Background: Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.Results: Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb). Conclusions:HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito's largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.

Natural hazards engineering plays an important role in minimizing the effects of natural hazards 9 on society through the design of resilient and sustainable infrastructure. The DesignSafe 10 cyberinfrastructure has been developed to enable and facilitate transformative research in natural 11 hazards engineering, which necessarily spans across multiple disciplines and can take advantage 12 of advancements in computation, experimentation, and data analysis. DesignSafe allows researchers to more effectively share and find data using cloud services, perform numerical 14 simulations using high performance computing, and integrate diverse datasets such that researchers can make discoveries that were previously unattainable. This paper describes the design principles used in the cyberinfrastructure development process, introduces the main components of the DesignSafe cyberinfrastructure, and illustrates the use of the DesignSafe cyberinfrastructure in research in natural hazards engineering through various examples.

Jetstream will be the first production cloud resource supporting general science and engineering research within the XD ecosystem. In this report we describe the motivation for proposing Jetstream, the configuration of the Jetstream system as funded by the NSF, the team that is implementing Jetstream, and the communities we expect to use this new system. Our hope and plan is that Jetstream, which will become available for production use in 2016, will aid thousands of researchers who need modest amounts of computing power interactively. The implementation of Jetstream should increase the size and disciplinary diversity of the US research community that makes use of the resources of the XD ecosystem.

We have investigated the lateral thermal oxidation of AlAs in water vapor in vertical cavity surface emitting laser structures. At low temperatures and short oxidation times, oxide growth was found to be reaction rate limited. Conversely, diffusion across the oxide was the rate controlling mechanism at higher temperatures and longer oxidation times. Lasers are typically processed at intermediate values of temperatures and time. The observed growth can be modeled by rate equations by which the two component growth mechanisms can be separated. Activation energies of 1.6 and 0.8 eV were determined for the reaction rate and diffusion limited mechanisms, respectively.

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