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.

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.

Enhanced robotic body extension with modular units

The adaptation of robots to changing tasks has been explored in modular self-reconfigurable robot research, where the robot structure is altered by adapting the connectivity of its constituent modules. As these modules are generally complex and large, an upper bound is imposed on the resolution of the built structures. Inspired by growth of plants or animals, robotic body extension (RBE) based on hot melt adhesives allows a robot to additively fabricate and assemble tools, and integrate them into its own body. This enables the robot to achieve tasks which it could not achieve otherwise. The RBE tools are constructed from hot melt adhesives and therefore generally small and only passive. In this paper, we seek to show physical extension of a robotic system in the order of magnitude of the robot, with actuation of integrated body parts, while maintaining the ability of RBE to construct parts with high resolution. Therefore, we present an enhancement of RBE based on hot melt adhesives with modular units, combining the flexibility of RBE with the advantages of simple modular units. We explain the concept of this new approach and demonstrate with two simple unit types, one fully passive and the other containing a single motor, how the physical range of a robot arm can be extended and additional actuation can be added to the robot body. © 2012 IEEE.