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1,456 results for “parallelism”
Files and plotting scripts for "Parallel tridiagonal matrix inversion with a hybrid multigrid--Thomas algorithm method"
<p>This archive contains the files required to reproduce the results and figures presented in <em>Parallel tridiagonal matrix inversion with a hybrid multigrid--Thomas algorithm method</em>, J. T. Parker, P. A. Hill, D. Dickinson and B. D. Dudson.</p> <p>Also available at the repository: https://gitlab.com/JosephThomasParker/files-and-plotting-scripts-for-parallel-tridiagonal-matrix-inversion-with-a-hybrid-multigrid-thomas-algorithm-method/</p> <p>Questions to joseph.parker@ukaea.uk.</p> <p>This version is before submission to journal.</p>
Parallel CUHRE regions for Genz 1abs in 5 dimensions
<p>Parallel CUHRE algorithm performance data from the Genz 1 function, absolute value, in 5 dimensions. The integrand is: $$ | \cos(4 v +5 w + 6 x +7 y + 8 z)/k |$$, with k = 0s .6371054. This integrand is only approximately normalized.</p> <p> </p> <p>These data were colllected with an uncertain version of the parallel algorithm.</p>
Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
<p>Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-reared <em>Bombus vosnesenskii</em> workers. We analyze bees reared from latitudinal (35.7–45.7°N) and altitudinal (7–2154 m) extremes of the species' range to correlate thermal tolerance and gene expression among populations from different climates. We find that critical thermal minima (CT<sub>MIN</sub>) exhibit strong associations with local minimums at the location of queen origin, while critical thermal maximum (CT<sub>MAX</sub>) was invariant among populations. Concordant patterns are apparent in gene expression data, with regional differentiation following cold exposure, and expression shifts invariant among populations under high temperatures. Furthermore, we identify several modules of co-expressed genes that tightly correlate with critical thermal limits and temperature at the region of origin. Our results reveal that local adaptation in thermal limits and gene expression may facilitate cold tolerance across a species range, whereas high temperature responses are likely constrained, both of which may have implications for climate change responses of bumble bees.</p>
Robustness of massively parallel sequencing platforms
<p>The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications. </p>
NIMROD growth rates (1/s) by finite element poly_degree (columns) and case from "The Impact of Collisionality, FLR and Parallel Closure Effects on Instabilities in the Tomakak Pedestal: Numerical Studies with the NIMROD code”
<p>NIMROD growth rates (1/s) by finite element poly_degree (columns) and case from "The Impact of Collisionality, FLR and Parallel Closure Effects on Instabilities in the Tomakak Pedestal: Numerical Studies with the NIMROD code” as submitted to Physics of Plasmas</p>
RPL: a domain-specific language for designing and implementing parallel C++ applications
<p>Parallelising sequential applications is usually a very hard job, due to many different ways in which an application can be parallelised and a large number of programming models (each with its own advantages and disadvantages) that can be used. In this paper, we describe a method to semi-automatically generate and evaluate different parallelisations of the same application, allowing programmers to find the best parallelisation without significant manual reengineering of the code. We describe a novel, high-level domain-specific language, Refactoring Pattern Language (RPL), that is used to represent the parallel structure of an application and to capture its extra-functional properties (such as service time). We then describe a set of RPL rewrite rules that can be used to generate alternative, but semantically equivalent, parallel structures (parallelisations) of the same application. We also describe the RPL Shell that can be used to evaluate these parallelisations, in terms of the desired extra-functional properties. Finally, we describe a set of C++ refactorings, targeting OpenMP, Intel TBB and FastFlow parallel programming models, that semi-automatically apply the desired parallelisation to the application's source code, therefore giving a parallel version of the code. We demonstrate how the RPL and the refactoring rules can be used to derive efficient parallelisations of two realistic C++ use cases (Image Convolution and Ant Colony Optimisation).</p>
Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking
<p>Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown. We generated high-frequency, genome-wide allele frequency data from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December, a period of ~12 generations. Adaptation throughout the fundamental ecological phases of population expansion, peak density, and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of allele frequency change to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveal fitness-relevance of standing variation that is likely to be masked by inference approaches based on static population sampling, or insufficiently resolved time-series data. We propose such fine-scaled temporally fluctuating selection may be an important force maintaining functional genetic variation in natural populations and an important stochastic force affecting levels of standing genetic variation genome-wide.</p>
Figure 2 in Parallel evolution in molar outline of murine rodents: the case of the extinct Malpaisomys insularis (Eastern Canary Islands)
Figure 2. Schematic representation of the modern and fossil murine rodents compared to Malpaisomys. Top, molecular phylogeny after Chevret (1994) and Chevret et al. (2001). A calibration of the time of divergence between taxa is given by reference to the divergence of the Rattus rattus lineage, estimated as having occurred 12 Mya (Chevret et al., 2001). The grey box includes the arvicanthine rodents, characterized by a herbivorous diet. Bottom, fossil lineages with investigated localities. Thick grey lines indicate taxa with stephanodont characteristics, thick black lines, complete stephanodonty. Crosses indicate extinct taxa.
Dataset: Exploring Techniques for the Analysis of Spontaneous Asynchronicity in MPI-Parallel Applications
<p>Dataset used in the paper "Exploring Techniques for the Analysis of Spontaneous Asynchronicity in MPI-Parallel Applications"</p>
Underlying dataset for battery pack degradation - Understanding aging in parallel-connected lithium-ion batteries under thermal gradients
<p>This record constitutes the raw data underlying the paper "<i>Battery pack degradation - Understanding aging in parallel-connected lithium-ion batteries under thermal gradients</i>" (<a href="https://www.researchsquare.com/article/rs-2535223/v1">preprint link</a>)</p><p>The dataset contains all raw data, processed data and analysis codes used to generate figures in the publication. Abstract is as follows:</p><blockquote><p>Practical lithium-ion battery systems require parallelisation of tens to hundreds of cells, however understanding of how pack-level thermal gradients influence lifetime performance remains a research gap. Here we present an experimental study of surface cooled parallel-string battery packs (temperature range 20-45 °C), and identify two main operational modes; convergent degradation with homogeneous temperatures, and (the more detrimental) divergent degradation driven by thermal gradients. We attribute the divergent case to the, often overlooked, cathode impedance growth. This was negatively correlated with temperature and can cause positive feedback where the impedance of cells in parallel diverge over time; increasing heterogeneous current and state-of-charge distributions. These conclusions are supported by current distribution measurements, decoupled impedance measurements and degradation mode analysis. From this, mechanistic explanations are proposed, alongside a publicly available aging dataset, which highlights the critical role of capturing cathode degradation in parallel-connected batteries; a key insight for battery pack developers.</p></blockquote>
Nupe-English Parallel Corpus
<p>This is the first ever Nupe - English Parallel Corpus and Nupe Monolingual Corpora curated from diverse sources including poems,idioms, proverbs, religpoius text etc. The aim of this data collection is to make available a cultural-aware Nupe-english corpus for NLP Tasks such as machine translation.</p>
Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales
<p>The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change.</p> <p>We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes.</p> <p>Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high <em>in</em> <em>situ</em> diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae.</p> <p>The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid <em>in</em> <em>situ</em> diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high <em>in</em> <em>situ</em><strong> </strong>diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.</p>
Text-fig. 3. Pinaceae, Taxaceae. a: Pinus needle fascicle with 3 needles, UAPC-ALTA S 25088A. b: Pinus needle fascicle with at least 4 needles, UAPC-ALTA S 59496. c: Articulate Pinus seed (section Diploxylon) showing seed body partly detached from wing, BBM-PAL-P000007. d: Winged pinaceous seed with elongate, flattened wing and narrow seed body, BBM-PAL-P000048. e: Another winged pinaceous seed with very narrow seed body, BBM-PAL-P000008. f: Amentotaxus leaf, UAPC-ALTA S S25086A. g: Higher magnification counterpart of (f) showing abaxial (lower) leaf surface with two parallel stomatal bands and tapered leaf tip S 25086B. h: Higher magnification of specimen in (f) showing adaxial (upper) leaf surface with detail of single midvein. Scale bars: a–e, g, h = 1 cm, f = 2 cm. in The Early Eocene Flora Of Horsefly, British Columbia, Canada And Its Phytogeographic Significance
Text-fig. 3. Pinaceae, Taxaceae. a: Pinus needle fascicle with 3 needles, UAPC-ALTA S 25088A. b: Pinus needle fascicle with at least 4 needles, UAPC-ALTA S 59496. c: Articulate Pinus seed (section Diploxylon) showing seed body partly detached from wing, BBM-PAL-P000007. d: Winged pinaceous seed with elongate, flattened wing and narrow seed body, BBM-PAL-P000048. e: Another winged pinaceous seed with very narrow seed body, BBM-PAL-P000008. f: Amentotaxus leaf, UAPC-ALTA S S25086A. g: Higher magnification counterpart of (f) showing abaxial (lower) leaf surface with two parallel stomatal bands and tapered leaf tip S 25086B. h: Higher magnification of specimen in (f) showing adaxial (upper) leaf surface with detail of single midvein. Scale bars: a–e, g, h = 1 cm, f = 2 cm.
Text-fig. 4. Monocots. a, b: Large monocot leaf part and counterpart, UAPC-ALTA S 17955A, B. a: Wide leaf showing entire margin at left. b: Counterpart showing dark wide midrib, and and secondaries parallel to one another, arising at low acute angle. c–e: Monocot leaf with parallel venation. c: Overview of elongate monocot leaf with parallel veins horizontal and linear to oval structures and smaller leaf fragment of same type lacking them (at lower right), UAPC-ALTA S 59491. d: Higher magnification of the smaller fragment with weak cross veins. e: Higher magnification of larger specimen with linear to oval structures between parallel veins. f, g: Monocot leaf with parallel venation. Fig. (f) shows higher magnification and (g) shows overview, BBM-PAL-P000009. Scale bars: a, b = 5 cm, c = 4 cm, d–f = 1 cm, g = 2 cm. in The Early Eocene Flora Of Horsefly, British Columbia, Canada And Its Phytogeographic Significance
Text-fig. 4. Monocots. a, b: Large monocot leaf part and counterpart, UAPC-ALTA S 17955A, B. a: Wide leaf showing entire margin at left. b: Counterpart showing dark wide midrib, and and secondaries parallel to one another, arising at low acute angle. c–e: Monocot leaf with parallel venation. c: Overview of elongate monocot leaf with parallel veins horizontal and linear to oval structures and smaller leaf fragment of same type lacking them (at lower right), UAPC-ALTA S 59491. d: Higher magnification of the smaller fragment with weak cross veins. e: Higher magnification of larger specimen with linear to oval structures between parallel veins. f, g: Monocot leaf with parallel venation. Fig. (f) shows higher magnification and (g) shows overview, BBM-PAL-P000009. Scale bars: a, b = 5 cm, c = 4 cm, d–f = 1 cm, g = 2 cm.
Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?
<p>When populations colonise new environments they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes, and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (> 22X coverage) in Berthelot's pipit (<em>Anthus berthelotii</em>), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. Firstly, we quantify how genomic divergence accumulates across the speciation continuum, i.e., among Berthelot's pipit populations, between subspecies across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (<em>Anthus campestris</em>). Across these colonisation timeframes (2.1 million – <em>ca.</em> 8,000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism, and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism, and immune defence.</p>
GloMPO (Globally Managed Parallel Optimization) Benchmark Test Data
<p>Dataset associated with:<br> M. Freitas Gustavo and T. Verstraelen (2021), "GloMPO (Globally Managed Parallel Optimization) - a tool for expensive, black-box optimizations: application to ReaxFF reparameterizations".</p> <p>Contains optimization trajectories using the CMA-ES optimizer applied to various benchmark functions and ReaxFF reparameterizations. Compares optimization results using the GloMPO framework (github.com/mfgustavo/glompo) to unmanaged optimization results.</p>
Cast Away in the Adriatic: Low Degree of Parallel Genetic Differentiation in Three-Spined Sticklebacks
<p>This repository incorporates data and scripts associated with the paper "Cast Away in the Adriatic: Low Degree of Parallel Genetic Divergence in Three-Spined Sticklebacks".</p> <p>Included in the repository are the following compressed folders: </p> <ul> <li>Moments_models&data.zip: two-population demographic models and SFS to run in <em>moments.</em></li> <li>Stairwayplot.zip: blueprint files for multiple mutation rates and results for StairwayPlots.</li> <li>TreeMix.zip: pipeline to infer population splits and mixture events from allele frequency data using TreeMix, including input files.</li> <li>VCF.zip: a filtered VCF file for all three-spined stickleback samples.</li> </ul> <p>The scripts for TreeMix and demographic analyses in <em>moments</em> are also available on <a href="https://github.com/carolindahms">GitHub</a>.</p>
Probing Ion Channel Functional Architecture and Domain Recombination Compatibility by Massively Parallel Domain Insertion Profiling
<p>Supplementary Data for a large insertional profiling study described in Coyote-Maestas et al. (2021) Nature Communications.</p>
Data from: Rapid, parallel evolution of field mustard (Brassica rapa) under experimental drought
<p>Climate change is driving evolutionary and plastic responses in populations, but predicting these responses remains challenging. Studies that combine experimental evolution with ancestor-descendant comparisons allow assessment of the causes, parallelism, and adaptive nature of evolutionary responses, although such studies remain rare, particularly in a climate change context. Here, we created experimental populations of Brassica rapa derived from the same natural population and exposed these replicated populations to experimental drought or watered conditions for four generations. We then grew ancestors and descendants concurrently, following the resurrection approach. Experimental populations under drought showed rapid evolution of earlier flowering time and increased specific leaf area, consistent with a drought escape strategy and observations in natural populations. Evolutionary shifts followed the direction of selection and increased fitness under drought, indicative of adaptive evolution. Evolution to drought also occurred largely in parallel among replicate populations. Further, traits showed phenotypic plasticity to drought, but the direction and effect size of plasticity varied. Our results demonstrate parallel evolution to experimental drought, suggesting that evolution to strong, consistent selection may be predictable. Broadly, our study demonstrates the utility of combining experimental evolution with the resurrection approach to investigate responses to climate change.</p>
apomixis_parallel_evolution, and Fortunella hindsii (Citrus hindsii )Genome sequencing and assembly
<p>##The assemble(genome) files</p> <p>Citrus hindsii (Mini citrus)Genome assembly</p> <p>Citrus hindsii (Mini citrus)Genome assembly gene model gff3 file</p> <p>Citrus hindsii (Mini citrus)Genome assembly function annotation</p> <p>Citrus hindsii (Mini citrus)Genome assembly TE gff3 file</p> <p>##The population dataset</p> <p>LD_pur.vcf.gz //The LD purning SNP vcfs (1.4 M sites) used in analysis</p> <p><br> log10_auxin.txt //The expression (log10) related to auxin pathway</p> <p><br> sjg.temergedref.fasta.gz //The TE insertion modify genome in popTE2 analysis</p> <p><br> SVs.vcf.gz //The SV vcfs used in the paper</p> <p><br> te-hierarchy.txt //The TE classfication in popTE2 analysis</p> <p><br> TPM_count.txt //All samples expression in TMP count</p> <p><br> unfiltered.vcf.gz //The unfiltered vcfs file (7.3 M sites, within 0.4 M indels) </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.