A Primer on High-Throughput Computing for Genomic Selection

High-throughput computing (HTC) uses computer clusters to solve advanced computational problems, with the goal of accomplishing high-throughput over relatively long periods of time. In genomic selection, for example, a set of markers covering the entire genome is used to train a model based on known data, and the resulting model is used to predict the genetic merit of selection candidates. Sophisticated models are very computationally demanding and, with several traits to be evaluated sequentially, computing time is long, and output is low. In this paper, we present scenarios and basic principles of how HTC can be used in genomic selection, implemented using various techniques from simple batch processing to pipelining in distributed computer clusters. Various scripting languages, such as shell scripting, Perl, and R, are also very useful to devise pipelines. By pipelining, we can reduce total computing time and consequently increase throughput. In comparison to the traditional data processing pipeline residing on the central processors, performing general-purpose computation on a graphics processing unit provide a new-generation approach to massive parallel computing in genomic selection. While the concept of HTC may still be new to many researchers in animal breeding, plant breeding, and genetics, HTC infrastructures have already been built in many institutions, such as the University of Wisconsin–Madison, which can be leveraged for genomic selection, in terms of central processing unit capacity, network connectivity, storage availability, and middleware connectivity. Exploring existing HTC infrastructures as well as general-purpose computing environments will further expand our capability to meet increasing computing demands posed by unprecedented genomic data that we have today. We anticipate that HTC will impact genomic selection via better statistical models, faster solutions, and more competitive products (e.g., from design of marker panels to realized genetic gain). Eventually, HTC may change our view of data analysis as well as decision-making in the post-genomic era of selection programs in animals and plants, or in the study of complex diseases in humans

Visual Simulation of Multiple Fluids in Computer Graphics: A State-of-the-Art Report

Realistic animation of various interactions between multiple fluids, possibly undergoing phase change, is a challenging task in computer graphics. The visual scope of multi-phase multi-fluid phenomena covers complex tangled surface structures and rich color variations, which can greatly enhance visual effect in graphics applications. Describing such phenomena requires more complex models to handle challenges involving the calculation of interactions, dynamics and spatial distribution of multiple phases, which are often involved and hard to obtain real-time performance. Recently, a diverse set of algorithms have been introduced to implement the complex multi-fluid phenomena based on the governing physical laws and novel discretization methods to accelerate the overall computation while ensuring numerical stability. By sorting through the target phenomena of recent research in the broad subject of multiple fluids, this state-of-the-art report summarizes recent advances on multi-fluid simulation in computer graphics

Revealing the Concealed:Alternatives to Random Dots for Stereograms

Investigations of stereoscopic depth perception were transformed via the use of computer-generated random-dot stereograms in the 1960s. They realized Wheatstone’s wish of demonstrating binocular depth without monocular object recognition, and they have been the dominant stimulus for studying stereopsis since then. Alternative carrier patterns to random dots, based on graphics, photographs, and their combinations, are presented as anaglyphs and for free fusion. A wider range of concealed patterns can be revealed with these alternatives, and presenting them as anaglyphs can yield patterns that have visual appeal independent of the depth they conceal.<br/

FASTSWARM: A Data-driven FrAmework for Real-time Flying InSecT SWARM Simulation

Insect swarms are common phenomena in nature and therefore have been actively pursued in computer animation. Realistic insect swarm simulation is difficult due to two challenges: high‐fidelity behaviors and large scales, which make the simulation practice subject to laborious manual work and excessive trial‐and‐error processes. To address both challenges, we present a novel data‐driven framework, FASTSWARM, to model complex behaviors of flying insects based on real‐world data and simulate plausible animations of flying insect swarms. FASTSWARM has a linear time complexity and achieves real‐time performance for large swarms. The high‐fidelity behavior model of FASTSWARM explicitly takes into consideration the most common behaviors of flying insects, including the interactions among insects such as repulsion and attraction, self‐propelled behaviors such as target following and obstacle avoidance, and other characteristics such as random movements. To achieve scalability, an energy minimization problem is formed with different behaviors modeled as energy terms, where the minimizer is the desired behavior. The minimizer is computed from the real‐world data, which ensures the plausibility of the simulation results. Extensive simulation results and evaluations show that FASTSWARM is versatile in simulating various swarm behaviors, high fidelity measured by various metrics, easily controllable in inducing user controls and highly scalable

NASA Tech Briefs, June 1987

Topics include: NASA TU Services; New Product Ideas; Electronic Components and Circuits; Electronic Systems; Physical Sciences; Materials; Computer Programs; Mechanics; Fabrication Technology; Machinery; Mathematics and Information Sciences; Life Sciences

Electromechanical modeling, performance testing, and design of piezoelectric polymer film ultrasound transducers

The frequency-dependent lossy properties of piezoelectric polymer films prohibit the direct application of classical electromechanical circuit models. As a result, techniques have been unavailable for accurate simulation of piezo film ultrasound transducer performance;The first part of this work describes a method for determining the piezoelectric constants and the frequency-dependent dielectric properties for the polymers, from analysis of air-loaded broadband impedance measurements. It is then shown how to account for the frequency-dependent lossy properties of these films in a simple impedance circuit model and a modified Mason\u27s model. Comparisons between the models and actual film transducers show excellent broadband simulation of both electrical input impedance and ultrasonic pulse-echo performance;In the second part of this work, the modified Mason\u27s models were incorporated into an interactive design/simulation computer program. The simulation program provides an investigator with the means for performing 180 different quantitative tests of a prototype design, using any tuning or matching scheme;In the third part of this work, submersible P(VF[subscript]2-VF[subscript]3) ultrasound transducer probes were constructed and tests revealed excellent broadband ultrasonic performance. Comparisons between actual and predicted pulse-echo ultrasonic waveforms confirmed the accuracy and reliability of the derived modified Mason\u27s models and simulation techniques

Modeling and Visualization of Multi-material Volumes

The terminology of multi-material volumes is discussed. The classification of the multi-material volumes is given from the spatial partitions, spatial domain for material distribution, types of involved scalar fields and types of models for material distribution and composition of several materials points of view. In addition to the technical challenges of multi-material volume representations, a range of key challenges are considered before such representations can be adopted as mainstream practice