Gene expression for simulation of biological tissue

BioDynaMo is a biological processes simulator developed by an international community of researchers and software engineers working closely with neuroscientists. The authors have been working on gene expression, i.e. the process by which the heritable information in a gene - the sequence of DNA base pairs - is made into a functional gene product, such as protein or RNA. Typically, gene regulatory models employ either statistical or analytical approaches, being the former already well understood and broadly used. In this paper, we utilize analytical approaches representing the regulatory networks by means of differential equations, such as Euler and Runge-Kutta methods. The two solutions are implemented and have been submitted for inclusion in the BioDynaMo project and are compared for accuracy and performance

Size Matters: Microservices Research and Applications

In this chapter we offer an overview of microservices providing the introductory information that a reader should know before continuing reading this book. We introduce the idea of microservices and we discuss some of the current research challenges and real-life software applications where the microservice paradigm play a key role. We have identified a set of areas where both researcher and developer can propose new ideas and technical solutions.Comment: arXiv admin note: text overlap with arXiv:1706.0735

Parametric Protocol-Driven Agents and their Integration in JADE

Abstract. In this paper we introduce "Template Global Types" which extend Constrained Global Types to support a more generic and modular approach to define protocols, meant as patterns of events of a given type. Protocols can be used both for monitoring the behavior of distributed computational entities and for driving it. In this paper we show the potential of Template Global Types in the domain of protocol-driven intelligent software agents. The interpreter for "executing" Template Global Types has a very natural implementation in Prolog which can easily implement the transition rules for moving from one state to another one, given that an event has been perceived (in case of monitoring) or generated for execution (in case of protocol-driven behavior). This interpreter has been integrated into the Jason logic-based agent framework with limited effort, thanks to the native support that Jason offers to Prolog. In order to demonstrate the flexibility and portability of our approach, which goes beyond the boundaries of logic-based frameworks, in this paper we discuss the integration of the protocol-driven interpreter into the JADE agent framework, entirely implemented in Java

Cyber-Storms Come from Clouds: Security of Cloud Computing in the IoT Era

The Internet of Things (IoT) is rapidly changing our society to a world where every "thing" is connected to the Internet, making computing pervasive like never before. This tsunami of connectivity and data collection relies more and more on the Cloud, where data analytics and intelligence actually reside. Cloud computing has indeed revolutionized the way computational resources and services can be used and accessed, implementing the concept of utility computing whose advantages are undeniable for every business. However, despite the benefits in terms of flexibility, economic savings, and support of new services, its widespread adoption is hindered by the security issues arising with its usage. From a security perspective, the technological revolution introduced by IoT and Cloud computing can represent a disaster, as each object might become inherently remotely hackable and, as a consequence, controllable by malicious actors. While the literature mostly focuses on security of IoT and Cloud computing as separate entities, in this article we provide an up-to-date and well-structured survey of the security issues of Cloud computing in the IoT era. We give a clear picture of where security issues occur and what their potential impact is. As a result, we claim that it is not enough to secure IoT devices, as cyber-storms come from Clouds

Um protocolo de autenticação e autorização seguro para arquiteturas orientadas a serviços

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Ciência da Computação, 2014.A DITEC, Divisão de Tecnologia da Polícia Civil do Distrito Federal - (PCDF), tem como responsabilidade estratégica o desenvolvimento dos softwares da instituição, muitas vezes apresentando necessidades de integração e compartilhamento de informações sensíveis com órgãos conveniados. Dada a criticidade desses sistemas e informações compartilhadas, preocupações relacionadas a segurança devem ser tratadas sob uma perspectiva arquitetural dentro da instituição, que atualmente adota diferentes alternativas de integração, desde Web Services até a replicação das bases de dados para instituições parceiras. Essa dissertação descreve um protocolo de autenticação e autorização seguro, aderente a arquitetura Representational State Transfer (REST), que tem como finalidade possibilitar que uma arquitetura orientada a serviços possa ser adotada como alternativa única de integração, balanceando os requisitos de segurança com outros atributos de qualidade, em particular o tempo de processamento das requisições. O protocolo proposto foi especificado e analisado formalmente utilizando-se a lógica BAN. O protocolo é voltado para ambientes fechados, onde os potenciais clientes do serviço são conhecidos de forma antecipada e com isso torna-se viável o estabelecimento prévio de contratos para a utilização dos serviços ofertados pela Polícia Civil do Distrito Federal. Isso traz forte influência sob os mecanismos que podem ser usados no processo de autenticação e autorização. Com a realização deste trabalho foi possível realizar um mapeamento sistemático da literatura com a identificação e classificação dos trabalhos primários que discutem aspectos de segurança relacionados à computação orientada a serviços. Também foi definida uma arquitetura de referência que pode ser usada na integração de processos de negócio que podem envolver diferentes instituições utilizando computação orientada a serviços. Além disto, foram realizados testes automatizados em um protótipo funcional que permitiu investigar o impacto da adoção do protocolo em termos do custo adicional no tempo de resposta às requisições e throughput. ______________________________________________________________________________ ABSTRACTDITEC, Technology Division Civil Police of the Federal District, is responsible for the software's institution strategic development, often presenting needs of integration and sharing of sensitive information with government insured. Given the criticality of these systems and shared information, security concerns should be treated under an architectural perspective within the institution, which currently adopts di_erent integration alternatives, from Web Services to the replication of databases for partner institutions. This dissertation describes a secure protocol for authentication and authorization, adherent architecture Representational State Transfer(REST), which aims to enable a serviceoriented architecture can be adopted as the sole alternative integration, balancing security requirements with other quality attributes, particularly time processing of requests. The proposed protocol is specified, and formally assessed using the BAN logic. The protocol is designed for closed environments, where potential customers of the service are known in advance and it becomes feasible the prior establishment of contracts for the use of services offered by Civil Police of the Federal District. This has a strong influence on the mechanisms that can be used in the authentication and authorization process. With this work it was possible to conduct a systematic mapping of literature with the identification and classification of primary studies that discuss security issues related to service-oriented computing. Was also defined a reference architecture that can be used in the integration of business processes that may involve dfferent institutions using service-oriented computing. Besides this, automated tests were performed in a functional prototype which allowed to investigate the impact of the adoption of the protocol in terms the additional cost in response time to requests and throughput

Skalierbare Ausführung von Prozessanwendungen in dienstorientierten Umgebungen

Die Strukturierung und Nutzung von unternehmensinternen IT-Infrastrukturen auf Grundlage dienstorientierter Architekturen (SOA) und etablierter XML-Technologien ist in den vergangenen Jahren stetig gewachsen. Lag der Fokus anfänglicher SOA-Realisierungen auf der flexiblen Ausführung klassischer, unternehmensrelevanter Geschäftsprozesse, so bilden heutzutage zeitnahe Datenanalysen sowie die Überwachung von geschäftsrelevanten Ereignissen weitere wichtige Anwendungsklassen, um sowohl kurzfristig Probleme des Geschäftsablaufes zu identifizieren als auch um mittel- und langfristige Veränderungen im Markt zu erkennen und die Geschäftsprozesse des Unternehmens flexibel darauf anzupassen. Aufgrund der geschichtlich bedingten, voneinander unabhängigen Entwicklung der drei Anwendungsklassen, werden die jeweiligen Anwendungsprozesse gegenwärtig in eigenständigen Systemen modelliert und ausgeführt. Daraus resultiert jedoch eine Reihe von Nachteilen, welche diese Arbeit aufzeigt und ausführlich diskutiert. Vor diesem Hintergrund beschäftigte sich die vorliegende Arbeit mit der Ableitung einer konsolidierten Ausführungsplattform, die es ermöglicht, Prozesse aller drei Anwendungsklassen gemeinsam zu modellieren und in einer SOA-basierten Infrastruktur effizient auszuführen. Die vorliegende Arbeit adressiert die Probleme einer solchen konsolidierten Ausführungsplattform auf den drei Ebenen der Dienstkommunikation, der Prozessausführung und der optimalen Verteilung von SOA-Komponenten in einer Infrastruktur

Dynamic Formation and Strategic Management of Web Services Communities

In the last few years, communities of services have been studied in a certain numbers of proposals as virtual pockets of similar expertise. The motivation is to provide these services with high chance of discovery through better visibility, and to enhance their capabilities when it comes to provide requested functionalities. There are some proposed mechanisms and models on aggregating web services and making them cooperate within their communities. However, forming optimal and stable communities as coalitions to maximize individual and group efficiency and income for all the involved parties has not been addressed yet. Moreover, in the proposed frameworks of these communities, a common assumption is that residing services, which are supposed to be autonomous and intelligent, are competing over received requests. However, those services can also exhibit cooperative behaviors, for instance in terms of substituting each other. When competitive and cooperative behaviors and strategies are combined, autonomous services are said to be "coopetitive". Deciding to compete or cooperate inside communities is a problem yet to be investigated. In this thesis, we first identify the problem of defining efficient algorithms for coalition formation mechanisms. We study the community formation problem in two different settings: 1) communities with centralized manager having complete information using cooperative game-theoretic techniques; and 2) communities with distributed decision making mechanisms having incomplete information using training methods. We propose mechanisms for community membership requests and selections of web services in the scenarios where there is interaction between one community and many web services and scenarios where web services can join multiple established communities. Then in order to address the coopetitive relation within communities of web services, we propose a decision making mechanism for our web services to efficiently choose competition or cooperation strategies to maximize their payoffs. We prove that the proposed decision mechanism is efficient and can be implemented in time linear in the length of the time period considered for the analysis and the number of services in the community. Moreover, we conduct extensive simulations, analyze various scenarios, and confirm the obtained theoretical results using parameters from a real web services dataset

A context -and template- based data compression approach to improve resource-constrained IoT systems interoperability.

170 p.El objetivo del Internet de las Cosas (the Internet of Things, IoT) es el de interconectar todo tipo de cosas, desde dispositivos simples, como una bombilla o un termostato, a elementos más complejos y abstractoscomo una máquina o una casa. Estos dispositivos o elementos varían enormemente entre sí, especialmente en las capacidades que poseen y el tipo de tecnologías que utilizan. Esta heterogeneidad produce una gran complejidad en los procesos integración en lo que a la interoperabilidad se refiere.Un enfoque común para abordar la interoperabilidad a nivel de representación de datos en sistemas IoT es el de estructurar los datos siguiendo un modelo de datos estándar, así como formatos de datos basados en texto (e.g., XML). Sin embargo, el tipo de dispositivos que se utiliza normalmente en sistemas IoT tiene capacidades limitadas, así como recursos de procesamiento y de comunicación escasos. Debido a estas limitaciones no es posible integrar formatos de datos basados en texto de manera sencilla y e1ciente en dispositivos y redes con recursos restringidos. En esta Tesis, presentamos una novedosa solución de compresión de datos para formatos de datos basados en texto, que está especialmente diseñada teniendo en cuenta las limitaciones de dispositivos y redes con recursos restringidos. Denominamos a esta solución Context- and Template-based Compression (CTC). CTC mejora la interoperabilidad a nivel de los datos de los sistemas IoT a la vez que requiere muy pocos recursos en cuanto a ancho de banda de las comunicaciones, tamaño de memoria y potencia de procesamiento

A context -and template- based data compression approach to improve resource-constrained IoT systems interoperability.

170 p.El objetivo del Internet de las Cosas (the Internet of Things, IoT) es el de interconectar todo tipo de cosas, desde dispositivos simples, como una bombilla o un termostato, a elementos más complejos y abstractoscomo una máquina o una casa. Estos dispositivos o elementos varían enormemente entre sí, especialmente en las capacidades que poseen y el tipo de tecnologías que utilizan. Esta heterogeneidad produce una gran complejidad en los procesos integración en lo que a la interoperabilidad se refiere.Un enfoque común para abordar la interoperabilidad a nivel de representación de datos en sistemas IoT es el de estructurar los datos siguiendo un modelo de datos estándar, así como formatos de datos basados en texto (e.g., XML). Sin embargo, el tipo de dispositivos que se utiliza normalmente en sistemas IoT tiene capacidades limitadas, así como recursos de procesamiento y de comunicación escasos. Debido a estas limitaciones no es posible integrar formatos de datos basados en texto de manera sencilla y e1ciente en dispositivos y redes con recursos restringidos. En esta Tesis, presentamos una novedosa solución de compresión de datos para formatos de datos basados en texto, que está especialmente diseñada teniendo en cuenta las limitaciones de dispositivos y redes con recursos restringidos. Denominamos a esta solución Context- and Template-based Compression (CTC). CTC mejora la interoperabilidad a nivel de los datos de los sistemas IoT a la vez que requiere muy pocos recursos en cuanto a ancho de banda de las comunicaciones, tamaño de memoria y potencia de procesamiento