Seminars

Overview of LIS Projects

Seminar giving an overview of LIS projects, where every member gave a 3 minute presentation.

Access control in Multiversion Geographic Databases

Issues on how to manage access control for geographic data, when there are multiple versions thereof, in a collaborative design environment

Study of biochemical and sensorial kinetics of diferent types of brazilian beer

Beer is a beverage obtained through alcoholic fermentation of malt wort, usually made of barley, which could be added of other cereals, such as corn, rice or wheat. Its alcoholic content is between 3% and 8%. The beer can be considered a good source of polyphenols derived both from malt or hop. Due to its antioxidant capacity and low alcoholic content, it’s able to improve plasma antioxidant activity, reducing the risk of cardiovascular diseases, without the negative effects of high doses of alcohol. The beer is an unstable product that is involved in a series of chemical, physical and sensorial transformations during its shelf life. The objective of this study is to evaluate the oxidative profile of three different types of beer during their shelf life, analyzed through biochemical and sensorial assays. Samples were aged in a natural (4 months) and forced way (6 days at 42°C), and tests were performed periodically along this period. The applied tests were: Total polyphenol content, hydrogen-donating ability (DPPH), total antioxidant status (ABTS.+), reducing power, copper reducing activity, quantitative descriptive analysis and consumer acceptance. Results showed that polyphenol content decreased during the first 2 weeks of aging and remained constant after that. The antioxidant capacity of beer decreased up to 50% of its initial value during the aging period. The biochemical tests applied to the beer submitted to forced aging had no changes in total polyphenol content or antioxidant capacity. The descriptive tests showed an increase in cardboard aroma and flavor, which are the most important sensorial indicators of the oxidative process in beer, a decrease in bitter taste and a higher sweet taste perception. Product acceptance was satisfactory to all samples, and it seems not to be related to the type of beer or aging period.

Aondê: An Ontology Web Service for Interoperability across Biodiversity Information Systems

Biodiversity research requires associating data about living beings and their habitats, constructing sophisticated models and correlating all kinds of information. Data handled are inherently heterogeneous, being provided by distinct (and distributed) research groups, which collect these data using different vocabularies, assumptions, methodologies and goals, and under varying spatio-temporal frames. This poses many kinds of challenges in Computer Science research, from the physical (e.g., diversity of data structures) to the conceptual level (e.g., diversity of perspectives and of knowledge domains). Ontologies have been proposed as a means to help solve heterogeneity issues. However, this raises new research issues concerning ontology design, management and sharing. This dissertation presents a new kind of Web Service whose goal is to help in solving such issues. Aondê (which means "owl" in Tupi, the main branch of native Brazilian languages) is a Web Service that provides a wide range of operations for storage, management, search, ranking, analysis and integration of ontologies. The text covers the specification and implementation of Aondê, which have been validated by a prototype tested with large ontologies and real biodiversity case studies.

Windows Workflow Foundation - Building Custom Scientific Workflows

Presentation about the work developed during the second internship of Luciano Digiampietri at Microsoft Research.

LIS - redistribution of management tasks

Reassignment of software and network administration tasks among students

LIS software and administration

Discussion of recent overhauls in the LIS lab

Gerenciamento de workflows científicos em bioinformática [pré-defesa 2]

Atividades em bioinformática estão crescendo por todo o mundo, acompanhadas por uma proliferação de dados e ferramentas. Isto traz novos desafios, por exemplo, como entender e organizar esses recursos, como compartilhar e re-usar experimentos bem sucedidos (ferramentas e dados), e como prover interoperabilidade entre dados e ferramentas de diferentes locais e utilizados por usuários com perfis distintos. Esta tese propõe uma infra-estrutura computacional para resolver tais problemas. A infra-estrutura permite projetar, re-usar, anotar, validar, compartilhar e documentar experimentos de bioinformática. Workflows científicos são os mecanismos utilizados para representar tais experimentos. Combinando pesquisa em bancos de dados, workflows científicos, inteligência artificial e Web semântica, a infra-estrutura se beneficia do uso de ontologias para permitir a especificação e anotação de workflows de bioinformática e para servir como base aos mecanismos de rastreabilidade. Além disso, ela usa técnicas de planejamento em inteligência artificial para prover as composições automática, iterativa e supervisionada de tarefas para satisfazer as necessidades dos diferentes tipos de usuários. Os aspectos de integração de dados e interoperabilidade são resolvidos através da combinação do uso de ontologias, mapeamento entre estruturas e algoritmos de casamento de interfaces. A infra-estrutura implementada em um protótipo e validada com dados reais de bioinformática.

Um Serviço de Ontologias para Sistemas de Biodiversidade

Prévia da apresentação do artigo no SEMISH 2007 - XXXIV Seminário Integrado de Software e Hardware, no dia 05/07/2007.

OMS/OPAS/Bireme and the ISIS Network-based Platform Project

Milton Lapido, da Bireme, irá apresentar diversos portais científicos que constituem a Biblioteca Virtual em Saúde e irá comentar sobre o novo projeto ISIS-NBP.

Implantação de Novo Processo de Desenvolvimento no WebMAPS

Será apresentado o novo processo de desenvolvimento de software a ser adotado no projeto WebMAPS. Este processo envolve conceitos como controle de versão, teste automático e revisão de código, todos apoiados por um ferramental a ser apresentado na reunião

An architecture to query biodiversity data on the Web

Prévia da defesa de mestrado que ocorrerá no dia 18/05/2007.

Tools for e-Science: The Webmaps 2 Vision

O projeto Webmaps 2 pode vir a ser o protótipo de um framework mais genérico para a construção de ferramentas em e-Science. Nesta apresentação iremos discutir a reformulação do Webmaps I, a arquitetura proposta para a versão 2 e a metodologia de trabalho a ser adotada. A metodologia transcende o contexto exclusivo deste projeto e está sendo um esforço coletivo de diversos membros para que seja atingido um nível de excelência em toda a produção científica do laboratório.

Gerenciamento de workflows científicos em bioinformática [pré-defesa 1]

Atividades em bioinformática estão crescendo por todo o mundo, acompanhadas por uma proliferação de dados e ferramentas. Isto traz novos desafios, por exemplo, como entender e organizar esses recursos, como compartilhar e re-usar experimentos bem sucedidos (ferramentas e dados), e como prover interoperabilidade entre dados e ferramentas de diferentes locais e utilizados por usuários com perfis distintos. Esta tese propõe uma infra-estrutura computacional para resolver tais problemas. A infra-estrutura permite projetar, re-usar, anotar, validar, compartilhar e documentar experimentos de bioinformática. Workflows científicos são os mecanismos utilizados para representar tais experimentos. Combinando pesquisa em bancos de dados, workflows científicos, inteligência artificial e Web semântica, a infra-estrutura se beneficia do uso de ontologias para permitir a especificação e anotação de workflows de bioinformática e para servir como base aos mecanismos de rastreabilidade. Além disso, ela usa técnicas de planejamento em inteligência artificial para prover as composições automática, iterativa e supervisionada de tarefas para satisfazer as necessidades dos diferentes tipos de usuários. Os aspectos de integração de dados e interoperabilidade são resolvidos através da combinação do uso de ontologias, mapeamento entre estruturas e algoritmos de casamento de interfaces. A infra-estrutura implementada em um protótipo e validada com dados reais de bioinformática.

Disponibilização de Dados de Sensores Usando Serviços Web

An Invariant Shape Descriptor based on the Multiscale Fractal Dimension

This seminar presents a new shape descriptor based on the Multiscale Fractal Dimension. Preliminary results show that the proposed descriptor is invariant towards scaling, rotation and translation.

An Infrastructure based on Web Service Choreography for Activity Coordination in Supply Chains

Prévia da defesa de mestrado que ocorrerá no dia 24/03/2007.

How to use and manage LIS web portal

Rodrigo Senra will give a brief tutorial about how to use and manage LIS web portal.

Workflow-based sensor data management (part 2)

Sensors and sensor networks produce large quantities of heterogeneous data. This work proposes using Digital Content Components (DCCs) for encapsulating sensors, workflows for managing these DCCs, and Semantic Web related techniques to annotate data production. This aids data publication (on the Web).

Access Control in Multiversion Geographic Database

The purpose of this research is to present an access control mechanism for multiversion geographic database. Actual access control mechanisms do not take into account the existence of version in geographic database. This is essential for enabling cooperative work in Geographic Information System (GIS).

Workflow-based sensor data management

Sensors and sensor networks produce large quantities of heterogeneous data. This work proposes using Digital Content Components (DCCs) for encapsulating sensors and workflows for managing these DCCs. This aids data publication (on the Web).

Shape descriptors based on Tensor Scale

The purpose of this presentation is to show the current state of my MSc research which is the design of shape descriptors based on Tensor Scale. Tensor Scale is a morphometric parameter that unifies the representation of local thickness, orientation and anisotropy; and can be used in several computer vision and image processing tasks. I present Tensor Scale concepts, algorithms and its use for shape description. I also compare the method being proposed to other recent shape descriptors, using MPEG-7 image dataset.

Escience projects - common problems and trends

The seminar presented a few directions of Escience research, discussed during the Microsoft Escience workshop in Baltimore, Oct 13-15, 2006, commenting on similarities and trends.

Contract Negotiation on Agricultural Supply Chains

Trading relations inside a supply chain comprise a huge amount of commercial transactions and are subject to legal commitments. The increasing use of computational means to perform commercial transactions demands the replacement of contracts by their electronic counterparts, and performing live negotiation through software agents. Electronic contracts and electronic negotiation are often researched as problems in computer networks. However, they also raise interesting database problems, such as: (i) the negotiators must agree on a mutually known set of concepts and names, (ii) contracts (and their versions) must be recorded and their execution must be tracked in order to check if partners have fulfilled (or are fulfilling) their duties (audit), (iii) audit procedures may have to take into account temporal and spatial constraints mentioned in a contract, (iv) a negotiation process may raise a number of inter-related contracts, demanding special care to enforce consistency among them in case the agreement is renegotiated. Our proposal encompasses a negotiation framework focusing on agricultural supply chains that combines research on computer networks and databases to try to solve these four issues.

An Ontology Server to support Biodiversity Information System

This is a preview of the presentation on WTDBD (Workshop of Thesis and Dissertations on Database). It describes the current state of my master research which consists in the specification of an ontology service requirements to biodiversity context on WeBios project.

Efficient and effective content-based image retrieval framework for fingerprint databases

Two kinds of fingerprint identification approaches have been proposed in the literature to reduce the number of one-to-many comparisons during fingerprint image retrieval, namely, exclusive and continuous classification. Although exclusive classification approaches reduce the number of comparisons, they present some shortcomings, including fingerprint ambiguous classification, and unbalanced fingerprint classification distribution. On the other side, continuous classification approaches have not been further studied. In this context, we propose an original continuous approach to guide the search and the retrieval in fingerprint image databases considering both effectiveness and retrieval speed. For that purposes, we use feature extraction and indexing methods considering the textural and directional information contained in fingerprint images. Preliminary results of our work involves a comparative study of several textural image descriptors obtained by combining different types of the Wavelet Transform with similarity measures. From our experiments we can conclude that the best retrieval accuracy was achieved by combining Gabor Wavelets (GWs) with the Square Chord similarity measure. Furthermore, the presence of noise and distortions in fingerprint images have affected the overall retrieval accuracy.

Bioinformatics scientific workflows: combining databases, AI and Web services

Bioinformatics activities present new challenges, such as how to exchange and reuse successful experimental procedures, tools and data, and how to understand and provide interoperability among data and tools across different sites, for distinct user profiles. This thesis is an effort towards these directions. It is based on combining research on databases, AI and scientific workflows, on the Semantic Web, to design, reuse, annotate and document bioinformatics experiments.

Content-based image retrieval framework for fingerprint databases

This seminar presents a framework to improve the fingerprint identification process in terms of retrieval accuracy and speed by considering the textural information inherent to fingerprint images.

WeBios Coleta

The work objective is understand and redesign one existing database, from a project called WeBios. This database was used to store biological data collected in a previous work. This project aims to organize the current data, the database schema and create one web interface to improve the data manipulation. Additionally was added to the original project, resources to keep track of modifications in records, maintaining one historical log of events.

Model for Activity Coordination in Agricultural Supply Chain

This presentation describes the current state of my master research which aims to specify a model for agricultural supply chain activity coordination based on Web services orchestration and choreography.

Fluid Web and Digital Content Components: from a document-centric perspective to a content-centric perspective

This is a preview of the presentation of my PhD thesis, which comprises a model to produce/share/reuse digital content, named Digital Content Component (DCC), and an infrastructure to support its use/storage/deployment.