BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Air traffic control with an expected value criterion

in this contribution we discuss a stochastic framework for air traffic conflict resolution. The conflict resolution task is posed as the problem of optimizing an expected value criterion. Optimization is carried out by Monte Carlo Markov Chain (MCMC) simulation. A numerical example illustrates the proposed strategy. Copyright © 2005 IFAC.

Monte Carlo optimization strategies for air-traffic control

The safety of the flights, and in particular conflict resolution for separation assurance, is one of the main tasks of Air Traffic Control. Conflict resolution requires decision making in the face of the considerable levels of uncertainty inherent in the motion of aircraft. We present a Monte Carlo framework for conflict resolution which allows one to take into account such levels of uncertainty through the use of a stochastic simulator. A simulation example inspired by current air traffic control practice illustrates the proposed conflict resolution strategy. Copyright © 2005 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology.BarraCUDA is currently available from http://seqbarracuda.sf.net.

Design methodology for composite structures: A small low air-speed wind turbine blade case study

A small low air-speed wind turbine blade case study is used to demonstrate the effectiveness of a materials and design selection methodology described by Monroy Aceves et al. (2008) [24] for composite structures. The blade structure comprises a shell of uniform thickness and a unidirectional reinforcement. The shell outer geometry is fixed by aerodynamic considerations. A wide range of lay-ups are considered for the shell and reinforcement. Structural analysis is undertaken using the finite element method. Results are incorporated into a database for analysis using material selection software. A graphical selection stage is used to identify the lightest blade meeting appropriate design constraints. The proposed solution satisfies the design requirements and improves on the prototype benchmark by reducing the mass by almost 50%. The flexibility of the selection software in allowing identification of trends in the results and modifications to the selection criteria is demonstrated. Introducing a safety factor of two on the material failure stresses increases the mass by only 11%. The case study demonstrates that the proposed design methodology is useful in preliminary design where a very wide range of cases should be considered using relatively simple analysis. © 2011 Elsevier Ltd.

Air quality and public health impacts of UK airports. Part I: Emissions

The potential adverse human health and climate impacts of emissions from UK airports have become a significant political issue, yet the emissions, air quality impacts and health impacts attributable to UK airports remain largely unstudied. We produce an inventory of UK airport emissions - including aircraft landing and takeoff (LTO) operations and airside support equipment - with uncertainties quantified. The airports studied account for more than 95% of UK air passengers in 2005. We estimate that in 2005, UK airports emitted 10.2 Gg [-23 to +29%] of NOx, 0.73 Gg [-29 to +32%] of SO2, 11.7 Gg [-42 to +77%] of CO, 1.8 Gg [-59 to +155%] of HC, 2.4 Tg [-13 to +12%] of CO2, and 0.31 Gg [-36 to +45%] of PM2.5. This translates to 2.5 Tg [-12 to +12%] CO2-eq using Global Warming Potentials for a 100-year time horizon. Uncertainty estimates were based on analysis of data from aircraft emissions measurement campaigns and analyses of aircraft operations.The First-Order Approximation (FOA3) - currently the standard approach used to estimate particulate matter emissions from aircraft - is compared to measurements and it is shown that there are discrepancies greater than an order of magnitude for 40% of cases for both organic carbon and black carbon emissions indices. Modified methods to approximate organic carbon emissions, arising from incomplete combustion and lubrication oil, and black carbon are proposed. These alterations lead to factor 8 and a 44% increase in the annual emissions estimates of black and organic carbon particulate matter, respectively, leading to a factor 3.4 increase in total PM2.5 emissions compared to the current FOA3 methodology. Our estimates of emissions are used in Part II to quantify the air quality and health impacts of UK airports, to assess mitigation options, and to estimate the impacts of a potential London airport expansion. © 2011 Elsevier Ltd.

The deposition of small particles from a turbulent air flow in a curved duct

The paper describes an experimental and theoretical study of the deposition of small spherical particles from a turbulent air flow in a curved duct. The objective was to investigate the interaction between the streamline curvature of the primary flow and the turbulent deposition mechanisms of diffusion and turbophoresis. The experiments were conducted with particles of uranine (used as a fluorescent tracer) produced by an aerosol generator. The particles were entrained in an air flow which passed vertically downwards through a long straight channel of rectangular cross-section leading to a 90° bend. The inside surfaces of the channel and bend were covered with tape to collect the deposited particles. Following a test run the tape was removed in sections, the uranine was dissolved in sodium hydroxide solution and the deposition rates established by measuring the uranine concentration with a luminescence spectrometer. The experimental results were compared with calculations of particle deposition in a curved duct using a computer program that solved the ensemble-averaged particle mass and momentum conservation equations. A particle density-weighted averaging procedure was used and the equations were expressed in terms of the particle convective, rather than total, velocity. This approach provided a simpler formulation of the particle turbulence correlations generated by the averaging process. The computer program was used to investigate the distance required to achieve a fully-developed particle flow in the straight entry channel as well as the variation of the deposition rate around the bend. The simulations showed good agreement with the experimental results. © 2012 Elsevier Ltd.

A simple prediction model for asphalt surface texture incorporating mix gradation and air voids

This paper presents the results of a preliminary study that seeks to show how asphalt grading and air voids are related to the texture depth of asphalt. The fiftieth percentile particle size (D50) is shown to be a good predictor of texture depth measurements from a collected database of field and laboratory studies. The D50 is used to normalise collected texture data and this 'relative texture' is shown to correlate with air voids. Regression analyses confirm that air voids should be included along with a measure of gradation in the interpretation of asphalt surface texture.The derived formulae are used to develop correlation charts.

Effects of preferential transport in turbulent bluff-body-stabilized lean premixed CH 4/air flames

Preferential species diffusion is known to have important effects on local flame structure in turbulent premixed flames, and differential diffusion of heat and mass can have significant effects on both local flame structure and global flame parameters, such as turbulent flame speed. However, models for turbulent premixed combustion normally assume that atomic mass fractions are conserved from reactants to fully burnt products. Experiments reported here indicate that this basic assumption may be incorrect for an important class of turbulent flames. Measurements of major species and temperature in the near field of turbulent, bluff-body stabilized, lean premixed methane-air flames (Le=0.98) reveal significant departures from expected conditional mean compositional structure in the combustion products as well as within the flame. Net increases exceeding 10% in the equivalence ratio and the carbon-to-hydrogen atom ratio are observed across the turbulent flame brush. Corresponding measurements across an unstrained laminar flame at similar equivalence ratio are in close agreement with calculations performed using Chemkin with the GRI 3.0 mechanism and multi-component transport, confirming accuracy of experimental techniques. Results suggest that the large effects observed in the turbulent bluff-body burner are cause by preferential transport of H 2 and H 2O through the preheat zone ahead of CO 2 and CO, followed by convective transport downstream and away from the local flame brush. This preferential transport effect increases with increasing velocity of reactants past the bluff body and is apparently amplified by the presence of a strong recirculation zone where excess CO 2 is accumulated. © 2011 The Combustion Institute.