Semantic search components:a blueprint for effective query language interfaces

Formulating complex queries is hard, especially when users cannot understand all the data structures of multiple complex knowledge bases. We see a gap between simplistic but user friendly tools and formal query languages. Building on an example comparison search, we propose an approach in which reusable search components take an intermediary role between the user interface and formal query languages.

Europeana Creative. EDM Endpoint. Custom Views

The paper discusses the Europeana Creative project which aims to facilitate re-use of cultural heritage metadata and content by the creative industries. The paper focuses on the contribution of Ontotext to the project activities. The Europeana Data Model (EDM) is further discussed as a new proposal for structuring the data that Europeana will ingest, manage and publish. The advantages of using EDM instead of the current ESE metadata set are highlighted. Finally, Ontotext’s EDM Endpoint is presented, based on OWLIM semantic repository and SPARQL query language. A user-friendly RDF view is presented in order to illustrate the possibilities of Forest - an extensible modular user interface framework for creating linked data and semantic web applications.

Development of a mathematical and computer model to assess water quality impacts of hazardous compounds from minor gasoline spills in the inter-tidal zone of the Miami River, Florida

The objective of this study was to develop a model to predict transport and fate of gasoline components of environmental concern in the Miami River by mathematically simulating the movement of dissolved benzene, toluene, xylene (BTX), and methyl-tertiary-butyl ether (MTBE) occurring from minor gasoline spills in the inter-tidal zone of the river. Computer codes were based on mathematical algorithms that acknowledge the role of advective and dispersive physical phenomena along the river and prevailing phase transformations of BTX and MTBE. Phase transformations included volatilization and settling. ^ The model used a finite-difference scheme of steady-state conditions, with a set of numerical equations that was solved by two numerical methods: Gauss-Seidel and Jacobi iterations. A numerical validation process was conducted by comparing the results from both methods with analytical and numerical reference solutions. Since similar trends were achieved after the numerical validation process, it was concluded that the computer codes algorithmically were correct. The Gauss-Seidel iteration yielded at a faster convergence rate than the Jacobi iteration. Hence, the mathematical code was selected to further develop the computer program and software. The model was then analyzed for its sensitivity. It was found that the model was very sensitive to wind speed but not to sediment settling velocity. ^ A computer software was developed with the model code embedded. The software was provided with two major user-friendly visualized forms, one to interface with the database files and the other to execute and present the graphical and tabulated results. For all predicted concentrations of BTX and MTBE, the maximum concentrations were over an order of magnitude lower than current drinking water standards. It should be pointed out, however, that smaller concentrations than the latter reported standards and values, although not harmful to humans, may be very harmful to organisms of the trophic levels of the Miami River ecosystem and associated waters. This computer model can be used for the rapid assessment and management of the effects of minor gasoline spills on inter-tidal riverine water quality. ^

Capacity-based cost modeling for light rail and bus rapid transit systems

Choosing between Light Rail Transit (LRT) and Bus Rapid Transit (BRT) systems is often controversial and not an easy task for transportation planners who are contemplating the upgrade of their public transportation services. These two transit systems provide comparable services for medium-sized cities from the suburban neighborhood to the Central Business District (CBD) and utilize similar right-of-way (ROW) categories. The research is aimed at developing a method to assist transportation planners and decision makers in determining the most feasible system between LRT and BRT. ^ Cost estimation is a major factor when evaluating a transit system. Typically, LRT is more expensive to build and implement than BRT, but has significantly lower Operating and Maintenance (OM) costs than BRT. This dissertation examines the factors impacting capacity and costs, and develops cost models, which are a capacity-based cost estimate for the LRT and BRT systems. Various ROW categories and alignment configurations of the systems are also considered in the developed cost models. Kikuchi's fleet size model (1985) and cost allocation method are used to develop the cost models to estimate the capacity and costs. ^ The comparison between LRT and BRT are complicated due to many possible transportation planning and operation scenarios. In the end, a user-friendly computer interface integrated with the established capacity-based cost models, the LRT and BRT Cost Estimator (LBCostor), was developed by using Microsoft Visual Basic language to facilitate the process and will guide the users throughout the comparison operations. The cost models and the LBCostor can be used to analyze transit volumes, alignments, ROW configurations, number of stops and stations, headway, size of vehicle, and traffic signal timing at the intersections. The planners can make the necessary changes and adjustments depending on their operating practices. ^

An integrated functional mapping and source localization platform for brain research

The premise of this dissertation is to create a highly integrated platform that combines the most current recording technologies for brain research through the development of new algorithms for three-dimensional (3D) functional mapping and 3D source localization. The recording modalities that were integrated include: Electroencephalography (EEG), Optical Topographic Maps (OTM), Magnetic Resonance Imaging (MRI), and Diffusion Tensor Imaging (DTI). This work can be divided into two parts: The first part involves the integration of OTM with MRI, where the topographic maps are mapped to both the skull and cortical surface of the brain. This integration process is made possible through the development of new algorithms that determine the probes location on the MRI head model and warping the 2D topographic maps onto the 3D MRI head/brain model. Dynamic changes of the brain activation can be visualized on the MRI head model through a graphical user interface. The second part of this research involves augmenting a fiber tracking system, by adding the ability to integrate the source localization results generated by commercial software named Curry. This task involved registering the EEG electrodes and the dipole results to the MRI data. Such Integration will allow the visualization of fiber tracts, along with the source of the EEG, in a 3D transparent brain structure. The research findings of this dissertation were tested and validated through the participation of patients from Miami Children Hospital (MCH). Such an integrated platform presented to the medical professionals in the form of a user-friendly graphical interface is viewed as a major contribution of this dissertation. It should be emphasized that there are two main aspects to this research endeavor: (1) if a dipole could be situated in time at its different positions, its trajectory may reveal additional information on the extent and nature of the brain malfunction; (2) situating such a dipole trajectory with respect to the fiber tracks could ensure the preservation of these fiber tracks (axons) during surgical interventions, preserving as a consequence these parts of the brain that are responsible for information transmission.

Design of an automated book reader as an assistive technology tool for blind persons

This dissertation introduces a novel automated book reader as an assistive technology tool for persons with blindness. The literature shows extensive work in the area of optical character recognition, but the current methodologies available for the automated reading of books or bound volumes remain inadequate and are severely constrained during document scanning or image acquisition processes. The goal of the book reader design is to automate and simplify the task of reading a book while providing a user-friendly environment with a realistic but affordable system design. This design responds to the main concerns of (a) providing a method of image acquisition that maintains the integrity of the source (b) overcoming optical character recognition errors created by inherent imaging issues such as curvature effects and barrel distortion, and (c) determining a suitable method for accurate recognition of characters that yields an interface with the ability to read from any open book with a high reading accuracy nearing 98%. This research endeavor focuses in its initial aim on the development of an assistive technology tool to help persons with blindness in the reading of books and other bound volumes. But its secondary and broader aim is to also find in this design the perfect platform for the digitization process of bound documentation in line with the mission of the Open Content Alliance (OCA), a nonprofit Alliance at making reading materials available in digital form. The theoretical perspective of this research relates to the mathematical developments that are made in order to resolve both the inherent distortions due to the properties of the camera lens and the anticipated distortions of the changing page curvature as one leafs through the book. This is evidenced by the significant increase of the recognition rate of characters and a high accuracy read-out through text to speech processing. This reasonably priced interface with its high performance results and its compatibility to any computer or laptop through universal serial bus connectors extends greatly the prospects for universal accessibility to documentation.

Design and implementation of a web based shop floor control system to maintain schedule feasibility in a dynamic job shop environment

The effective control of production activities in dynamic job shop with predetermined resource allocation for all the jobs entering the system is a unique manufacturing environment, which exists in the manufacturing industry. In this thesis a framework for an Internet based real time shop floor control system for such a dynamic job shop environment is introduced. The system aims to maintain the schedule feasibility of all the jobs entering the manufacturing system under any circumstance. The system is capable of deciding how often the manufacturing activities should be monitored to check for control decisions that need to be taken on the shop floor. The system will provide the decision maker real time notification to enable him to generate feasible alternate solutions in case a disturbance occurs on the shop floor. The control system is also capable of providing the customer with real time access to the status of the jobs on the shop floor. The communication between the controller, the user and the customer is through web based user friendly GUI. The proposed control system architecture and the interface for the communication system have been designed, developed and implemented.

Integração da simulação termoenergética com o processo de projeto: a análise de 6 casos

This work consists of the integrated design process analyses with thermal energetic simulation during the early design stages, based on six practical cases. It aims to schematize the integration process, identifying the thermal energetic analyses contributions at each design phase and identifying the highest impact parameters on building performance. The simulations were run in the DesignBuilder energy tool, which has the same EnergyPlus engine, validated. This tool was chosen due to the flexible and user friendly graphic interface for modeling and output assessment, including the parametric simulation to compare design alternatives. The six case studies energy tools are three architectural and three retrofit projects, and the author the simulations as a consultant or as a designer. The case studies were selected based on the commitment of the designers in order to achieve performance goals, and their availability to share the process since the early pre-design analyses, allowing schematizing the whole process, and supporting the design decisions with quantifications, including energy targets. The thermoenergetic performance analyses integration is feasible since the early stages, except when only a short time is available to run the simulations. The simulation contributions are more important during the sketch and detail phases. The predesign phase can be assisted by means of reliable bioclimatic guidelines. It was verified that every case study had two dominant design variables on the general performance. These variables differ according the building characteristics and always coincide with the local bioclimatic strategies. The adaptation of alternatives to the design increases as earlier it occurs. The use of simulation is very useful: to prove and convince the architects; to quantify the cost benefits and payback period to the retrofit designer; and to the simulator confirm the desirable result and report the performance to the client

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.

EIR – sistema inteligente para detecção e classificação de calcificações em mamografias

Dissertação (mestrado)—Universidade de Brasília, Faculdade Gama, Programa de Pós-Graduação em Engenharia Biomédica, 2016.

Feasibility study and flow scheduling optimization of a multi-product pipeline system

The first goal of this study is to analyse a real-world multiproduct onshore pipeline system in order to verify its hydraulic configuration and operational feasibility by constructing a simulation model step by step from its elementary building blocks that permits to copy the operation of the real system as precisely as possible. The second goal is to develop this simulation model into a user-friendly tool that one could use to find an “optimal” or “best” product batch schedule for a one year time period. Such a batch schedule could change dynamically as perturbations occur during operation that influence the behaviour of the entire system. The result of the simulation, the ‘best’ batch schedule is the one that minimizes the operational costs in the system. The costs involved in the simulation are inventory costs, interface costs, pumping costs, and penalty costs assigned to any unforeseen situations. The key factor to determine the performance of the simulation model is the way time is represented. In our model an event based discrete time representation is selected as most appropriate for our purposes. This means that the time horizon is divided into intervals of unequal lengths based on events that change the state of the system. These events are the arrival/departure of the tanker ships, the openings and closures of loading/unloading valves of storage tanks at both terminals, and the arrivals/departures of trains/trucks at the Delivery Terminal. In the feasibility study we analyse the system’s operational performance with different Head Terminal storage capacity configurations. For these alternative configurations we evaluated the effect of different tanker ship delay magnitudes on the number of critical events and product interfaces generated, on the duration of pipeline stoppages, the satisfaction of the product demand and on the operative costs. Based on the results and the bottlenecks identified, we propose modifications in the original setup.

FDOT District Six Pedestrian Safety Web GIS Application

A group of four applications including Top 20 Pedestrian Crash Locations: This application is designed to display top 20 pedestrian crash locations into both map- view and detailed information view. FDOT Crash Reporting Tool: This application is designed to simplify the usage and sharing of CAR data. The application can load raw data from CAR and display it into a web map interface. FDOT Online Document Portal: This application is designed for FDOT project managers to be able to share and manage documents through a user friendly, GIS enable web interface GIS Data Collection for Pedestrian Safety Tool: FIU-GIS Center was responsible for data collection and processing work for the project of Pedestrian Safety Tool Project. The outcome of this task is present by a simple web-GIS application design to host GIS by projects.

Modelling the infrastructure of the “Śivadharma Database”

A Digital Scholarly Edition is a conceptually and structurally sophisticated entity. Throughout the centuries, diverse methodologies have been employed to reconstruct a text transmitted through one or multiple sources, resulting in various edition types. With the advent of digital technology in philology, these practices have undergone a significant transformation, compelling scholars to reconsider their approach in light of the web. In the digital age, philologists are expected to possess (too) advanced technical skills to prepare interactive and enriched editions, even though, in most cases, only mechanical or documentary editions are published online. The Śivadharma Database is a web Content Management System (CMS) designed to facilitate the preparation, publication, and updating of Digital Scholarly Editions. By providing scholars with a user-friendly CRUD web application to reconstruct and annotate a text, they can prepare their textus with additional components such as apparatus, notes, translations, citations, and parallels. It is possible by leveraging an annotation system based on HTML and graph data structure. This choice is made because the text entity is multidimensional and multifaceted, even if its sequential presentation constrains it. In particular, editions of South Asian texts of the Śivadharma corpus, the case study of this research, contain a series of phenomena that are difficult to manage formally, such as overlapping hierarchies. Hence, it becomes necessary to establish the data structure best suited to represent this complexity. In Śivadharma Database, the textus is an HTML file readily displayable. Textual fragments, annotated via an interface without requiring philologists to write code and saved in the backend, form the atomic unit of multiple relationships organised in a graph database. This approach enables the formal representation of complex and overlapping textual phenomena, allowing for good annotation expressiveness with minimal effort to learn the relevant technologies during the editing workflow.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Spatial Technologies: What use are they to managers of environmental lands?

This paper reviews the potential use of three types of spatial technology to land managers, namely satellite imagery, satellite positioning systems and supporting computer software. Developments in remote sensing and the relative advantages of multispectral and hyperspectral images are discussed. The main challenge to the wider use of remote sensing as a land management tool is seen as uncertainty whether apparent relationships between biophysical variables and spectral reflectance are direct and causal, or artefacts of particular images. Developments in satellite positioning systems are presented in the context of land managers’ need for position estimates in situations where absolute precision may or may not be required. The role of computer software in supporting developments in spatial technology is described. Spatial technologies are seen as having matured beyond empirical applications to the stage where they are useful and reliable land management tools. In addition, computer software has become more user-friendly and this has facilitated data collection and manipulation by semi-expert as well as specialist staff.