Data Science and Ebola

Data Science---Today, everybody and everything produces data. People produce large amounts of data in social networks and in commercial transactions. Medical, corporate, and government databases continue to grow. Sensors continue to get cheaper and are increasingly connected, creating an Internet of Things, and generating even more data. In every discipline, large, diverse, and rich data sets are emerging, from astrophysics, to the life sciences, to the behavioral sciences, to finance and commerce, to the humanities and to the arts. In every discipline people want to organize, analyze, optimize and understand their data to answer questions and to deepen insights. The science that is transforming this ocean of data into a sea of knowledge is called data science. This lecture will discuss how data science has changed the way in which one of the most visible challenges to public health is handled, the 2014 Ebola outbreak in West Africa.Comment: Inaugural lecture Leiden Universit

Jeeva: Enterprise Grid-enabled Web Portal for Protein Secondary Structure Prediction

This paper presents a Grid portal for protein secondary structure prediction developed by using services of Aneka, a .NET-based enterprise Grid technology. The portal is used by research scientists to discover new prediction structures in a parallel manner. An SVM (Support Vector Machine)-based prediction algorithm is used with 64 sample protein sequences as a case study to demonstrate the potential of enterprise Grids.Comment: 7 page

Parallel evolutionary algorithms for scheduling on heterogeneous computing and grid environments

This thesis studies the application of sequential and parallel evolutionary algorithms to the scheduling problem in heterogeneous computing and grid environments, a key problem when executing tasks in distributed computing systems. Since the 1990's, this class of systems has been increasingly employed to provide support for solving complex problems using high-performance computing techniques. The scheduling problem in heterogeneous computing systems is an NP-hard optimization problem, which has been tackled using several optimization methods in the past. Among many new techniques for optimization, evolutionary computing methods have been successfully applied to this class of problems. In this work, several evolutionary algorithms in their sequential and parallel variants are specically designed to provide accurate solutions for the problem, allowing to compute an eficient planning for heterogeneous computing and grid environments. New problem instances, far more complex than those existing in the related literature, are introduced in this thesis in order to study the scalability of the presented parallel evolutionary algorithms. In addition, a new parallel micro-CHC algorithm is developed, inspired by useful ideas from the multiobjective optimization field. Eficient numerical results of this algorithm are reported in the experimental analysis performed on both well-known problem instances and the large instances specially designed in this work. The comparative study including traditional methods and evolutionary algorithms shows that the new parallel micro-CHC is able to achieve a high problem solving eficacy, outperforming previous results already reported for the problem and also having a good scalability behavior when solving high dimension problem instances.In addition, two variants of the scheduling problem in heterogeneous environments are also tackled, showing the versatility of the proposed approach using parallel evolutionary algorithms to deal with both dynamic and multi-objective scenarios.Esta tesis estudia la aplicación de algoritmos evolutivos secuenciales y paralelos para el problema de planicación de tareas en entornos de cómputo heterogéneos y de computación grid. Desde la década de 1990, estos sistemas computacionales han sido utilizados con éxito para resolver problemas complejos utilizando técnicas de computación de alto desempeo. El problema de planificación de tareas en entornos heterogéneos es un problema de optimización NP-difícil que ha sido abordado utilizando diversas técnicas. Entre las técnicas emergentes para optimización combinatoria, los algoritmos evolutivos han sido aplicados con éxito a esta clase de problemas. En este trabajo, varios algoritmos evolutivos en sus versiones secuenciales y paralelas han sido especificamente diseados para alcanzar soluciones precisas para el problema de planicación de tareas en entornos de heterogéneos, permitiendo calcular planificaciones eficientes para entornos que modelan clusters de computadores y plataformas de computación grid. Nuevas instancias del problema, con una complejidad mucho mayor que las previamente existentes en la literatura relacionada, son presentadas en esta tesis con el objetivo de analizar la escalabilidad de los algoritmos evolutivos propuestos. Complementariamente, un nuevo método, el micro-CHC paralelo es desarrollado, inspirado en ideas ítiles provenientes del área de optimización multiobjetivo. Resultados numéricos precisos y eficientes se reportan en el análisis experimental realizado sobre instancias estándar del problema y sobre las nuevas instancias especificamente diseñadas en este trabajo.El estudio comparativo que incluye a métodos tradicionales para planificación de tareas, los nuevos métodos propuestos y algoritmos evolutivos previamente aplicados al problema, demuestra que el nuevo micro-CHC paralelo es capaz de alcanzar altos valores de eficacia, superando a los mejores resultados previamente reportados en la literatura del área y mostrando un buen comportamiento de escalabilidad para resolver las instancias de gran dimensión. Además, dos variantes del problema de planificación de tareas en entornos heterogéneos han sido inicialmente estudiadas, comprobándose la versatilidad del enfoque propuesto para resolver las variantes dinámica y multiobjetivo del problema

Hybrid ant colony system algorithm for static and dynamic job scheduling in grid computing

Grid computing is a distributed system with heterogeneous infrastructures. Resource management system (RMS) is one of the most important components which has great influence on the grid computing performance. The main part of RMS is the scheduler algorithm which has the responsibility to map submitted tasks to available resources. The complexity of scheduling problem is considered as a nondeterministic polynomial complete (NP-complete) problem and therefore, an intelligent algorithm is required to achieve better scheduling solution. One of the prominent intelligent algorithms is ant colony system (ACS) which is implemented widely to solve various types of scheduling problems. However, ACS suffers from stagnation problem in medium and large size grid computing system. ACS is based on exploitation and exploration mechanisms where the exploitation is sufficient but the exploration has a deficiency. The exploration in ACS is based on a random approach without any strategy. This study proposed four hybrid algorithms between ACS, Genetic Algorithm (GA), and Tabu Search (TS) algorithms to enhance the ACS performance. The algorithms are ACS(GA), ACS+GA, ACS(TS), and ACS+TS. These proposed hybrid algorithms will enhance ACS in terms of exploration mechanism and solution refinement by implementing low and high levels hybridization of ACS, GA, and TS algorithms. The proposed algorithms were evaluated against twelve metaheuristic algorithms in static (expected time to compute model) and dynamic (distribution pattern) grid computing environments. A simulator called ExSim was developed to mimic the static and dynamic nature of the grid computing. Experimental results show that the proposed algorithms outperform ACS in terms of best makespan values. Performance of ACS(GA), ACS+GA, ACS(TS), and ACS+TS are better than ACS by 0.35%, 2.03%, 4.65% and 6.99% respectively for static environment. For dynamic environment, performance of ACS(GA), ACS+GA, ACS+TS, and ACS(TS) are better than ACS by 0.01%, 0.56%, 1.16%, and 1.26% respectively. The proposed algorithms can be used to schedule tasks in grid computing with better performance in terms of makespan

The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

Energy-aware scheduling in distributed computing systems

Distributed computing systems, such as data centers, are key for supporting modern computing demands. However, the energy consumption of data centers has become a major concern over the last decade. Worldwide energy consumption in 2012 was estimated to be around 270 TWh, and grim forecasts predict it will quadruple by 2030. Maximizing energy efficiency while also maximizing computing efficiency is a major challenge for modern data centers. This work addresses this challenge by scheduling the operation of modern data centers, considering a multi-objective approach for simultaneously optimizing both efficiency objectives. Multiple data center scenarios are studied, such as scheduling a single data center and scheduling a federation of several geographically-distributed data centers. Mathematical models are formulated for each scenario, considering the modeling of their most relevant components such as computing resources, computing workload, cooling system, networking, and green energy generators, among others. A set of accurate heuristic and metaheuristic algorithms are designed for addressing the scheduling problem. These scheduling algorithms are comprehensively studied, and compared with each other, using statistical tools to evaluate their efficacy when addressing realistic workloads and scenarios. Experimental results show the designed scheduling algorithms are able to significantly increase the energy efficiency of data centers when compared to traditional scheduling methods, while providing a diverse set of trade-off solutions regarding the computing efficiency of the data center. These results confirm the effectiveness of the proposed algorithmic approaches for data center infrastructures.Los sistemas informáticos distribuidos, como los centros de datos, son clave para satisfacer la demanda informática moderna. Sin embargo, su consumo de energético se ha convertido en una gran preocupación. Se estima que mundialmente su consumo energético rondó los 270 TWh en el año 2012, y algunos prevén que este consumo se cuadruplicará para el año 2030. Maximizar simultáneamente la eficiencia energética y computacional de los centros de datos es un desafío crítico. Esta tesis aborda dicho desafío mediante la planificación de la operativa del centro de datos considerando un enfoque multiobjetivo para optimizar simultáneamente ambos objetivos de eficiencia. En esta tesis se estudian múltiples variantes del problema, desde la planificación de un único centro de datos hasta la de una federación de múltiples centros de datos geográficmentea distribuidos. Para esto, se formulan modelos matemáticos para cada variante del problema, modelado sus componentes más relevantes, como: recursos computacionales, carga de trabajo, refrigeración, redes, energía verde, etc. Para resolver el problema de planificación planteado, se diseñan un conjunto de algoritmos heurísticos y metaheurísticos. Estos son estudiados exhaustivamente y su eficiencia es evaluada utilizando una batería de herramientas estadísticas. Los resultados experimentales muestran que los algoritmos de planificación diseñados son capaces de aumentar significativamente la eficiencia energética de un centros de datos en comparación con métodos tradicionales planificación. A su vez, los métodos propuestos proporcionan un conjunto diverso de soluciones con diferente nivel de compromiso respecto a la eficiencia computacional del centro de datos. Estos resultados confirman la eficacia del enfoque algorítmico propuesto

Advances in Grid Computing

This book approaches the grid computing with a perspective on the latest achievements in the field, providing an insight into the current research trends and advances, and presenting a large range of innovative research papers. The topics covered in this book include resource and data management, grid architectures and development, and grid-enabled applications. New ideas employing heuristic methods from swarm intelligence or genetic algorithm and quantum encryption are considered in order to explain two main aspects of grid computing: resource management and data management. The book addresses also some aspects of grid computing that regard architecture and development, and includes a diverse range of applications for grid computing, including possible human grid computing system, simulation of the fusion reaction, ubiquitous healthcare service provisioning and complex water systems