testing, use cases, tools, and lessons learnt. The conference topics covered classical and advanced methodologies, open source, agile software, as well as software deployment and software economics and education. The conference had the following tracks: Advances in fundamentals for software development Advanced mechanisms for software development Advanced design tools for developing software Software engineering for service computing (SOA and Cloud) Advanced facilities for accessing software Software performance Software security, privacy, safeness Advances in software testing Specialized software advanced applications Web Accessibility Open source software Agile and Lean approaches in software engineering Software deployment and maintenance Software engineering techniques, metrics, and formalisms Software economics, adoption, and education Business technology Improving productivity in research on software engineering Trends and achievements Similar to the previous edition, this event continued to be very competitive in its selection process and very well perceived by the international software engineering community. As such, it is attracting excellent contributions and active participation from all over the world. We were very pleased to receive a large amount of top quality contributions. We take here the opportunity to warmly thank all the members of the ICSEA 2021 technical program committee as well as the numerous reviewers. The creation of such a broad and high quality conference program would not have been possible without their involvement. We also kindly thank all the authors that dedicated much of their time and efforts to contribute to the ICSEA 2021. We truly believe that thanks to all these efforts, the final conference program consists of top quality contributions. This event could also not have been a reality without the support of many individuals, organizations and sponsors. We also gratefully thank the members of the ICSEA 2021 organizing committee for their help in handling the logistics and for their work that is making this professional meeting a success. We hope the ICSEA 2021 was a successful international forum for the exchange of ideas and results between academia and industry and to promote further progress in software engineering research

Automatic Algorithm Selection for Complex Simulation Problems

To select the most suitable simulation algorithm for a given task is often difficult. This is due to intricate interactions between model features, implementation details, and runtime environment, which may strongly affect the overall performance. The thesis consists of three parts. The first part surveys existing approaches to solve the algorithm selection problem and discusses techniques to analyze simulation algorithm performance.The second part introduces a software framework for automatic simulation algorithm selection, which is evaluated in the third part.Die Auswahl des passendsten Simulationsalgorithmus für eine bestimmte Aufgabe ist oftmals schwierig. Dies liegt an der komplexen Interaktion zwischen Modelleigenschaften, Implementierungsdetails und Laufzeitumgebung. Die Arbeit ist in drei Teile gegliedert. Der erste Teil befasst sich eingehend mit Vorarbeiten zur automatischen Algorithmenauswahl, sowie mit der Leistungsanalyse von Simulationsalgorithmen. Der zweite Teil der Arbeit stellt ein Rahmenwerk zur automatischen Auswahl von Simulationsalgorithmen vor, welches dann im dritten Teil evaluiert wird

How To Touch a Running System

The increasing importance of distributed and decentralized software architectures entails more and more attention for adaptive software. Obtaining adaptiveness, however, is a difficult task as the software design needs to foresee and cope with a variety of situations. Using reconfiguration of components facilitates this task, as the adaptivity is conducted on an architecture level instead of directly in the code. This results in a separation of concerns; the appropriate reconfiguration can be devised on a coarse level, while the implementation of the components can remain largely unaware of reconfiguration scenarios. We study reconfiguration in component frameworks based on formal theory. We first discuss programming with components, exemplified with the development of the cmc model checker. This highly efficient model checker is made of C++ components and serves as an example for component-based software development practice in general, and also provides insights into the principles of adaptivity. However, the component model focuses on high performance and is not geared towards using the structuring principle of components for controlled reconfiguration. We thus complement this highly optimized model by a message passing-based component model which takes reconfigurability to be its central principle. Supporting reconfiguration in a framework is about alleviating the programmer from caring about the peculiarities as much as possible. We utilize the formal description of the component model to provide an algorithm for reconfiguration that retains as much flexibility as possible, while avoiding most problems that arise due to concurrency. This algorithm is embedded in a general four-stage adaptivity model inspired by physical control loops. The reconfiguration is devised to work with stateful components, retaining their data and unprocessed messages. Reconfiguration plans, which are provided with a formal semantics, form the input of the reconfiguration algorithm. We show that the algorithm achieves perceived atomicity of the reconfiguration process for an important class of plans, i.e., the whole process of reconfiguration is perceived as one atomic step, while minimizing the use of blocking of components. We illustrate the applicability of our approach to reconfiguration by providing several examples like fault-tolerance and automated resource control

The cropping-plan decision-making : a farm level modelling and simulation approach

L'assolement' c'est à dire l'attribution des cultures sur les différentes parcelles de l'exploitation agricole' est un élément fondamental de la stratégie de l'agriculteur. Il provient d'un équilibre entre des contraintes et objectifs multiples alliant les dimensions sociale' économique' agronomique et environnementale (utilisation des ressources). Il reflète deux dimensions: une dimension stratégique (lié aux orientations de l'exploitation) et une dimension tactique plus lié à l'adaptation des attributions suite à des contextes changeant (climatique' prix). Afin représenter ces deux niveaux et ainsi structurer les enjeux relatifs aux choix d'assolement à l'échelle de l'exploitation nous proposons une approche basées sur : i) une analyse du processus décisionnel par le biais d'enquêtes en exploitation; ii) une modélisation dynamique aussi bien sur des processus biophysiques (modèles de culture) que sur des processus de gestion (modèle de décision) pour comprendre et simuler. ABSTRACT : Evolutions of the institutional and environmental contexts are driving search for alternative cropping systems to reduce water use while maintaining high levels of productivity. This thesis is an account of the long tradition of research on cropping-plan choices at the farm level. It concerns the scope of modelling agricultural systems with an opening to economy. The objective of the research described in this thesis is to produce formalised knowledge on farmers’ croppingplan choices under uncertain environment (price and weather) by analysing and modelling their decision-making processes. Formalising and modelling decision-making processes is becoming a crucial point to develop decision support systems that go beyond limitations of formerly developed prescriptive approaches. This thesis contributes to the development of a formalised and integrated methodology to study and model complex decision-making process. This methodology enables to fill the gap between field surveys and decision-model implementation. The methodology is drawn upon a theoretical background of the decision-making' and consistently combined tools to respectively survey' analyse' model and implement coupled agent and biophysical models. In this thesis' I address the question of uncertainty in two directions. I first analyse the spatio-temporal dynamic of individual farmers’ decision-making process. Then I estimate farmers’ aversion to risk by comparing stated and revealed elicitation methods. On the basis of field survey results' I develop a decision model called CRASH. The approach to develop the model stresses on explicit formalisation of the decision-making process in its temporal and spatial dimensions' and representation of the domain knowledge through generic concepts that are close to ones used by decision-makers. The implementation of developed models is carried out on the RECORD platform as trail blazing project. The originality relies on the use of dynamic models on both the biophysical and management processes. This research opens new perspectives for developing farm specific decision support systems that are based on simulating farmers’ decisionmaking processes. The modelling and simulating the cropping-plan decision-making processes should enable to design with farmers cropping systems that re-conciliate the required adaptive capacities and needs to maintain cropping systems productivity

Semantic systems biology of prokaryotes : heterogeneous data integration to understand bacterial metabolism

The goal of this thesis is to improve the prediction of genotype to phenotypeassociations with a focus on metabolic phenotypes of prokaryotes. This goal isachieved through data integration, which in turn required the development ofsupporting solutions based on semantic web technologies. Chapter 1 providesan introduction to the challenges associated to data integration. Semantic webtechnologies provide solutions to some of these challenges and the basics ofthese technologies are explained in the Introduction. Furthermore, the ba-sics of constraint based metabolic modeling and construction of genome scalemodels (GEM) are also provided. The chapters in the thesis are separated inthree related topics: chapters 2, 3 and 4 focus on data integration based onheterogeneous networks and their application to the human pathogen M. tu-berculosis; chapters 5, 6, 7, 8 and 9 focus on the semantic web based solutionsto genome annotation and applications thereof; and chapter 10 focus on thefinal goal to associate genotypes to phenotypes using GEMs. Chapter 2 provides the prototype of a workflow to efficiently analyze in-formation generated by different inference and prediction methods. This me-thod relies on providing the user the means to simultaneously visualize andanalyze the coexisting networks generated by different algorithms, heteroge-neous data sets, and a suite of analysis tools. As a show case, we have ana-lyzed the gene co-expression networks of M. tuberculosis generated using over600 expression experiments. Hereby we gained new knowledge about theregulation of the DNA repair, dormancy, iron uptake and zinc uptake sys-tems. Furthermore, it enabled us to develop a pipeline to integrate ChIP-seqdat and a tool to uncover multiple regulatory layers. In chapter 3 the prototype presented in chapter 2 is further developedinto the Synchronous Network Data Integration (SyNDI) framework, whichis based on Cytoscape and Galaxy. The functionality and usability of theframework is highlighted with three biological examples. We analyzed thedistinct connectivity of plasma metabolites in networks associated with highor low latent cardiovascular disease risk. We obtained deeper insights froma few similar inflammatory response pathways in Staphylococcus aureus infec-tion common to human and mouse. We identified not yet reported regulatorymotifs associated with transcriptional adaptations of M. tuberculosis.In chapter 4 we present a review providing a systems level overview ofthe molecular and cellular components involved in divalent metal homeosta-sis and their role in regulating the three main virulence strategies of M. tu-berculosis: immune modulation, dormancy and phagosome escape. With theuse of the tools presented in chapter 2 and 3 we identified a single regulatorycascade for these three virulence strategies that respond to limited availabilityof divalent metals in the phagosome. The tools presented in chapter 2 and 3 achieve data integration throughthe use of multiple similarity, coexistence, coexpression and interaction geneand protein networks. However, the presented tools cannot store additional(genome) annotations. Therefore, we applied semantic web technologies tostore and integrate heterogeneous annotation data sets. An increasing num-ber of widely used biological resources are already available in the RDF datamodel. There are however, no tools available that provide structural overviewsof these resources. Such structural overviews are essential to efficiently querythese resources and to assess their structural integrity and design. There-fore, in chapter 5, I present RDF2Graph, a tool that automatically recoversthe structure of an RDF resource. The generated overview enables users tocreate complex queries on these resources and to structurally validate newlycreated resources. Direct functional comparison support genotype to phenotype predictions.A prerequisite for a direct functional comparison is consistent annotation ofthe genetic elements with evidence statements. However, the standard struc-tured formats used by the public sequence databases to present genome an-notations provide limited support for data mining, hampering comparativeanalyses at large scale. To enable interoperability of genome annotations fordata mining application, we have developed the Genome Biology OntologyLanguage (GBOL) and associated infrastructure (GBOL stack), which is pre-sented in chapter 6. GBOL is provenance aware and thus provides a consistentrepresentation of functional genome annotations linked to the provenance.The provenance of a genome annotation describes the contextual details andderivation history of the process that resulted in the annotation. GBOL is mod-ular in design, extensible and linked to existing ontologies. The GBOL stackof supporting tools enforces consistency within and between the GBOL defi-nitions in the ontology. Based on GBOL, we developed the genome annotation pipeline SAPP (Se-mantic Annotation Platform with Provenance) presented in chapter 7. SAPPautomatically predicts, tracks and stores structural and functional annotationsand associated dataset- and element-wise provenance in a Linked Data for-mat, thereby enabling information mining and retrieval with Semantic Webtechnologies. This greatly reduces the administrative burden of handling mul-tiple analysis tools and versions thereof and facilitates multi-level large scalecomparative analysis. In turn this can be used to make genotype to phenotypepredictions. The development of GBOL and SAPP was done simultaneously. Duringthe development we realized that we had to constantly validated the data ex-ported to RDF to ensure coherence with the ontology. This was an extremelytime consuming process and prone to error, therefore we developed the Em-pusa code generator. Empusa is presented in chapter 8. SAPP has been successfully used to annotate 432 sequenced Pseudomonas strains and integrate the resulting annotation in a large scale functional com-parison using protein domains. This comparison is presented in chapter 9.Additionally, data from six metabolic models, nearly a thousand transcrip-tome measurements and four large scale transposon mutagenesis experimentswere integrated with the genome annotations. In this way, we linked gene es-sentiality, persistence and expression variability. This gave us insight into thediversity, versatility and evolutionary history of the Pseudomonas genus, whichcontains some important pathogens as well some useful species for bioengi-neering and bioremediation purposes. Genome annotation can be used to create GEM, which can be used to betterlink genotypes to phenotypes. Bio-Growmatch, presented in chapter 10, istool that can automatically suggest modification to improve a GEM based onphenotype data. Thereby integrating growth data into the complete processof modelling the metabolism of an organism. Chapter 11 presents a general discussion on how the chapters contributedthe central goal. After which I discuss provenance requirements for data reuseand integration. I further discuss how this can be used to further improveknowledge generation. The acquired knowledge could, in turn, be used to de-sign new experiments. The principles of the dry-lab cycle and how semantictechnologies can contribute to establish these cycles are discussed in chapter11. Finally a discussion is presented on how to apply these principles to im-prove the creation and usability of GEM’s.</p