Computer-aided design for building multipurpose routing processes in discrete event simulation models

Good domain-modeling enables an appropriate separation of concerns that improves quality properties in the simulation models, such as modifiability and maintainability. In this paper, the interplay of abstraction and concreteness in advancing the theory and practice of Modelling and Simulation is improved using the Model-Driven Engineering levels for building simulation models devoted to routing processes. The definition of this type of processes is detailed as a domain-model conceived as an abstraction defined in a graph model. Such abstraction turns into a set of formal simulation models that are (later) translated into an executable implementation. The final simulation models are specified using Routed DEVS formalism. The methodological proposal is accomplished with the development of a Modelling and Simulation graphical software tool that uses the set of models (defined in terms of the Model-Driven Engineering approach) as the core of its operation. This graphical software tool is developed as a plug-in for Eclipse Integrated Development Environment with aims to take advantage of existent Modeling and Simulation software. Therefore, the usefulness of graphical modeling for supporting the development of the simulation models is empowered with a Model-Driven Engineering process. The main benefit obtained when the Model-Driven Engineering approach is used for modeling an abstraction of the final simulation model is a clear reduction of formalization and implementation times.Fil: Blas, María Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Gonnet, Silvio Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentin

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

Second Generation General System Theory: Perspectives in Philosophy and Approaches in Complex Systems

Following the classical work of Norbert Wiener, Ross Ashby, Ludwig von Bertalanffy and many others, the concept of System has been elaborated in different disciplinary fields, allowing interdisciplinary approaches in areas such as Physics, Biology, Chemistry, Cognitive Science, Economics, Engineering, Social Sciences, Mathematics, Medicine, Artificial Intelligence, and Philosophy. The new challenge of Complexity and Emergence has made the concept of System even more relevant to the study of problems with high contextuality. This Special Issue focuses on the nature of new problems arising from the study and modelling of complexity, their eventual common aspects, properties and approaches—already partially considered by different disciplines—as well as focusing on new, possibly unitary, theoretical frameworks. This Special Issue aims to introduce fresh impetus into systems research when the possible detection and correction of mistakes require the development of new knowledge. This book contains contributions presenting new approaches and results, problems and proposals. The context is an interdisciplinary framework dealing, in order, with electronic engineering problems; the problem of the observer; transdisciplinarity; problems of organised complexity; theoretical incompleteness; design of digital systems in a user-centred way; reaction networks as a framework for systems modelling; emergence of a stable system in reaction networks; emergence at the fundamental systems level; behavioural realization of memoryless functions

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

A model-based systems engineering methodology to make engineering analysis of discrete-event logistics systems more cost-accessible

This dissertation supports human decision-making with a Model-Based Systems Engineering methodology enabling engineering analysis, and in particular Operations Research analysis of discrete-event logistics systems, to be more widely used in a cost-effective and correct manner. A methodology is a collection of related processes, methods, and tools, and the process of interest is posing a question about a system model and then identifying and building answering analysis models. Methods and tools are the novelty of this dissertation, which when applied to the process will enable the dissertation's goal. One method which directly enables the goal is adding automation to analysis model-building. Another method is abstraction, to make explicit a frequently-used bridge to analysis and also expose analysis model-building repetition to justify automation. A third method is formalization, to capture knowledge for reuse and also enable automation without human interpreters. The methodology, which is itself a contribution, also includes two supporting tool contributions. A tool to support the abstraction method is a definition of a token-flow network, an abstract concept which generalizes many aspects of discrete-event logistics systems and underlies many analyses of them. Another tool to support the formalization method is a definition of a well-formed question, the result of an initial study of semantics, categories, and patterns in questions about models which induce engineering analysis. This is more general than queries about models in any specific modeling language, and also more general than queries answerable by navigating through a model and retrieving recorded information. A final contribution follows from investigating tools for the automation method. Analysis model-building is a model-to-model transformation, and languages and tools for model-to-model transformation already exist in Model-Driven Architecture of software. The contribution considers if and how these tools can be re-purposed by contrasting software object-oriented code generation and engineering analysis model-building. It is argued that both use cases share a common transformation paradigm but executed at different relative levels of abstraction, and the argument is supported by showing how several Operations Research analyses can be defined in an object-oriented way across multiple layered instance-of abstraction levels. Enabling Operations Research analysis of discrete-event logistics systems to be more widely used in a cost-effective and correct manner requires considering fundamental questions about what knowledge is required to answer a question about a system, how to formally capture that knowledge, and what that capture enables. Developments here are promising, but provide only limited answers and leave much room for future work.Ph.D

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

Fifth Conference on Artificial Intelligence for Space Applications

The Fifth Conference on Artificial Intelligence for Space Applications brings together diverse technical and scientific work in order to help those who employ AI methods in space applications to identify common goals and to address issues of general interest in the AI community. Topics include the following: automation for Space Station; intelligent control, testing, and fault diagnosis; robotics and vision; planning and scheduling; simulation, modeling, and tutoring; development tools and automatic programming; knowledge representation and acquisition; and knowledge base/data base integration

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