Virtual Communication Stack: Towards Building Integrated Simulator of Mobile Ad Hoc Network-based Infrastructure for Disaster Response Scenarios

Responses to disastrous events are a challenging problem, because of possible damages on communication infrastructures. For instance, after a natural disaster, infrastructures might be entirely destroyed. Different network paradigms were proposed in the literature in order to deploy adhoc network, and allow dealing with the lack of communications. However, all these solutions focus only on the performance of the network itself, without taking into account the specificities and heterogeneity of the components which use it. This comes from the difficulty to integrate models with different levels of abstraction. Consequently, verification and validation of adhoc protocols cannot guarantee that the different systems will work as expected in operational conditions. However, the DEVS theory provides some mechanisms to allow integration of models with different natures. This paper proposes an integrated simulation architecture based on DEVS which improves the accuracy of ad hoc infrastructure simulators in the case of disaster response scenarios.Comment: Preprint. Unpublishe

Avoiditals: Enhanced Cyber-Attack Taxonomy In Securing Information Technology Infrastructure

An operation of an organization is currently using a digital environment which opens to potential cyber-attacks. These phenomena become worst as the cyberattack landscape is changing rapidly. The impact of cyber-attacks varies depending on the scope of the organization and the value of assets that need to be protected. It is difficult to assess the damage to an organization from cyberattacks due to a lack of understanding of tools, metrics, and knowledge on the type of attacks and their impacts. Hence, this paper aims to identify domains and sub-domains of cyber-attack taxonomy to facilitate the understanding of cyber-attacks. Four phases are carried in this research: identify existing cyber-attack taxonomy, determine and classify domains and sub-domains of cyber-attack, and construct the enhanced cyber-attack taxonomy. The existing cyber-attack taxonomies are analyzed, domains and sub-domains are selected based on the focus and objectives of the research, and the proposed taxonomy named AVOIDITALS Cyber-attack Taxonomy is constructed. AVOIDITALS consists of 8 domains, 105 sub-domains, 142 sub-sub-domains, and 90 other sub-sub-domains that act as a guideline to assist administrators in determining cyber-attacks through cyber-attacks pattern identification that commonly occurred on digital infrastructure and provide the best prevention method to minimize impact. This research can be further developed in line with the emergence of new types and categories of current cyberattacks and the future

Iterchanging Discrete Event Simulationprocess Interaction Modelsusing The Web Ontology Language - Owl

Discrete event simulation development requires significant investments in time and resources. Descriptions of discrete event simulation models are associated with world views, including the process interaction orientation. Historically, these models have been encoded using high-level programming languages or special purpose, typically vendor-specific, simulation languages. These approaches complicate simulation model reuse and interchange. The current document-centric World Wide Web is evolving into a Semantic Web that communicates information using ontologies. The Web Ontology Language OWL, was used to encode a Process Interaction Modeling Ontology for Discrete Event Simulations (PIMODES). The PIMODES ontology was developed using ontology engineering processes. Software was developed to demonstrate the feasibility of interchanging models from commercial simulation packages using PIMODES as an intermediate representation. The purpose of PIMODES is to provide a vendor-neutral open representation to support model interchange. Model interchange enables reuse and provides an opportunity to improve simulation quality, reduce development costs, and reduce development times

Towards a Formal Theory of Interoperability

This dissertation proposes a formal theory of interoperability that explains 1) what interoperability is as opposed to how it works, 2) how to tell whether two or more systems can interoperate and 3) how to identify whether systems are interoperating or merely exchanging bits and bytes. The research provides a formal model of data in M&S that captures all possible representations of a real or imagined thing and distinguishes between existential dependencies and transformational dependencies. Existential dependencies capture the relationships within a model while transformational dependencies capture the relationships between interactions with a model. These definitions are used to formally specify interoperation, the ability to exchange information, as a necessary condition for interoperability. Theorems of interoperation that capture the nature and boundaries of the interoperation space and how to measure it are formulated. Interoperability is formally captured as a subset of the interoperation space for which transformational dependencies can be fulfilled. Theorems of interoperability that capture the interoperability space and how to measure it are presented. Using graph theory and complexity theory, the model of data is reformulated as a graph, and the complexity of interoperation and interoperability is shown to be at least NP-Complete. Model Based Data Engineering (MBDE) is formally defined using the model of data introduced earlier and transformed into a heuristic that supports interoperability. This heuristic is shown to be more powerful than current approaches in that it is consistent and can easily be verified

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

Computer Science & Technology Series : XVI Argentine Congress of Computer Science - Selected papers

CACIC’10 was the sixteenth Congress in the CACIC series. It was organized by the School of Computer Science of the University of Moron. The Congress included 10 Workshops with 104 accepted papers, 1 main Conference, 4 invited tutorials, different meetings related with Computer Science Education (Professors, PhD students, Curricula) and an International School with 5 courses. (http://www.cacic2010.edu.ar/). CACIC 2010 was organized following the traditional Congress format, with 10 Workshops covering a diversity of dimensions of Computer Science Research. Each topic was supervised by a committee of three chairs of different Universities. The call for papers attracted a total of 195 submissions. An average of 2.6 review reports were collected for each paper, for a grand total of 507 review reports that involved about 300 different reviewers. A total of 104 full papers were accepted and 20 of them were selected for this book.Red de Universidades con Carreras en Informática (RedUNCI

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

Fourth Conference on Artificial Intelligence for Space Applications

Proceedings of a conference held in Huntsville, Alabama, on November 15-16, 1988. The Fourth 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: space applications of expert systems in fault diagnostics, in telemetry monitoring and data collection, in design and systems integration; and in planning and scheduling; knowledge representation, capture, verification, and management; robotics and vision; adaptive learning; and automatic programming

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