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.

Improving model quality through computer controlled saturation

In dynamic centrifuge modelling, fluids with enhanced viscosity are often used to correct for the discrepancy in time scaling. However, great care must be taken when using a high viscosity fluid that hydraulic gradients during saturation do not become high enough to cause excessive model disturbance. This paper introduces the CAM-Sat system which aims to improve the saturation process by continually controlling the fluid flow into the model, limiting it to rates low enough to avoid model disturbance. A new method for measuring the fluid flow rate is then described, and its implementation & improvement to the system is discussed. © 2010 Taylor & Francis Group, London.

A computer algorithm for determining the tensile strength of float glass

The extrinsic tensile strength of glass can be determined explicitly if the characteristics of the critical surface flaw are known, or stochastically if the critical flaw characteristics are unknown. This paper makes contributions to both these approaches. Firstly it presents a unified model for determining the strength of glass explicitly, by accounting for both the inert strength limit and the sub-critical crack growth threshold. Secondly, it describes and illustrates the use of a numerical algorithm, based on the stochastic approach, that computes the characteristic tensile strength of float glass by piecewise summation of the surface stresses. The experimental validation and sensitivity analysis reported in this paper show that the proposed computer algorithm provides an accurate and efficient means of determining the characteristic strength of float glass. The algorithm is particularly useful for annealed and thermally treated float glass used in the construction industry. © 2012 Elsevier Ltd.

Computer Vision and Pattern Recognition Technologies for Construction

This book will be of particular interest to academics, researchers, and graduate students at universities and industrial practitioners seeking to apply mobile and pervasive computing systems to improve construction industry productivity.

A Computer integrated unified modelling approach to responsive manufacturing

Computer modelling approaches have significant potential to enable decision-making about various aspects of responsive manufacturing. In order to understand the system prior to the selection of any responsiveness strategy, multiple process segments of organisations need to be modelled. The article presents a novel systematic approach for creating coherent sets of unified enterprise, simulation and other supporting models that collectively facilitate responsiveness. In this approach, enterprise models are used to explicitly define relatively enduring relationships between (i) production planning and control (PPC) processes, that implement a particular strategy and (ii) process-oriented elements of production systems, that are work loaded by the PPC processes. Coherent simulation models, can in part be derived from the enterprise models, so that they computer execute production system behaviours. In this way, time-based performance outcomes can be simulated; so that the impacts of alternative PPC strategies on the planning and controlling historical or forecasted patterns of workflow, through (current and possible future) production system models, can be analysed. The article describes the unified modelling approach conceived and its application in a furniture industry case study small and medium enterprise (SME). Copyright © 2010 Inderscience Enterprises Ltd.