qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software

Background qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools. It is built as an umbrella package that enables outbred genotype probabilities to be calculated and/or imported into the software package R/qtl. Findings Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and efficient algorithm developed for analyzing arbitrarily large datasets (included in the package) or imported from other sources such as the web-based tool, GridQTL. Conclusion qtl.outbred will improve the speed for calculating probabilities and the ability to analyse large future datasets. This package enables the user to analyse outbred line cross data accurately, but with similar effort than inbred line cross data.

User perspectives on the Swedish Maternal Health Care Register

Background: Established in 1999, the Swedish Maternal Health Care Register (MHCR) collects data on pregnancy, birth, and the postpartum period for most pregnant women in Sweden. Antenatal care (ANC) midwives manually enter data into the Web-application that is designed for MHCR. The aim of this study was to investigate midwives? experiences, opinions and use of the MHCR. Method: A national, cross-sectional, questionnaire survey, addressing all Swedish midwives working in ANC, was conducted January to March 2012. The questionnaire included demographic data, preformed statements with six response options ranging from zero to five (0 = totally disagree and 5 = totally agree), and opportunities to add information or further clarification in the form of free text comments. Parametric and non-parametric methods and logistic regression analyses were applied, and content analysis was used for free text comments. Results: The estimated response rate was 53.1%. Most participants were positive towards the Web-application and the included variables in the MHCR. Midwives exclusively engaged in patient-related work tasks perceived the register as burdensome (70.3%) and 44.2% questioned the benefit of the register. The corresponding figures for midwives also engaged in administrative supervision were 37.8% and 18.5%, respectively. Direct electronic transfer of data from the medical records to the MHCR was emphasised as significant future improvement. In addition, the midwives suggested that new variables of interest should be included in the MHCR ? e.g., infertility, outcomes of previous pregnancy and birth, and complications of the index pregnancy. Conclusions: In general, the MHCR was valued positively, although perceived as burdensome. Direct electronic transfer of data from the medical records to the MHCR is a prioritized issue to facilitate the working situation for midwives. Finally, the data suggest that the MHCR is an underused source for operational planning and quality assessment in local ANC centres.

Transparent Provenance Derivation for User Decisions

It is rare for data's history to include computational processes alone. Even when software generates data, users ultimately decide to execute software procedures, choose their configuration and inputs, reconfigure, halt and restart processes, and so on. Understanding the provenance of data thus involves understanding the reasoning of users behind these decisions, but demanding that users explicitly document decisions could be intrusive if implemented naively, and impractical in some cases. In this paper, therefore, we explore an approach to transparently deriving the provenance of user decisions at query time. The user reasoning is simulated, and if the result of the simulation matches the documented decision, the simulation is taken to approximate the actual reasoning. The plausibility of this approach requires that the simulation mirror human decision -making, so we adopt an automated process explicitly modelled on human psychology. The provenance of the decision is modelled in OPM, allowing it to be queried as part of a larger provenance graph, and an OPM profile is provided to allow consistent querying of provenance across user decisions.

A Resource Centric Approach For Advancing Collaboration Through Hydrologic Data And Model Sharing

HydroShare is an online, collaborative system being developed for open sharing of hydrologic data and models. The goal of HydroShare is to enable scientists to easily discover and access hydrologic data and models, retrieve them to their desktop or perform analyses in a distributed computing environment that may include grid, cloud or high performance computing model instances as necessary. Scientists may also publish outcomes (data, results or models) into HydroShare, using the system as a collaboration platform for sharing data, models and analyses. HydroShare is expanding the data sharing capability of the CUAHSI Hydrologic Information System by broadening the classes of data accommodated, creating new capability to share models and model components, and taking advantage of emerging social media functionality to enhance information about and collaboration around hydrologic data and models. One of the fundamental concepts in HydroShare is that of a Resource. All content is represented using a Resource Data Model that separates system and science metadata and has elements common to all resources as well as elements specific to the types of resources HydroShare will support. These will include different data types used in the hydrology community and models and workflows that require metadata on execution functionality. The HydroShare web interface and social media functions are being developed using the Drupal content management system. A geospatial visualization and analysis component enables searching, visualizing, and analyzing geographic datasets. The integrated Rule-Oriented Data System (iRODS) is being used to manage federated data content and perform rule-based background actions on data and model resources, including parsing to generate metadata catalog information and the execution of models and workflows. This presentation will introduce the HydroShare functionality developed to date, describe key elements of the Resource Data Model and outline the roadmap for future development.

Parameterization Of Turbulence Models Using 3DVAR Data Assimilation

In this research the 3DVAR data assimilation scheme is implemented in the numerical model DIVAST in order to optimize the performance of the numerical model by selecting an appropriate turbulence scheme and tuning its parameters. Two turbulence closure schemes: the Prandtl mixing length model and the two-equation k-ε model were incorporated into DIVAST and examined with respect to their universality of application, complexity of solutions, computational efficiency and numerical stability. A square harbour with one symmetrical entrance subject to tide-induced flows was selected to investigate the structure of turbulent flows. The experimental part of the research was conducted in a tidal basin. A significant advantage of such laboratory experiment is a fully controlled environment where domain setup and forcing are user-defined. The research shows that the Prandtl mixing length model and the two-equation k-ε model, with default parameterization predefined according to literature recommendations, overestimate eddy viscosity which in turn results in a significant underestimation of velocity magnitudes in the harbour. The data assimilation of the model-predicted velocity and laboratory observations significantly improves model predictions for both turbulence models by adjusting modelled flows in the harbour to match de-errored observations. 3DVAR allows also to identify and quantify shortcomings of the numerical model. Such comprehensive analysis gives an optimal solution based on which numerical model parameters can be estimated. The process of turbulence model optimization by reparameterization and tuning towards optimal state led to new constants that may be potentially applied to complex turbulent flows, such as rapidly developing flows or recirculating flows.

Power flow for primary distribution networks considering uncertainty in demand and user connection

This paper presents a method for calculating the power flow in distribution networks considering uncertainties in the distribution system. Active and reactive power are used as uncertain variables and probabilistically modeled through probability distribution functions. Uncertainty about the connection of the users with the different feeders is also considered. A Monte Carlo simulation is used to generate the possible load scenarios of the users. The results of the power flow considering uncertainty are the mean values and standard deviations of the variables of interest (voltages in all nodes, active and reactive power flows, etc.), giving the user valuable information about how the network will behave under uncertainty rather than the traditional fixed values at one point in time. The method is tested using real data from a primary feeder system, and results are presented considering uncertainty in demand and also in the connection. To demonstrate the usefulness of the approach, the results are then used in a probabilistic risk analysis to identify potential problems of undervoltage in distribution systems. (C) 2012 Elsevier Ltd. All rights reserved.

EthoSeq: A tool for phylogenetic analysis and data mining in behavioral sequences

This article introduces the software program called EthoSeq, which is designed to extract probabilistic behavioral sequences (tree-generated sequences, or TGSs) from observational data and to prepare a TGS-species matrix for phylogenetic analysis. The program uses Graph Theory algorithms to automatically detect behavioral patterns within the observational sessions. It includes filtering tools to adjust the search procedure to user-specified statistical needs. Preliminary analyses of data sets, such as grooming sequences in birds and foraging tactics in spiders, uncover a large number of TGSs which together yield single phylogenetic trees. An example of the use of the program is our analysis of felid grooming sequences, in which we have obtained 1,386 felid grooming TGSs for seven species, resulting in a single phylogeny. These results show that behavior is definitely useful in phylogenetic analysis. EthoSeq simplifies and automates such analyses, uncovers much of the hidden patterns of long behavioral sequences, and prepares this data for further analysis with standard phylogenetic programs. We hope it will encourage many empirical studies on the evolution of behavior.

Coordinated views to assist exploration of spatio-temporal data: a case study

In this paper we focus on providing coordinated visual strategies to assist users in performing tasks driven by the presence of temporal and spatial attributes. We introduce temporal visualization techniques targeted at such tasks, and illustrate their use with an application involving a climate classification process. The climate classification requires extensive Processing of a database containing daily rain precipitation values collected along over fifty years at several spatial locations in the São Paulo state, Brazil. We identify user exploration tasks typically conducted as part of the data preparation required in this process, and then describe how such tasks may be assisted by the multiple visual techniques provided. Issues related to the use of the multiple techniques by an end-user are also discussed.

Conceptual model for adaptable and extensible visual data exploration

Interactive visual representations complement traditional statistical and machine learning techniques for data analysis, allowing users to play a more active role in a knowledge discovery process and making the whole process more understandable. Though visual representations are applicable to several stages of the knowledge discovery process, a common use of visualization is in the initial stages to explore and organize a sometimes unknown and complex data set. In this context, the integrated and coordinated - that is, user actions should be capable of affecting multiple visualizations when desired - use of multiple graphical representations allows data to be observed from several perspectives and offers richer information than isolated representations. In this paper we propose an underlying model for an extensible and adaptable environment that allows independently developed visualization components to be gradually integrated into a user configured knowledge discovery application. Because a major requirement when using multiple visual techniques is the ability to link amongst them, so that user actions executed on a representation propagate to others if desired, the model also allows runtime configuration of coordinated user actions over different visual representations. We illustrate how this environment is being used to assist data exploration and organization in a climate classification problem.

Evaluation of tropospheric and ionospheric effects on the geographic localization of data collection platforms

The Brazilian National Institute for Space Research (INPE) is operating the Brazilian Environmental Data Collection System that currently amounts to a user community of around 100 organizations and more than 700 data collection platforms installed in Brazil. This system uses the SCD-1, SCD-2, and CBERS-2 low Earth orbit satellites to accomplish the data collection services. The main system applications are hydrology, meteorology, oceanography, water quality, and others. One of the functionalities offered by this system is the geographic localization of the data collection platforms by using Doppler shifts and a batch estimator based on least-squares technique. There is a growing demand to improve the quality of the geographical location of data collection platforms for animal tracking. This work presents an evaluation of the ionospheric and tropospheric effects on the Brazilian Environmental Data Collection System transmitter geographic location. Some models of the ionosphere and troposphere are presented to simulate their impacts and to evaluate performance of the platform location algorithm. The results of the Doppler shift measurements, using the SCD-2 satellite and the data collection platform (DCP) located in Cuiabá town, are presented and discussed.

User Manual for the Gender Equality Observatory for Latin America and the Caribbean

Includes bibliography

A multi-agent architecture for intelligent data analysis

The present study introduces a multi-agent architecture designed for doing automation process of data integration and intelligent data analysis. Different from other approaches the multi-agent architecture was designed using a multi-agent based methodology. Tropos, an agent based methodology was used for design. Based on the proposed architecture, we describe a Web based application where the agents are responsible to analyse petroleum well drilling data to identify possible abnormalities occurrence. The intelligent data analysis methods used was the Neural Network.

LUTS: A lightweight user-level transaction scheduler

Software Transactional Memory (STM) systems have poor performance under high contention scenarios. Since many transactions compete for the same data, most of them are aborted, wasting processor runtime. Contention management policies are typically used to avoid that, but they are passive approaches as they wait for an abort to happen so they can take action. More proactive approaches have emerged, trying to predict when a transaction is likely to abort so its execution can be delayed. Such techniques are limited, as they do not replace the doomed transaction by another or, when they do, they rely on the operating system for that, having little or no control on which transaction should run. In this paper we propose LUTS, a Lightweight User-Level Transaction Scheduler, which is based on an execution context record mechanism. Unlike other techniques, LUTS provides the means for selecting another transaction to run in parallel, thus improving system throughput. Moreover, it avoids most of the issues caused by pseudo parallelism, as it only launches as many system-level threads as the number of available processor cores. We discuss LUTS design and present three conflict-avoidance heuristics built around LUTS scheduling capabilities. Experimental results, conducted with STMBench7 and STAMP benchmark suites, show LUTS efficiency when running high contention applications and how conflict-avoidance heuristics can improve STM performance even more. In fact, our transaction scheduling techniques are capable of improving program performance even in overloaded scenarios. © 2011 Springer-Verlag.

Is it possible to make pixel-based radar image classification user-friendly?

In this paper we would like to shed light the problem of efficiency and effectiveness of image classification in large datasets. As the amount of data to be processed and further classified has increased in the last years, there is a need for faster and more precise pattern recognition algorithms in order to perform online and offline training and classification procedures. We deal here with the problem of moist area classification in radar image in a fast manner. Experimental results using Optimum-Path Forest and its training set pruning algorithm also provided and discussed. © 2011 IEEE.

Mobile application as a tool for urban traffic data collection and generation to advanced traveler information systems using Wi-Fi networks available in urban centers

This paper presents an Advanced Traveler Information System (ATIS) developed on Android platform, which is open source and free. The developed application has as its main objective the free use of a Vehicle-to- Infrastructure (V2I) communication through the wireless network access points available in urban centers. In addition to providing the necessary information for an Intelligent Transportation System (ITS) to a central server, the application also receives the traffic data close to the vehicle. Once obtained this traffic information, the application displays them to the driver in a clear and efficient way, allowing the user to make decisions about his route in real time. The application was tested in a real environment and the results are presented in the article. In conclusion we present the benefits of this application. © 2012 IEEE.