Search

MotivationThe recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research lab and into the front lines of surveillance and outbreak response requires user-friendly, reproducible, and scalable pipelines that have been well validated.ResultsSNVPhyl (Single Nucleotide Variant Phylogenomics) is a bioinformatics pipeline for identifying high-quality SNVs and constructing a whole genome phylogeny from a collection of WGS reads and a reference genome. Individual pipeline components are integrated into the Galaxy bioinformatics framework, enabling data analysis in a user-friendly, reproducible, and scalable environment. We show that SNVPhyl can detect SNVs with high sensitivity and specificity and identify and remove regions of high SNV density (indicative of recombination). SNVPhyl is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds, or in the presence of contamination.AvailabilitySNVPhyl is available as a Galaxy workflow, Docker and virtual machine images, and a Unix-based command-line application. SNVPhyl is released under the Apache 2.0 license and available at http://snvphyl.readthedocs.io/ or at https://github.com/phac-nml/snvphyl-galaxy.

The paper describes e2v technologies' successful development of the MPT583x series of solid-state modulators. These offer superior performance with good pulse fidelity and many safety features to give a long system life. The paper covers the choice of switch element and configuration, identifies the technical problems we encountered along the way, and what we have done to overcome them. The resulting modulator series is exceptionally robust and reliable. Finally future developments are touched upon.

The paper describes the MPT5838/9, a successful development and commercial application of pulsed RF power manifested in a solid state modulator and magnetron as an RF source at a sub system level. The design is rated at 55 kV peak pulse amplitude at 250 A peak current with 10 kW mean power continuous operation driving high power magnetrons with output RF power of up to 5MW peak and 4 kW mean. It is based substantially on the FET- based solid-state direct-switched repetitive pulse modulator developed in the early part of the 21st century (Ref ). We highlight the key technical challenges addressed during the development, including performance issues, fault handling, and control of a compact solid state modulator. (4 pages)

Active modulators using pulse transformers are an option for pulsing magnetrons. In this context, active implies a single or a number of paralleled or a number of series connected or a series/parallel combination of semiconductor switches used to pulse a magnetron via a step up pulse transformer. The pulse is delivered by a large capacitor bank (pulse energy is very much less than the capacitor stored energy) and the switches must be of a type that can be turned both on and off such as MOSFETs or IGBTs. A problem can arise because of the biased diode nature of the magnetron load (typically a magnetron that works at 20 kV/20 A will draw very little current at 16 kV, ref figure 1). Thus when the active switches are turned off the current pulse in the magnetron is terminated. The stray capacitance on the output of the pulse transformer however remains charged to almost full voltage. This can give rise to a complex series of events which can damage the active switches. This paper will carefully define the problem and describe a solution.