Towards data warehousing and mining of protein unfolding simulation data

OBJECTIVES: The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. METHODS: To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. RESULTS: To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. CONCLUSIONS: Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

Grid warehousing of molecular dynamics protein unfolding data

With the increasing awareness of protein folding disorders, the explosion of genomic information, and the need for efficient ways to predict protein structure, protein folding and unfolding has become a central issue in molecular sciences research. Molecular dynamics computer simulations are increasingly employed to understand the folding and unfolding of proteins. Running protein unfolding simulations is computationally expensive and finding ways to enhance performance is a grid issue on its own. However, more and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. This paper describes efforts to provide a grid-enabled data warehouse for protein unfolding data. We outline the challenge and present first results in the design and implementation of the data warehouse.

P-found: grid-enabling distributed repositories of protein folding and unfolding simulations for data mining

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform data mining and other analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data that is used to populate the second component, and a data warehouse that contains important molecular properties. These properties may be used for data mining studies. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular, we look at two aspects: firstly, how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories — this is an important and challenging aspect of P-found, due to the large data volumes involved and the desire of scientists to maintain control of their own data. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling scientific discovery.

Towards the design of a unified semantics model for OLTP and OLAP systems

The concepts of on-line transactional processing (OLTP) and on-line analytical processing (OLAP) are often confused with the technologies or models that are used to design transactional and analytics based information systems. This in some way has contributed to existence of gaps between the semantics in information captured during transactional processing and information stored for analytical use. In this paper, we propose the use of a unified semantics design model, as a solution to help bridge the semantic gaps between data captured by OLTP systems and the information provided by OLAP systems. The central focus of this design approach is on enabling business intelligence using not just data, but data with context.

Teknik för en flerskiktadwebbapplikation

The report analyses if some common problems can be avoided by using modern technology. As a reference system “Fartygsrapporteringssystemet” is used. It is an n-tier web application built with modern technology at time, 2003-2004. The aim is to examine whether ASP.Net MVC, Windows Communication Foundation, Workflow Foundation and SQL Server 2005 Service Broker can be used to create an n-tier web application which also communicate with other systems and facilitate automated testing. The report describes the construction of a prototype in which the presentation layer uses ASP.Net MVC to separate presentation and business logic. Communication with the business layer is done through the Windows Communication Foundation. Hard coded processes are broken out and dealt with by Workflow Foundation. Asynchronous communication with other systems is done by using Microsoft SQL Server 2005 Service Broker. The results of the analysis is that these techniques can be used to create a n-tier web application, but that ASP.Net MVC, which at present only available in a preview release, is not sufficiently developed yet.

Data mining : aplicação voltada a geração de informações para tomada de decisão na Secretaria de Estado da Educação de São Paulo

Trata da aplicação de ferramentas de Data Mining e do conceito de Data Warehouse à coleta e análise de dados obtidos a partir das ações da Secretaria de Estado da Educação de São Paulo. A variável dependente considerada na análise é o resultado do rendimento das escolas estaduais obtido através das notas de avaliação do SARESP (prova realizada no estado de São Paulo). O data warehouse possui ainda dados operacionais e de ações já realizadas, possibilitando análise de influência nos resultados

Modelo de gerenciamento de versões para evolução de Data Warehouses

Sistemas de tomada de decisão baseados em Data Warehouse (DW) estão sendo cada dia mais utilizados por grandes empresas e organizações. O modelo multidimensional de organização dos dados utilizado por estes sistemas, juntamente com as técnicas de processamento analítico on-line (OLAP), permitem análises complexas sobre o histórico dos negócios através de uma simples e intuitiva interface de consulta. Apesar dos DWs armazenarem dados históricos por natureza, as estruturas de organização e classificação destes dados, chamadas de dimensões, não possuem a rigor uma representação temporal, refletindo somente a estrutura corrente. Para um sistema destinado à análise de dados, a falta do histórico das dimensões impossibilita consultas sobre o ambiente real de contextualização dos dados passados. Além disso, as alterações dos esquemas multidimensionais precisam ser assistidas e gerenciadas por um modelo de evolução, de forma a garantir a consistência e integridade do modelo multidimensional sem a perda de informações relevantes. Neste trabalho são apresentadas dezessete operações de alteração de esquema e sete operações de alteração de instâncias para modelos multidimensionais de DW. Um modelo de versões, baseado na associação de intervalos de validade aos esquemas e instâncias, é proposto para o gerenciamento dessas operações. Todo o histórico de definições e de dados do DW é mantido por esse modelo, permitindo análises completas dos dados passados e da evolução do DW. Além de suportar consultas históricas sobre as definições e as instâncias do DW, o modelo também permite a manutenção de mais de um esquema ativo simultaneamente. Isto é, dois ou mais esquemas podem continuar a ter seus dados atualizados periodicamente, permitindo assim que as aplicações possam consultar dados recentes utilizando diferentes versões de esquema.

A utilização de raciocínio baseado em casos para a análise de crédito e cobrança

Data Warehouse (DW) é um processo que aglutina dados de fontes heterogêneas, incluindo dados históricos e dados externos para atender à necessidade de consultas estruturadas e ad-hoc, relatórios analíticos e de suporte de decisão. Já um Case-Based Reasoning (CBR) é uma técnica de Inteligência Artificial (AI – Artificial Intelligence) para a representação de conhecimento e inferência, que propõe a solução de novos problemas adaptando soluções que foram usadas para resolver problemas anteriores. A descrição de um problema existente, ou um caso é utilizado para sugerir um meio de resolver um novo problema, avisar o usuário de possíveis falhas que ocorreram anteriormente e interpretar a situação atual. Esta dissertação tem por objetivo apresentar um estudo do uso de um DW combinado com um CBR para a verificação de “risco” de inadimplência no setor de telecomunicações. Setor este que devido as grandes mudanças que ocorreram no mercado, que passam desde a privatização do setor e a entrada de novas operadoras fixas e celulares, criando um ambiente de concorrência, anteriormente inexistente, possibilitando assim ao cliente trocar de operadora ou até mesmo deixar a telefonia fixa e ficar somente com a celular, e vai até ao fato da estabilização econômica e as novas práticas de mercado, que determinou a baixa das multas, tornando assim compensador aos clientes deixar as faturas vencidas a perder juros de aplicações ou pagar juros bancários para quitar a sua dívida, visto que a empresa telefônica só pode aplicar as sanções com o prazo de 30 dias. Este trabalho mostra o desenvolvimento de um CBR para aplicação na área de Crédito e Cobrança, onde são detalhados os vários passos, a utilização do mesmo junto ao um DW, o que proporciona a comparação com desenvolvimento de outros sistemas similares e as diferenças (vantagens e desvantagens) que isso traz ao mesmo.

Electrical consumers data clustering through optimum-path forest

Non-technical losses identification has been paramount in the last decade. Since we have datasets with hundreds of legal and illegal profiles, one may have a method to group data into subprofiles in order to minimize the search for consumers that cause great frauds. In this context, a electric power company may be interested in to go deeper a specific profile of illegal consumer. In this paper, we introduce the Optimum-Path Forest (OPF) clustering technique to this task, and we evaluate the behavior of a dataset provided by a brazilian electric power company with different values of an OPF parameter. © 2011 IEEE.

Um método de análise de dados temporais para o Cadastro Territorial Multifinalitário Urbano

Pós-graduação em Ciências Cartográficas - FCT

Inteligência competitiva organizacional: um modelo apoiado nos comportamentos de busca, compartilhamento e uso de informação e de TIC

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The SB-index and the HSB-index: efficient indices for spatial data warehouses

Spatial data warehouses (SDWs) allow for spatial analysis together with analytical multidimensional queries over huge volumes of data. The challenge is to retrieve data related to ad hoc spatial query windows according to spatial predicates, avoiding the high cost of joining large tables. Therefore, mechanisms to provide efficient query processing over SDWs are essential. In this paper, we propose two efficient indices for SDW: the SB-index and the HSB-index. The proposed indices share the following characteristics. They enable multidimensional queries with spatial predicate for SDW and also support predefined spatial hierarchies. Furthermore, they compute the spatial predicate and transform it into a conventional one, which can be evaluated together with other conventional predicates by accessing a star-join Bitmap index. While the SB-index has a sequential data structure, the HSB-index uses a hierarchical data structure to enable spatial objects clustering and a specialized buffer-pool to decrease the number of disk accesses. The advantages of the SB-index and the HSB-index over the DBMS resources for SDW indexing (i.e. star-join computation and materialized views) were investigated through performance tests, which issued roll-up operations extended with containment and intersection range queries. The performance results showed that improvements ranged from 68% up to 99% over both the star-join computation and the materialized view. Furthermore, the proposed indices proved to be very compact, adding only less than 1% to the storage requirements. Therefore, both the SB-index and the HSB-index are excellent choices for SDW indexing. Choosing between the SB-index and the HSB-index mainly depends on the query selectivity of spatial predicates. While low query selectivity benefits the HSB-index, the SB-index provides better performance for higher query selectivity.

Intelligence systems methodology: a systemic approach to the organizational intelligence function

Organizational intelligence can be seen as a function of the viable structure of an organization. With the integration of the Viable System Model and Soft Systems Methodology (systemic approaches of organizational management) focused on the role of the intelligence function, it is possible to elaborate a model of action with a structured methodology to prospect, select, treat and distribute information to the entire organization that improves the efficacy and efficiency of all processes. This combination of methodologies is called Intelligence Systems Methodology (ISM) whose assumptions and dynamics are delimited in this paper. The ISM is composed of two simultaneous activities: the Active Environmental Mapping and the Stimulated Action Cycle. The elaboration of the formal ISM description opens opportunities for applications of the methodology on real situations, offering a new path for this specific issue of systems thinking: the intelligence systems. Knowledge Management Research & Practice (2012) 10, 141-152. doi:10.1057/kmrp.2011.44

Análisis del comportamiento de los viajeros del transporte interurbano en la isla de Gran Canaria

Máster Universitario en Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería (SIANI)

Confronto di performance tra applicazioni web SQL e NoSQL su grandi quantità di dati

Lo scopo di questa tesi è di mettere a confronto le performance, su grandi quantità di dati, tra applicazioni web basate su database a modello relazionale, noti come RDBMS, e applicazioni web basate su database a modello non-relazionale, meglio conosciuti con l'appellativo NoSQL. Sono stati selezionati sette casi d'uso appartenenti ad una applicazione reale per effettuare il confronto di prestazioni tra i seguenti database: MySQL, Microsoft SQL Server, OrientDB, MongoDB e BaseX.