Analysis of case histories on deep excavations in marine clay

Two case histories on deep excavation of marine clay are used to study the use of a decision-making tool based on a new deign method called the Mobilized Strength Design (MSD) method which allows the designer to use a simple method of predicting ground displacements during deep excavation. This application can approximately satisfy both safety and serviceability requirements by predicting stresses and displacements under working conditions by introducing the concept of "Mobilizable soil strength". The new method accommodates a number of features which are important to design of underground construction between retaining walls, including different deformation mechanism in different stages of excavation. The influence of wall depth, wall flexibility and stratified ground are the major focus of this paper. These developments should make it possible for a design engineer to take informed decisions on the influence of wall stiffness, or on the need for a jet-grouted base slab, for example, without having to conduct project-specific Finite Element Analysis.

Supporting excavations in clay - From analysis to decision-making

Finite Element Analysis (FEA) is used to calibrate a decision-making tool based on an extension of the Mobilized Strength Design (MSD) method which permits the designer an extremely simple method of predicting ground displacements during construction. This newly extended MSD approach accommodates a number of issues which are important in underground construction between in-situ walls, including: alternative base heave mechanisms suitable either for wide excavations in relatively shallow soft clay strata, or narrow excavations in relatively deep soft strata; the influence of support system stiffness in relation to the sequence of propping of the wall; and the capability of dealing with stratified ground. These developments should make it possible for a design engineer to take informed decisions on the relationship between prop spacing and ground movements, or the influence of wall stiffness, or on the need for and influence of a jet-grouted base slab, for example, without having to conduct project-specific FEA. © 2009 Taylor & Francis Group.

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.