Performance analysis of a parallel, multi-node pipeline for DNA sequencing

Post-sequencing DNA analysis typically consists of read mapping followed by variant calling and is very time-consuming, even on a multi-core machine. Recently, we proposed Halvade, a parallel, multi-node implementation of a DNA sequencing pipeline according to the GATK Best Practices recommendations. The MapReduce programming model is used to distribute the workload among different workers. In this paper, we study the impact of different hardware configurations on the performance of Halvade. Benchmarks indicate that especially the lack of good multithreading capabilities in the existing tools (BWA, SAMtools, Picard, GATK) cause suboptimal scaling behavior. We demonstrate that it is possible to circumvent this bottleneck by using multiprocessing on high-memory machines rather than using multithreading. Using a 15-node cluster with 360 CPU cores in total, this results in a runtime of 1 h 31 min. Compared to a single-threaded runtime of similar to 12 days, this corresponds to an overall parallel efficiency of 53%

Bubble formation in ϕ6\phi^6 potential

Scalar field theory with an asymmetric potential is studied at zero temperature and high-temperature for $\phi^6$ potential. The equations of motion are solved numerically to obtain O(4) spherical symmetric and O(3) cylindrical symmetric bounce solutions. These solutions control the rates for tunneling from the false vacuum to the true vacuum by bubble formation. The range of validity of the thin-wall approximation (TWA) is investigated. An analytical solution for the bounce is presented, which reproduces the action in the thin-wall as well as the thick-wall limits.Comment: 22 pag

The European Network for Translational Research in Atrial Fibrillation (EUTRAF): objectives and initial results.

Atrial fibrillation (AF) is the most common sustained arrhythmia in the general population. As an age-related arrhythmia AF is becoming a huge socio-economic burden for European healthcare systems. Despite significant progress in our understanding of the pathophysiology of AF, therapeutic strategies for AF have not changed substantially and the major challenges in the management of AF are still unmet. This lack of progress may be related to the multifactorial pathogenesis of atrial remodelling and AF that hampers the identification of causative pathophysiological alterations in individual patients. Also, again new mechanisms have been identified and the relative contribution of these mechanisms still has to be established. In November 2010, the European Union launched the large collaborative project EUTRAF (European Network of Translational Research in Atrial Fibrillation) to address these challenges. The main aims of EUTRAF are to study the main mechanisms of initiation and perpetuation of AF, to identify the molecular alterations underlying atrial remodelling, to develop markers allowing to monitor this processes, and suggest strategies to treat AF based on insights in newly defined disease mechanisms. This article reports on the objectives, the structure, and initial results of this network

How musical selection impacts the performance of the interaction with the computer

In this busy society of ours people push their limits to work better and more in order to remain competitive with their peers. Nonetheless, working longer hours does not necessarily improves productivity nor performance. In order to prevent the negative consequences of this increasing trend, the evolution of performance throughout the day of work should be more closely monitored. This could avoid undesirable states or even breakdowns, which have social and economical implications. In this work we measure user performance through their interaction with the computer. We monitor its evolution during a day of work and how di erent types of music may increase or decrease its natural daily degradation. We conclude that the relationship between types of music and its e ects is not universal and depends, among other things, on the musical pro le of the individual. A prototype for a distributed music recommendation service is presented that suggests musics at an individual and group level, based on user musical pro les and objectives.This work is part-funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124-FEDER-028980 (PTDC/EEI-SII/1386/2012)

Tailoring the pressure-drop in multi-layered open-cell porous inconel structures

This study investigates the pressure-drop behaviour associated with airflow through bulk and structurally tailored multi-layered, open-cell porous Inconel structures over a wide airflow velocity range (0–50 m s-1). The effect of airflow velocity on the pressure-drop behaviour as a function of the sample thickness is presented and related to the flow behaviour corresponding to the relevant flow regimes (Darcy, Forchheimer, Turbulent and Postturbulent). Entrance effects are highlighted as a source of the pressure-drop increase for porous structures with air gaps, regardless of their sizes, as long as they are larger than those generated by loosely-stacked structures. The pressure-drops for gapped porous structures and the mathematical-summation of the pressure drop for the corresponding individual components, were in very good agreement, at lower airflow velocities. The potential for mass-efficient porous structures, providing a high pressure drop, was demonstrated using multiple thin porous laminates separated by air gaps

A Light Sterile Neutrino in the TopFlavor Model

A scenario based on the TopFlavor model is presented to explain the origin of a light sterile neutrino as indicated by all combined neutrino oscillation experiments. The model is phenomenologically well motivated and compatible with all available low-energy data. The derived nuetrino mass matrix can qualitatively explain the observed hierarchy in the neutrino mass splittings as indicated by the neutrino oscillation data. Numerical results are obtained for special cases.Comment: Plain Latex file, 12 page

Experimental investigation of pressure-drop characteristics across multi-layer porous metal structures

This study investigates the effect of airflow (in the range of 0–70 m s-1) on the pressure-drop characteristics for a novel multi-layered, nickel-based porous metal, as a function of thickness (affected by sectioning) and density (affected by compression). In addition to generating unique data for these materials, the study highlights the need for precise pinpointing of the different flow regimes (Darcy, Forchheimer and Turbulent) in order to enable accurate determination of the permeability (K) and form drag coefficient (C) defined by the Forchheimer equation and to understand the complex dependence of length-normalised pressure drop on sample thickness

Clinical use of Whole Genome Sequencing for Mycobacterium tuberculosis

Drug resistant tuberculosis (TB) remains a major challenge to global health and to healthcare in the UK. In 2014, England recorded 6520 cases of TB of which 1.4% were multi-drug resistant (MDR-TB). Extensively drug resistant TB (XDR-TB) occurs at a much lower rate, but the impact on the patient and hospital is severe. Current diagnostic methods such as drug susceptibility testing and targeted molecular tests are slow to return or examine only a limited number of target regions respectively. Faster, more comprehensive diagnostics will enable earlier use of the most appropriate drug regimen thus improving patient outcome and reducing overall healthcare costs. Whole genome sequencing has been shown to provide a rapid and comprehensive view of the genotype of the organism and thus enable reliable prediction of the drug susceptibility phenotype within a clinically relevant time frame. In addition it provides the highest resolution when investigating transmission events in possible outbreak scenarios. However, robust software and database tools need to be developed for the full potential to be realized in this specialized area of medicine

Spherical Harmonics - Finite Element Treatment of Neutron Transport in Cylindrical Geometry

A variational spherical harmonics (DPN) method is used in conjunction with the finite element method to solve the transport of neutron beams. The method is developed for finite axisymmetric cylindrical geometry. In this model, the angular distribution along the path of neutron travel is separated into two sub-ranges of the forward and the backward moving particles. The system of the model equations is cast in terms of an even and an odd vector analogue to the even-parity transport technique. The finite element method is applied in space to solve the resulting coupled system of equations. A source-free cylinder with specified incident flux on the z = 0 surface is considered in this study. The model is based on the DP1 and DP3 orders of expansion. The study demonstrates the advantages of the DPN method in accounting for the discontinuity of the angular flux in the direction of particles with no approximation. Results for the scalar flux are presented in isodose curve (contour) form for homogeneous and non-homogeneous media with different absorbing and purely scattering media. Numerical results compared favorably with those obtained by the exact solutions. © 1997 Elsevier Science Ltd. All rights reserved