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

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.

Electric times in olfaction.

Recent work established the spread of interglomerular excitation in the Drosophila antennal lobe. Two papers in this issue of Neuron, by Huang et al. and Yaksi and Wilson, show that cholinergic krasavietz local interneurons are a major substrate for this spread of excitation, predominantly via electrical coupling.

The experiment to evaluate the AC loss of 2G HTS windings in the application of rotating electric machines

This paper presents the design of an AC loss experiment using nitrogen boil-off method. This experiment is aimed at exploring the AC loss of HTS double race-track coils which will be installed on the rotor of a wind turbine generator. The operating environment is simulated by designing a cryostat with rotating magnetic field windings. Apart from the fact that the alternating magnetic field causes most of AC loss on the HTS coils, we also believe that the DC background field would be another important factor causing AC loss if the HTS coil is experiencing by both alternating magnetic field in the perpendicular direction and DC background field in the parallel direction. In order to perform the boil-off measurement, we present the method to estimate the heat leakage in the cryostat which might cause errors to the measurement. © 2011 IEEE.

Half-bridge SIC inverter for hybrid electric vehicles: Design, development and testing at higher operating temperature

In recent years, Silicon Carbide (SiC) semiconductor devices have shown promise for high density power electronic applications, due to their electrical and thermal properties. In this paper, the performance of SiC JFETs for hybrid electric vehicle (HEV) applications is investigated at heatsink temperatures of 100 °C. The thermal runaway characteristics, maximum current density and packaging temperature limitations of the devices are considered and the efficiency implications discussed. To quantify the power density capabilities of power transistors, a novel 'expression of rating' (EoR) is proposed. A prototype single phase, half-bridge voltage source inverter using SiC JFETs is also tested and its performance at 25 °C and 100 °C investigated.

AC loss estimation of HTS armature windings for electric machines

This paper studies 2G high-temperature superconducting (HTS) coils for electric machine armature windings, using finite element method (FEM) and H formulation. A FEM model for 2G HTS racetrack coil is built in COMSOL, and is well validated by comparing calculated ac loss with experimental measurements. The FEM model is used to calculate transport loss in HTS armature windings, using air-cored design. We find that distributed winding used in conventional machine design is an effective way to reduce transport loss of HTS armature winding, in terms of air-cored design. Based on our study, we give suggestions on the design of low loss HTS armature winding. © 2002-2011 IEEE.

Hierarchical orientation of crystallinity by block-copolymer patterning and alignment in an electric field

Electron and hole conducting 10-nm-wide polymer morphologies hold great promise for organic electro-optical devices such as solar cells and light emitting diodes. The self-assembly of block-copolymers (BCPs) is often viewed as an efficient way to generate such materials. Here, a functional block copolymer that contains perylene bismide (PBI) side chains which can crystallize via π-π stacking to form an electron conducting microphase is patterned harnessing hierarchical electrohydrodynamic lithography (HEHL). HEHL film destabilization creates a hierarchical structure with three distinct length scales: (1) micrometer-sized polymer pillars, containing (2) a 10-nm BCP microphase morphology that is aligned perpendicular to the substrate surface and (3) on a molecular length scale (0.35-3 nm) PBI π-π-stacks traverse the HEHL-generated plugs in a continuous fashion. The good control over BCP and PBI alignment inside the generated vertical microstructures gives rise to liquid-crystal-like optical dichroism of the HEHL patterned films, and improves the electron conductivity across the film by 3 orders of magnitude. © 2013 American Chemical Society.

Off-wall boundary conditions for turbulent flows obtained from buffer-layer minimal flow units

There is strong evidence that the transport processes in the buffer region of wall-bounded turbulence are common across various flow configurations, even in the embryonic turbulence in transition (Park et al., Phys. Fl. 24). We use this premise to develop off-wall boundary conditions for turbulent simulations. Boundary conditions are constructed from DNS databases using periodic minimal flow units and reduced order modeling. The DNS data was taken from a channel at Reτ=400 and a zero-pressure gradient transitional boundary layer (Sayadi et al., submitted to J. Fluid Mech.). Both types of boundary conditions were first tested on a DNS of the core of the channel flow with the aim of extending their application to LES and to spatially evolving flows.