A computationally efficient software application for calculating vibration from underground railways

The PiP model is a software application with a user-friendly interface for calculating vibration from underground railways. This paper reports about the software with a focus on its latest version and the plans for future developments. The software calculates the Power Spectral Density of vibration due to a moving train on floating-slab track with track irregularity described by typical values of spectra for tracks with good, average and bad conditions. The latest version accounts for a tunnel embedded in a half space by employing a toolbox developed at K.U. Leuven which calculates Green's functions for a multi-layered half-space. © 2009 IOP Publishing Ltd.

Security considerations in the design and peering of RFID discovery services

There is growing interest in Discovery Services for locating RFID and supply chain data between companies globally, to obtain product lifecycle information for individual objects. Discovery Services are heralded as a means to find serial-level data from previously unknown parties, however more realistically they provide a means to reduce the communications load on the information services, the network and the requesting client application. Attempts to design a standardised Discovery Service will not succeed unless security is considered in every aspect of the design. In this paper we clearly show that security cannot be bolted-on in the form of access control, although this is also required. The basic communication model of the Discovery Service critically affects who shares what data with whom, and what level of trust is required between the interacting parties. © 2009 IEEE.

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