Measurements, Models, Systems and Design

531 s.

Mathematics in Software Reliability and Quality Assurance

This monograph concerns the mathematical aspects of software reliability and quality assurance and consists of 11 technical papers in this emerging area. Included are the latest research results related to formal methods and design, automatic software testing, software verification and validation, coalgebra theory, automata theory, hybrid system and software reliability modeling and assessment

Fine-Grained Workflow Interoperability in Life Sciences

In den vergangenen Jahrzehnten führten Fortschritte in den Schlüsseltechnologien der Lebenswissenschaften zu einer exponentiellen Zunahme der zur Verfügung stehenden biologischen Daten. Um Ergebnisse zeitnah generieren zu können werden sowohl spezialisierte Rechensystem als auch Programmierfähigkeiten benötigt: Desktopcomputer oder monolithische Ansätze sind weder in der Lage mit dem Wachstum der verfügbaren biologischen Daten noch mit der Komplexität der Analysetechniken Schritt zu halten. Workflows erlauben diesem Trend durch Parallelisierungsansätzen und verteilten Rechensystemen entgegenzuwirken. Ihre transparenten Abläufe, gegeben durch ihre klar definierten Strukturen, ebenso ihre Wiederholbarkeit, erfüllen die Standards der Reproduzierbarkeit, welche an wissenschaftliche Methoden gestellt werden. Eines der Ziele unserer Arbeit ist es Forschern beim Bedienen von Rechensystemen zu unterstützen, ohne dass Programmierkenntnisse notwendig sind. Dafür wurde eine Sammlung von Tools entwickelt, welche jedes Kommandozeilenprogramm in ein Workflowsystem integrieren kann. Ohne weitere Anpassungen kann unser Programm zwei weit verbreitete Workflowsysteme unterstützen. Unser modularer Entwurf erlaubt zudem Unterstützung für weitere Workflowmaschinen hinzuzufügen. Basierend auf der Bedeutung von frühen und robusten Workflowentwürfen, haben wir außerdem eine wohl etablierte Desktop–basierte Analyseplattform erweitert. Diese enthält über 2.000 Aufgaben, wobei jede als Baustein in einem Workflow fungiert. Die Plattform erlaubt einfache Entwicklung neuer Aufgaben und die Integration externer Kommandozeilenprogramme. In dieser Arbeit wurde ein Plugin zur Konvertierung entwickelt, welches nutzerfreundliche Mechanismen bereitstellt, um Workflows auf verteilten Hochleistungsrechensystemen auszuführen—eine Aufgabe, die sonst technische Kenntnisse erfordert, die gewöhnlich nicht zum Anforderungsprofil eines Lebenswissenschaftlers gehören. Unsere Konverter–Erweiterung generiert quasi identische Versionen desselben Workflows, welche im Anschluss auf leistungsfähigen Berechnungsressourcen ausgeführt werden können. Infolgedessen werden nicht nur die Möglichkeiten von verteilten hochperformanten Rechensystemen sowie die Bequemlichkeit eines für Desktopcomputer entwickelte Workflowsystems ausgenutzt, sondern zusätzlich werden Berechnungsbeschränkungen von Desktopcomputern und die steile Lernkurve, die mit dem Workflowentwurf auf verteilten Systemen verbunden ist, umgangen. Unser Konverter–Plugin hat sofortige Anwendung für Forscher. Wir zeigen dies in drei für die Lebenswissenschaften relevanten Anwendungsbeispielen: Strukturelle Bioinformatik, Immuninformatik, und Metabolomik.Recent decades have witnessed an exponential increase of available biological data due to advances in key technologies for life sciences. Specialized computing resources and scripting skills are now required to deliver results in a timely fashion: desktop computers or monolithic approaches can no longer keep pace with neither the growth of available biological data nor the complexity of analysis techniques. Workflows offer an accessible way to counter against this trend by facilitating parallelization and distribution of computations. Given their structured and repeatable nature, workflows also provide a transparent process to satisfy strict reproducibility standards required by the scientific method. One of the goals of our work is to assist researchers in accessing computing resources without the need for programming or scripting skills. To this effect, we created a toolset able to integrate any command line tool into workflow systems. Out of the box, our toolset supports two widely–used workflow systems, but our modular design allows for seamless additions in order to support further workflow engines. Recognizing the importance of early and robust workflow design, we also extended a well–established, desktop–based analytics platform that contains more than two thousand tasks (each being a building block for a workflow), allows easy development of new tasks and is able to integrate external command line tools. We developed a converter plug–in that offers a user–friendly mechanism to execute workflows on distributed high–performance computing resources—an exercise that would otherwise require technical skills typically not associated with the average life scientist's profile. Our converter extension generates virtually identical versions of the same workflows, which can then be executed on more capable computing resources. That is, not only did we leverage the capacity of distributed high–performance resources and the conveniences of a workflow engine designed for personal computers but we also circumvented computing limitations of personal computers and the steep learning curve associated with creating workflows for distributed environments. Our converter extension has immediate applications for researchers and we showcase our results by means of three use cases relevant for life scientists: structural bioinformatics, immunoinformatics and metabolomics

Flexible and Intelligent Learning Architectures for SOS (FILA-SoS)

Multi-faceted systems of the future will entail complex logic and reasoning with many levels of reasoning in intricate arrangement. The organization of these systems involves a web of connections and demonstrates self-driven adaptability. They are designed for autonomy and may exhibit emergent behavior that can be visualized. Our quest continues to handle complexities, design and operate these systems. The challenge in Complex Adaptive Systems design is to design an organized complexity that will allow a system to achieve its goals. This report attempts to push the boundaries of research in complexity, by identifying challenges and opportunities. Complex adaptive system-of-systems (CASoS) approach is developed to handle this huge uncertainty in socio-technical systems

The DS-Pnet modeling formalism for cyber-physical system development

This work presents the DS-Pnet modeling formalism (Dataflow, Signals and Petri nets), designed for the development of cyber-physical systems, combining the characteristics of Petri nets and dataflows to support the modeling of mixed systems containing both reactive parts and data processing operations. Inheriting the features of the parent IOPT Petri net class, including an external interface composed of input and output signals and events, the addition of dataflow operations brings enhanced modeling capabilities to specify mathematical data transformations and graphically express the dependencies between signals. Data-centric systems, that do not require reactive controllers, are designed using pure dataflow models. Component based model composition enables reusing existing components, create libraries of previously tested components and hierarchically decompose complex systems into smaller sub-systems. A precise execution semantics was defined, considering the relationship between dataflow and Petri net nodes, providing an abstraction to define the interface between reactive controllers and input and output signals, including analog sensors and actuators. The new formalism is supported by the IOPT-Flow Web based tool framework, offering tools to design and edit models, simulate model execution on the Web browser, plus model-checking and software/hardware automatic code generation tools to implement controllers running on embedded devices (C,VHDL and JavaScript). A new communication protocol was created to permit the automatic implementation of distributed cyber-physical systems composed of networks of remote components communicating over the Internet. The editor tool connects directly to remote embedded devices running DS-Pnet models and may import remote components into new models, contributing to simplify the creation of distributed cyber-physical applications, where the communication between distributed components is specified just by drawing arcs. Several application examples were designed to validate the proposed formalism and the associated framework, ranging from hardware solutions, industrial applications to distributed software applications

Viiteraamistik turvariskide haldamiseks plokiahela abil

Turvalise tarkvara loomiseks on olemas erinevad programmid (nt OWASP), ohumudelid (nt STRIDE), turvariskide juhtimise mudelid (nt ISSRM) ja eeskirjad (nt GDPR). Turvaohud aga arenevad pidevalt, sest traditsiooniline tehnoloogiline infrastruktuur ei rakenda turvameetmeid kavandatult. Blockchain näib leevendavat traditsiooniliste rakenduste turvaohte. Kuigi plokiahelapõhiseid rakendusi peetakse vähem haavatavateks, ei saanud need erinevate turvaohtude eest kaitsmise hõbekuuliks. Lisaks areneb plokiahela domeen pidevalt, pakkudes uusi tehnikaid ja sageli vahetatavaid disainikontseptsioone, mille tulemuseks on kontseptuaalne ebaselgus ja segadus turvaohtude tõhusal käsitlemisel. Üldiselt käsitleme traditsiooniliste rakenduste TJ-e probleemi, kasutades vastumeetmena plokiahelat ja plokiahelapõhiste rakenduste TJ-t. Alustuseks uurime, kuidas plokiahel leevendab traditsiooniliste rakenduste turvaohte, ja tulemuseks on plokiahelapõhine võrdlusmudel (PV), mis järgib TJ-e domeenimudelit. Järgmisena esitleme PV-it kontseptualiseerimisega alusontoloogiana kõrgema taseme võrdlusontoloogiat (ULRO). Pakume ULRO kahte eksemplari. Esimene eksemplar sisaldab Cordat, kui lubatud plokiahelat ja finantsjuhtumit. Teine eksemplar sisaldab lubadeta plokiahelate komponente ja tervishoiu juhtumit. Mõlemad ontoloogiaesitlused aitavad traditsiooniliste ja plokiahelapõhiste rakenduste TJ-es. Lisaks koostasime veebipõhise ontoloogia parsimise tööriista OwlParser. Kaastööde tulemusel loodi ontoloogiapõhine turberaamistik turvariskide haldamiseks plokiahela abil. Raamistik on dünaamiline, toetab TJ-e iteratiivset protsessi ja potentsiaalselt vähendab traditsiooniliste ja plokiahelapõhiste rakenduste turbeohte.Various programs (e.g., OWASP), threat models (e.g., STRIDE), security risk management models (e.g., ISSRM), and regulations (e.g., GDPR) exist to communicate and reduce the security threats to build secure software. However, security threats continuously evolve because the traditional technology infrastructure does not implement security measures by design. Blockchain is appearing to mitigate traditional applications’ security threats. Although blockchain-based applications are considered less vulnerable, they did not become the silver bullet for securing against different security threats. Moreover, the blockchain domain is constantly evolving, providing new techniques and often interchangeable design concepts, resulting in conceptual ambiguity and confusion in treating security threats effectively. Overall, we address the problem of traditional applications’ SRM using blockchain as a countermeasure and the SRM of blockchain-based applications. We start by surveying how blockchain mitigates the security threats of traditional applications, and the outcome is a blockchain-based reference model (BbRM) that adheres to the SRM domain model. Next, we present an upper-level reference ontology (ULRO) as a foundation ontology and provide two instantiations of the ULRO. The first instantiation includes Corda as a permissioned blockchain and the financial case. The second instantiation includes the permissionless blockchain components and the healthcare case. Both ontology representations help in the SRM of traditional and blockchain-based applications. Furthermore, we built a web-based ontology parsing tool, OwlParser. Contributions resulted in an ontology-based security reference framework for managing security risks using blockchain. The framework is dynamic, supports the iterative process of SRM, and potentially lessens the security threats of traditional and blockchain-based applications.https://www.ester.ee/record=b551352