Soft windowing application to improve analysis of high-throughput phenotyping data.

MOTIVATION: High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximizes analytic power while minimizing noise from unspecified environmental factors. RESULTS: Here we introduce \u27soft windowing\u27, a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant P-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft-windowed and non-windowed approaches, respectively, from a set of 2082 mutant mouse lines. Our method is generalizable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources. AVAILABILITY AND IMPLEMENTATION: The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Use of the method of manufactured solutions for the verification of conjugate heat transfer solvers

This paper demonstrates the use of the method of manufactured solutions to verify the implementation of tightly coupled conjugate heat transfer for fluid–solid solvers. The interface conditions in the prescribed manufactured solutions were implemented to mimic real effects such as no-slip, and temperature/heat flux match between the solid and fluid domains. The newly developed solid heat transfer solver was verified in standalone mode using this prescribed manufactured solution and was found to have no apparent coding errors. Our pre-existing in-house compressible fluid solver (Eilmer) was used to demonstrate the conjugate heat transfer implementation. Both the fluid and solid solvers showed an expected spatial order of convergence of 2.0 in the standalone mode. The coupled conjugate heat transfer mode also showed no coding errors and demonstrated that the spatial order of convergence was again 2.0. The one-sided spatial discretisation utilised to enforce the tight coupling for the interface conditions were effectively equivalent to a central difference. Hence, the overall spatial order of the error convergence for the entire domain, including the interface, was 2.0. The method prescribed in this work can be extended for verification of other conjugate heat transfer solvers, in particular for compressible flow scenarios where analytical solutions may not be readily available

Metallic mesh and quartz wafer as emitter-filter for a thermophotovoltaic system

The use of metallic meshes as radiative material in a mesoscale combustor and thermophotovoltaic (TPV) system for power generation is investigated. A previous study showed promising results combining a silicon carbide (SiC) foam porous material as a radiator, and quartz wafers as optical filters. High temperature metallic meshes have a similar emissivity in the usable wavelength region for the TPV system. In addition, these present a clear advantage over SiC foams in terms of availability and cost. The previous study focusing in the SiC foam has been extended using two different thread count Kanthal meshes, also featuring different surface treatments. The results show higher achievable power with similar values of efficiency to the SiC cases. Moreover, the spatial discontinuities of the metallic mesh allow to stabilize the flame at different combustor heights independently of fuel-air mixture velocity. The effect of the flame location on power and efficiency has been assessed. The ideal flame location and importance of TPV placement with respect to the flame is described

On the effect of workload ordering for reacting flow simulations using GPUs

In reacting flow simulations, considerable computational effort is spent on updating the change of composition due to chemical reactions. As a means of accelerating the simulation of reacting flows, we have been investigating the use of graphics processing units (GPUs) to compute the chemistry update in a massively parallel manner. We have some evidence from previous work that our use of the GPU is less than optimal because of imbalances in the workload that is sent to the GPU. In the present work, we implement several new strategies to better order the workload of chemistry updates that are processed by the GPU and test the performance of these strategies. The results show that we can achieve a speed-up of 1.4x for a particular flow case with hydrogen/ oygen combustion when using a GPU accelerator. The results also show that the performance of the GPU accelerator is insensitive to the workload odering

Verification of RANS turbulence model in Eilmer using the Method of Manufactured Solutions

This paper presents the verification study of a ReynoldsAveraged Navier-Stokes (RANS) turbulence model using the Method of Manufactured Solutions (MMS) in a finite volume Computational Fluid Dynamics (CFD) code. The Eilmer CFD code is an open-source fluid solver which solves the compressible Navier-Stokes equations to provide time-accurate simulations of compressible flows in two and three dimensions. The turbulence model verified is Wilcox’s (2006) k −ω model. The turbulence model implementation is verified through the order of accuracy test. An expected spatial order of accuracy of 2 is demonstrated with mesh refinement, matching the formal order of Eilmer numerics. The verification process significantly facilitated the detection and removal of coding mistakes in our implementation. We also provide discussion of coding mistakes that were identified and corrected as part of our verification exercise

Suppression of instabilities in a premixed methane–air flame in a narrow channel via hydrogen/carbon monoxide addition

The effects of hydrogen and carbon monoxide addition on premixed methane/air flame dynamics in a heated narrow channel are numerically investigated using a time accurate, compressible flow solver along with the DRM-19 reaction mechanism. By adding a small amount of either H or CO, flame instabilities present for the pure CH/air combustion in the form of flame-extinction and re-ignition could be effectively suppressed. This suppression can be attributed to a few important elementary reactions, that play a dominant role in contributing to the heat release rate, getting enhanced with H or CO addition. This leads to a higher flame propagation speed and a shorter flame-extinction period, and eventually leads to flame stabilisation after a few cycles of spatial oscillations

On the effect of outflow boundary truncation for numerical simulation of narrow-channel flames

Premixed methane/air flame propagation in a two-dimensional, planar micro-channel is modelled by solving the transient, full Navier–Stokes equations with the reaction mechanism DRM- 19 using our in-house code (Eilmer). Effects of two different outflow boundary treatments, i.e. applying an outflow boundary truncation and using a domain-extension joining the combustor outlet are investigated, for both steady-state flames and periodically oscillating flames. It is found that the use of a domain truncation/extension mainly influences the acoustic wave damping time at the initial stage when the flame is initiated. For the steady-state flame case, there is no noticeable difference in final solutions between two outflow treatments. For the spatially oscillating flames, the characteristics in terms of the oscillation frequency and amplitude are slightly but not significantly affected when the flame settles into a consistent oscillatory pattern