Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Pattern Discovery from Biosequences

In this thesis we have developed novel methods for analyzing biological data, the primary sequences of the DNA and proteins, the microarray based gene expression data, and other functional genomics data. The main contribution is the development of the pattern discovery algorithm SPEXS, accompanied by several practical applications for analyzing real biological problems. For performing these biological studies that integrate different types of biological data we have developed a comprehensive web-based biological data analysis environment Expression Profiler (http://ep.ebi.ac.uk/)

Extending functional databases for use in text-intensive applications

This thesis continues research exploring the benefits of using functional databases based around the functional data model for advanced database applications-particularly those supporting investigative systems. This is a growing generic application domain covering areas such as criminal and military intelligence, which are characterised by significant data complexity, large data sets and the need for high performance, interactive use. An experimental functional database language was developed to provide the requisite semantic richness. However, heavy use in a practical context has shown that language extensions and implementation improvements are required-especially in the crucial areas of string matching and graph traversal. In addition, an implementation on multiprocessor, parallel architectures is essential to meet the performance needs arising from existing and projected database sizes in the chosen application area. [Continues.

On the Discovery of Significant Motifs in Genomic Sequences

In this thesis we study the statistical properties of some families of motifs of the same length. We develop a method for the approximation of the average number of frequent motifs in the family in random texts with independent characters. We give a bound on the approximation error and show that this bound is loose in practice. We develop a test which verifies whether the number of frequent motifs can be approximated to a Poisson distributio

Revisiting Actor Programming in C++

The actor model of computation has gained significant popularity over the last decade. Its high level of abstraction makes it appealing for concurrent applications in parallel and distributed systems. However, designing a real-world actor framework that subsumes full scalability, strong reliability, and high resource efficiency requires many conceptual and algorithmic additives to the original model. In this paper, we report on designing and building CAF, the "C++ Actor Framework". CAF targets at providing a concurrent and distributed native environment for scaling up to very large, high-performance applications, and equally well down to small constrained systems. We present the key specifications and design concepts---in particular a message-transparent architecture, type-safe message interfaces, and pattern matching facilities---that make native actors a viable approach for many robust, elastic, and highly distributed developments. We demonstrate the feasibility of CAF in three scenarios: first for elastic, upscaling environments, second for including heterogeneous hardware like GPGPUs, and third for distributed runtime systems. Extensive performance evaluations indicate ideal runtime behaviour for up to 64 cores at very low memory footprint, or in the presence of GPUs. In these tests, CAF continuously outperforms the competing actor environments Erlang, Charm++, SalsaLite, Scala, ActorFoundry, and even the OpenMPI.Comment: 33 page

Automating design intent capture for component based software reusability

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1998.Includes bibliographical references (leaves 119-122).by Siva Kumar Dirisala.M.S

Domain specific modeling and analysis

It is desirable to model software systems in such a way that analysis of the systems, and tool development for such analysis, is readily possible and feasible in the context of large scientific research projects. This thesis emphasizes the methodology that serves as a basis for such developments. I focus on methods for the design of data-languages and their corresponding tools.UBL - phd migration 201

Secure Remote Storage of Logs with Search Capabilities

Dissertação de Mestrado em Engenharia InformáticaAlong side with the use of cloud-based services, infrastructure and storage, the use of application logs in business critical applications is a standard practice nowadays. Such application logs must be stored in an accessible manner in order to used whenever needed. The debugging of these applications is a common situation where such access is required. Frequently, part of the information contained in logs records is sensitive. This work proposes a new approach of storing critical logs in a cloud-based storage recurring to searchable encryption, inverted indexing and hash chaining techniques to achieve, in a unified way, the needed privacy, integrity and authenticity while maintaining server side searching capabilities by the logs owner. The designed search algorithm enables conjunctive keywords queries plus a fine-grained search supported by field searching and nested queries, which are essential in the referred use case. To the best of our knowledge, the proposed solution is also the first to introduce a query language that enables complex conjunctive keywords and a fine-grained search backed by field searching and sub queries.A gerac¸ ˜ao de logs em aplicac¸ ˜oes e a sua posterior consulta s˜ao fulcrais para o funcionamento de qualquer neg´ocio ou empresa. Estes logs podem ser usados para eventuais ac¸ ˜oes de auditoria, uma vez que estabelecem uma baseline das operac¸ ˜oes realizadas. Servem igualmente o prop´ osito de identificar erros, facilitar ac¸ ˜oes de debugging e diagnosticar bottlennecks de performance. Tipicamente, a maioria da informac¸ ˜ao contida nesses logs ´e considerada sens´ıvel. Quando estes logs s˜ao armazenados in-house, as considerac¸ ˜oes relacionadas com anonimizac¸ ˜ao, confidencialidade e integridade s˜ao geralmente descartadas. Contudo, com o advento das plataformas cloud e a transic¸ ˜ao quer das aplicac¸ ˜oes quer dos seus logs para estes ecossistemas, processos de logging remotos, seguros e confidenciais surgem como um novo desafio. Adicionalmente, regulac¸ ˜ao como a RGPD, imp˜oe que as instituic¸ ˜oes e empresas garantam o armazenamento seguro dos dados. A forma mais comum de garantir a confidencialidade consiste na utilizac¸ ˜ao de t ´ecnicas criptogr ´aficas para cifrar a totalidade dos dados anteriormente `a sua transfer ˆencia para o servidor remoto. Caso sejam necess´ arias capacidades de pesquisa, a abordagem mais simples ´e a transfer ˆencia de todos os dados cifrados para o lado do cliente, que proceder´a `a sua decifra e pesquisa sobre os dados decifrados. Embora esta abordagem garanta a confidencialidade e privacidade dos dados, rapidamente se torna impratic ´avel com o crescimento normal dos registos de log. Adicionalmente, esta abordagem n˜ao faz uso do potencial total que a cloud tem para oferecer. Com base nesta tem´ atica, esta tese prop˜oe o desenvolvimento de uma soluc¸ ˜ao de armazenamento de logs operacionais de forma confidencial, integra e autˆ entica, fazendo uso das capacidades de armazenamento e computac¸ ˜ao das plataformas cloud. Adicionalmente, a possibilidade de pesquisa sobre os dados ´e mantida. Essa pesquisa ´e realizada server-side diretamente sobre os dados cifrados e sem acesso em momento algum a dados n˜ao cifrados por parte do servidor..