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.

Flame imaging of gas-turbine relight

High-altitude relight inside a lean-direct-injection gas-turbine combustor is investigated experimentally by highspeed imaging. Realistic operating conditions are simulated in a ground-based test facility, with two conditions being studied: one inside and one outside the combustor ignition loop. The motion of hot gases during the early stages of relight is recorded using a high-speed camera. An algorithm is developed to track the flame movement and breakup, revealing important characteristics of the flame development process, including stabilization timescales, spatial trajectories, and typical velocities of hot gas motion. Although the observed patterns of ignition failure are in broad agreement with results from laboratory-scale studies, other aspects of relight behavior are not reproduced in laboratory experiments employing simplified flow geometries and operating conditions. For example, when the spark discharge occurs, the air velocity below the igniter in a real combustor is much less strongly correlated to ignition outcome than laboratory studies would suggest. Nevertheless, later flame development and stabilization are largely controlled by the cold flowfield, implying that the location of the igniter may, in the first instance, be selected based on the combustor cold flow. Copyright © 2010.

Baroclinic waves in an air-filled thermally driven rotating annulus.

In this study an experimental investigation of baroclinic waves in air in a differentially heated rotating annulus is presented. Air has a Prandtl number of 0.707, which falls within a previously unexplored region of parameter space for baroclinic instability. The flow regimes encountered include steady waves, periodic amplitude vacillations, modulated amplitude vacillations, and either monochromatic or mixed wave number weak waves, the latter being characterized by having amplitudes less than 5% of the applied temperature contrast. The distribution of these flow regimes in parameter space are presented in a regime diagram. It was found that the progression of transitions between different regimes is, as predicted by recent numerical modeling results, in the opposite sense to that usually found in experiments with high Prandtl number liquids. No hysteresis in the flow type, with respect to variations in the rotation rate, was found in this investigation.

Synchronization of modulated traveling baroclinic waves in a periodically forced, rotating fluid annulus.

Frequency entrainment and nonlinear synchronization are commonly observed between simple oscillatory systems, but their occurrence and behavior in continuum fluid systems are much less well understood. Motivated by possible applications to geophysical fluid systems, such as in atmospheric circulation and climate dynamics, we have carried out an experimental study of the interaction of fully developed baroclinic instability in a differentially heated, rotating fluid annulus with an externally imposed periodic modulation of the thermal boundary conditions. In quasiperiodic and chaotic amplitude-modulated traveling wave regimes, the results demonstrate a strong interaction between the natural periodic modulation of the wave amplitude and the externally imposed forcing. This leads to partial or complete phase synchronization. Synchronization effects were observed even with very weak amplitudes of forcing, and were found with both 1:1 and 1:2 frequency ratios between forcing and natural oscillations.

Synchronization in a pair of thermally coupled rotating baroclinic annuli: understanding atmospheric teleconnections in the laboratory.

Synchronization phenomena in a fluid dynamical analogue of atmospheric circulation is studied experimentally by investigating the dynamics of a pair of thermally coupled, rotating baroclinic annulus systems. The coupling between the systems is in the well-known master-slave configuration in both periodic and chaotic regimes. Synchronization tools such as phase dynamics analysis are used to study the dynamics of the coupled system and demonstrate phase synchronization and imperfect phase synchronization, depending upon the coupling strength and parameter mismatch.