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.

Safety implications of reactivity variations in fast thorium ADSRs

Nuclear power generation offers a reliable, low-impact and large-scale alternative to fossil fuels. However, concerns exist over the safety and sustainability of this method of power production, and it remains unpopular with some governments and pressure groups throughout the world. Fast thorium fuelled accelerator-driven sub-critical reactors (ADSRs) offer a possible route to providing further re-assurance regarding these concerns on account of their properties of enhanced safety through sub-critical operation combined with reduced actinide waste production from the thorium fuel source. The appropriate sub-critical margin at which these reactors should operate is the subject of continued debate. Commercial interests favour a small sub-critical margin in order to minimise the size of the accelerator needed for a given power output, whilst enhanced safety would be better satisfied through larger sub-critical margins to further minimise the possibility of a criticality excursion. Against this background, this paper examines some of the issues affecting reactor safety inherent within thorium fuel sources resulting from the essential Th90232→Th90233→Pa91233→U92233 breeding chain. Differences in the decay half-lives and fission and capture cross-sections of 233Pa and 233U can result in significant changes in the reactivity of the fuel following changes in the reactor power. Reactor operation is represented using a homogeneous lumped fast reactor model that can simulate the evolution of actinides and reactivity variations to first-order accuracy. The reactivity of the fuel is shown to increase significantly following a loss of power to the accelerator. Where the sub-critical operating margins are small this can result in a criticality excursion unless some form of additional intervention is made, for example through the insertion of control rods. © 2012 Elsevier Ltd. All rights reserved.

A new apparatus for modelling excavations

Underground space is commonly exploited both to maximise the utility of costly land in urban development and to reduce the vertical load acting on the ground. Deep excavations are carried out to construct various types of underground infrastructure such as deep basements, subways and service tunnels. Although the soil response to excavation is known in principle, designers lack practical calculation methods for predicting both short- and long-term ground movements. As the understanding of how soil behaves around an excavation in both the short and long term is insufficient and usually empirical, the judgements used in design are also empirical and serious accidents are common. To gain a better understanding of the mechanisms involved in soil excavation, a new apparatus for the centrifuge model testing of deep excavations in soft clay has been developed. This apparatus simulates the field construction sequence of a multi-propped retaining wall during centrifuge flight. A comparison is given between the new technique and the previously used method of draining heavy fluid to simulate excavation in a centrifuge model. The new system has the benefit of giving the correct initial ground conditions before excavation and the proper earth pressure distribution on the retaining structures during excavation, whereas heavy fluid only gives an earth pressure coefficient of unity and is unable to capture any changes in the earth pressure coefficient of soil inside the zone of excavation, for example owing to wall movements. Settlements of the ground surface, changes in pore water pressure, variations in earth pressure, prop forces and bending moments in the retaining wall are all monitored during excavation. Furthermore, digital images taken of a cross-section during the test are analysed using particle image velocimetry to illustrate ground deformation and soil-structure interaction mechanisms. The significance of these observations is discussed.

Product scheduling for thermal energy reduction in papermaking industries

Papermaking is considered as an energy-intensive industry partly due to the fact that the machinery and procedures have been designed at the time when energy was both cheap and plentiful. A typical paper machine manufactures a variety of different products (grades) which impose variable per-unit raw material and energy costs to the mill. It is known that during a grade change operation the products are not market-worthy. Therefore, two different production regimes, i.e. steady state and grade transition can be recognised in papermaking practice. Among the costs associated with paper manufacture, the energy cost is 'more variable' due to (usually) day-to-day variations of the energy prices. Moreover, the production of a grade is often constrained by customer delivery time requirements. Given the above constraints and production modes, the product scheduling technique proposed in this paper aims at optimising the sequence of orders in a single machine so that the cost of production (mainly determined by the energy) is minimised. Simulation results obtained from a commercial board machine in the UK confirm the effectiveness of the proposed method. © 2011 IFAC.

Development of a new apparatus for modeling deep excavation related problems in geotechnical centrifuge

Underground space is commonly exploited both to maximise the utility of costly land in urban development and to reduce the vertical load acting on the ground. Deep excavations are carried out to construct various types of underground infrastructure such as deep basements, subways and service tunnels. Although the soil response to excavation is known in principle, designers lack practical calculation methods for predicting both short- and long-term ground movements. As the understanding of how soil behaves around an excavation in both the short and long term is insufficient and usually empirical, the judgements used in design are also empirical and serious accidents are common. To gain a better understanding of the mechanisms involved in soil excavation, a new apparatus for the centrifuge model testing of deep excavations in soft clay has been developed. This apparatus simulates the field construction sequence of a multi-propped retaining wall during centrifuge flight. A comparison is given between the new technique and the previously used method of draining heavy fluid to simulate excavation in a centrifuge model. The new system has the benefit of giving the correct initial ground conditions before excavation and the proper earth pressure distribution on the retaining structures during excavation, whereas heavy fluid only gives an earth pressure coefficient of unity and is unable to capture any changes in the earth pressure coefficient of soil inside the zone of excavation, for example owing to wall movements. Settlements of the ground surface, changes in pore water pressure, variations in earth pressure, prop forces and bending moments in the retaining wall are all monitored during excavation. Furthermore, digital images taken of a cross-section during the test are analysed using particle image velocimetry to illustrate ground deformation and soil–structure interaction mechanisms. The significance of these observations is discussed.

Modeling of SFR cores with Serpent-DYN3D codes sequence

DYN3D reactor dynamics nodal diffusion code was originally developed for the analysis of Light Water Reactors. In this paper, we demonstrate the feasibility of using DYN3D for modeling of fast spectrum reactors. A homogenized cross sections data library was generated using continuous energy Monte-Carlo code Serpent which provides significant modeling flexibility compared with traditional deterministic lattice transport codes and tolerable execution time. A representative sodium cooled fast reactor core was modeled with the Serpent-DYN3D code sequence and the results were compared with those produced by ERANOS code and with a 3D full core Monte-Carlo solution. Very good agreement between the codes was observed for the core integral parameters and power distribution suggesting that the DYN3D code with cross section library generated using Serpent can be reliably used for the analysis of fast reactors. © 2012 Elsevier Ltd. All rights reserved.

Characterization of light and heavy hydrated magnesium carbonates using thermal analysis

Upon heating, hydrated magnesium carbonates (HMCs) undergo a continuous sequence of decomposition reactions. This study aims to investigate the thermal decomposition of various commercially produced HMCs classified as light and heavy, highlight their differences, and provide an insight into their compositions in accordance with the results obtained from thermal analysis and microstructure studies. An understanding of the chemical compositions and microstructures, and a better knowledge of the reactions that take place during the decomposition of HMCs were achieved through the use of SEM, XRD, and TG/differential thermal analysis (DTA). The quantification of their CO 2 contents was provided by TG and dissolving the samples in HCl acid. Results show that variations exist within the microstructure and decomposition patterns of the two groups of HMCs, which do not exactly fit into the fixed stoichiometry of the known HMCs in the MgO-CO2-H2O system. The occurrence of an exothermic DTA peak was only observed for the heavy HMCs, which was attributed to their high CO2 contents and the relatively delayed decomposition pattern. © 2013 Akadémiai Kiadó, Budapest, Hungary.

Numerical study of the impact of process variations on the motional resistance of weakly coupled MEMS resonators

This paper presents a numerical study of the impact of process-induced variations on the achievable motional resistance Rx of one-dimensional, cyclic and cross-coupled architectures of electrostatically transduced MEMS resonators operating in the 250 kHz range. Monte Carlo numerical simulations which accounted for up to 0.75% variation in critical resonator feature sizes were initiated on 1, 2, 3, 4, 5 and 9 coupled MEMS resonators for three distinct coupling architectures. Improvements of 100X in the spread of Rx and 2.7X in mean achievable Rx are reported for the case of 9 resonators when implemented in the cross-coupled topology, as opposed to the traditional one-dimensional chain. © 2013 IEEE.