Bioinformática estrutural aplicada ao estudo de proteínas alvo do genoma do Mycobacterium tuberculosis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Subsídio à gestão ambiental hidroviária: o empreendimento hídrico Santa Maria da Serra

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Desenvolvimento de um sistema de alerta de enchente aplicado aos planos de defesa civil em áreas de risco no estado do Pará utilizando Sistema de Informações Geográficas (SIG), caso: cidade de Marabá

A presente dissertação desenvolveu um Sistema de Alerta de Enchentes para a Cidade de Marabá, localizada na confluência dos rios Itacaiúnas e Tocantins, a 440 km da cidade de Belém, capital do Estado do Pará. O Sistema de Alerta de Enchentes foi desenvolvido com base no modelo hidrológico MOD-4B incorporado a um Sistema de Informações Geográficas. Esse sistema permite prever as variações do nível do Rio Tocantins ao longo do ano, de modo a acompanhar a evolução da cheia com antecedência de 4 dias, o que torna possível uma ação eficiente da defesa civil. O modelo de previsão utilizou como referência as réguas linimétricas localizadas nos rios Tocantins e Araguaia nas cidades de Carolina e Conceição do Araguaia, distantes aproximadamente 225 e 270 km, respectivamente, da cidade de Marabá. O sistema utiliza o software de geoprocessamento ArcView 3.3, que teve implementada uma interface desenvolvida através da linguagem de programação orientada a objetos Avenue, com a finalidade de rodar o aplicativo do modelo hidrológico. O uso de menus e janelas customizados do sistema possibilitou o acesso a dados espaciais e tabelas de dados relacionais e/ou banco de dados cadastral, além de módulos de análise espacial e de visualização de dados geográficos em um Sistema de Informações Geográficas (SIG), possibilitando a previsão de enchentes na forma de mapas, tabelas e relatórios com a indicação das áreas inundadas para os períodos de 4, 3, 2 e 1 dia de antecedência do evento de enchente. O Sistema permitiu identificar os imóveis e as ruas atingidos, e possibilitará através de levantamentos futuros quantificar a população afetada e os prejuízos causados pelo desastre, facilitando que a defesa civil execute planos de ação para enfrentamento eficiente antes, durante e depois da ocorrência da enchente.

Planejamento integrado dos recursos hídricos na microbacia do córrego Três Barras no município de Marinópolis-SP

Pós-graduação em Agronomia - FEIS

Sensoriamento remoto e Sistemas de Informações Geográficas (SIG) na análise dos impactos referentes à cultura canavieira e reflorestamento: a subtração dos biomas nativos no município de Itirapina-SP

The main objective of this study was to perform a temporal analysis of land use and cover of Itirapina – São Paulo estate, Brazil, for 1962, 2000 and 2008 scenarios, indicating the rate of change in native vegetation and contextualizing its modifications. Based on photointerpretation performed by supervised classification using the method of Bhattacharya, the thematic classes were mapped and characterized in an area equivalent to 56400 hectares. Using remote sensing technologies and geographic information systems, was structured and implemented a georeferenced and relational database, allowing the analysis of the size of the area occupied. The results showed that the expansion of cultivation of cane sugar and reforestation in the past 45 years has been conditioned the fragmentation of natural vegetation cover in the city, which fell by 34793 ha (61,7%) in 1962 to 9765,2 ha (17,3%) in 2008, with the loss of 25027,8 hectares.

Desenvolvimento de um aplicativo para processamento de imagens obtidas por fotografias aéreas

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Desenvolvimento de um aplicativo para processamento de imagens obtidas por fotografias aéreas

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

Abstract Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

RelAndXML

Diese Dissertation stellt das neu entwickelte SystemRelAndXML vor, das für das Management und dieSpeicherung von hypertextzentrierten XML-Dokumenten und dendazugehörenden XSL-Stylesheets spezialisiert ist. DerAnwendungsbereich sind die Vorlesungsmaterialien anUniversitäten. RelAndXML speichert die XML-formatiertenÜbungsblätter in Textbausteinen und weiterenTeilen in einer speziellen Datenbank.Die Speicherung von XML-Dokumenten in Datenbanken ist seiteinigen Jahren ein wichtiges Thema der Datenbankforschung.Ansätze dafür gliedern sich in solche fürdatenzentrierte und andere für dokumentenzentrierteDokumente. Die Dissertation präsentiert einen Ansatzzur Speicherung von hypertextzentrierten XML-Dokumenten, derAspekte von datenzentrierten und dokumentenzentriertenAnsätzen kombiniert. Der Ansatz erlaubt dieWiederverwendung von Textbausteinen und speichert dieReihenfolge dort, wo sie wichtig ist. Mit RelAndXML könnennicht nur Elemente gespeichert werden, wie mit einigenanderen Ansätzen, sondern auch Attribute, Kommentareund Processing Instructions. Algorithmen für dieFragmentierung und Rekonstruktion von Dokumenten werdenbereit gestellt.RelAndXML wurde mit Java und unter Verwendung einerobjektrelationalen Datenbank implementiert. Das System hateine graphische Benutzungsoberfläche, die das Erstellenund Verändern der XML- und XSL-Dokumente, dasEinfügen von neuen oder schon gespeichertenTextbausteinen sowie das Erzeugen von HTML-Dokumenten zurVeröffentlichung ermöglicht.

Sviluppo di un'applicazione bioinformatica per la gestione dei dati di antibiotico sensibilità di isolati clinici

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica.

Algorithmen zur labelfreien quantitativen Proteomanalyse auf Basis datenunabhängig-akquirierter LC-MS-Daten

Moderne ESI-LC-MS/MS-Techniken erlauben in Verbindung mit Bottom-up-Ansätzen eine qualitative und quantitative Charakterisierung mehrerer tausend Proteine in einem einzigen Experiment. Für die labelfreie Proteinquantifizierung eignen sich besonders datenunabhängige Akquisitionsmethoden wie MSE und die IMS-Varianten HDMSE und UDMSE. Durch ihre hohe Komplexität stellen die so erfassten Daten besondere Anforderungen an die Analysesoftware. Eine quantitative Analyse der MSE/HDMSE/UDMSE-Daten blieb bislang wenigen kommerziellen Lösungen vorbehalten. rn| In der vorliegenden Arbeit wurden eine Strategie und eine Reihe neuer Methoden zur messungsübergreifenden, quantitativen Analyse labelfreier MSE/HDMSE/UDMSE-Daten entwickelt und als Software ISOQuant implementiert. Für die ersten Schritte der Datenanalyse (Featuredetektion, Peptid- und Proteinidentifikation) wird die kommerzielle Software PLGS verwendet. Anschließend werden die unabhängigen PLGS-Ergebnisse aller Messungen eines Experiments in einer relationalen Datenbank zusammengeführt und mit Hilfe der dedizierten Algorithmen (Retentionszeitalignment, Feature-Clustering, multidimensionale Normalisierung der Intensitäten, mehrstufige Datenfilterung, Proteininferenz, Umverteilung der Intensitäten geteilter Peptide, Proteinquantifizierung) überarbeitet. Durch diese Nachbearbeitung wird die Reproduzierbarkeit der qualitativen und quantitativen Ergebnisse signifikant gesteigert.rn| Um die Performance der quantitativen Datenanalyse zu evaluieren und mit anderen Lösungen zu vergleichen, wurde ein Satz von exakt definierten Hybridproteom-Proben entwickelt. Die Proben wurden mit den Methoden MSE und UDMSE erfasst, mit Progenesis QIP, synapter und ISOQuant analysiert und verglichen. Im Gegensatz zu synapter und Progenesis QIP konnte ISOQuant sowohl eine hohe Reproduzierbarkeit der Proteinidentifikation als auch eine hohe Präzision und Richtigkeit der Proteinquantifizierung erreichen.rn| Schlussfolgernd ermöglichen die vorgestellten Algorithmen und der Analyseworkflow zuverlässige und reproduzierbare quantitative Datenanalysen. Mit der Software ISOQuant wurde ein einfaches und effizientes Werkzeug für routinemäßige Hochdurchsatzanalysen labelfreier MSE/HDMSE/UDMSE-Daten entwickelt. Mit den Hybridproteom-Proben und den Bewertungsmetriken wurde ein umfassendes System zur Evaluierung quantitativer Akquisitions- und Datenanalysesysteme vorgestellt.

Distributed Data Management in 2020?

Work on distributed data management commenced shortly after the introduction of the relational model in the mid-1970's. 1970's and 1980's were very active periods for the development of distributed relational database technology, and claims were made that in the following ten years centralized databases will be an “antique curiosity” and most organizations will move toward distributed database managers [1]. That prediction has certainly become true, and all commercial DBMSs today are distributed.

Cloud Computing Service for Managing Large Medical Image Data-Sets Using Balanced Collaborative Agents

Managing large medical image collections is an increasingly demanding important issue in many hospitals and other medical settings. A huge amount of this information is daily generated, which requires robust and agile systems. In this paper we present a distributed multi-agent system capable of managing very large medical image datasets. In this approach, agents extract low-level information from images and store them in a data structure implemented in a relational database. The data structure can also store semantic information related to images and particular regions. A distinctive aspect of our work is that a single image can be divided so that the resultant sub-images can be stored and managed separately by different agents to improve performance in data accessing and processing. The system also offers the possibility of applying some region-based operations and filters on images, facilitating image classification. These operations can be performed directly on data structures in the database.

Cartography for cooperative manoeuvres with autonomous land vehicles

This article presents a cartographic system to facilitate cooperative manoeuvres among autonomous vehicles in a well-known environment. The main objective is to design an extended cartographic system to help in the navigation of autonomous vehicles. This system has to allow the vehicles not only to access the reference points needed for navigation, but also noticeable information such as the location and type of traffic signals, the proximity to a crossing, the streets en route, etc. To do this, a hierarchical representation of the information has been chosen, where the information has been stored in two levels. The lower level contains the archives with the Universal Traverse Mercator (UTM) coordinates of the points that define the reference segments to follow. The upper level contains a directed graph with the relational database in which streets, crossings, roundabouts and other points of interest are represented. Using this new system it is possible to know when the vehicle approaches a crossing, what other paths arrive at that crossing, and, should there be other vehicles circulating on those paths and arriving at the crossing, which one has the highest priority. The data obtained from the cartographic system is used by the autonomous vehicles for cooperative manoeuvres.