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1,456 results for “parallelism”
Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking
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ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization
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Survey results: PARALLEL COMP MATH Fall 2019
<p>We introduced GitHub Classroom and other new technology and asked the students for their feedback on these new technolgoies.</p>
Tagged original datasets for 'Genetically Optimized Massively Parallel Binary Neural Networks for Intrusion Detection Systems'
<p>Tagged, non-formatted, original datasets used in 'Genetically Optimized Massively Parallel Binary Neural Networks for Intrusion Detection Systems', T. Murovič, A. Trost.</p> <p>Available from the original authors:</p> <p>1. <a href="https://www.unsw.adfa.edu.au/unsw-canberra-cyber/cybersecurity/ADFA-NB15-Datasets/">https://www.unsw.adfa.edu.au/unsw-canberra-cyber/cybersecurity/ADFA-NB15-Datasets/</a> (UNWS-NB15 dataset)</p> <p>2. <a href="https://www.unb.ca/cic/datasets/nsl.html">https://www.unb.ca/cic/datasets/nsl.html</a> (NSL-KDD dataset)</p>
Efficient ensemble data assimilation for coupled models with the Parallel Data Assimilation Framework: Example of AWI-CM - output files and plot scripts
<p>This archive outputs_plotting.zip contains the raw output files (STDOUT) from the scaling runs performed for the paper "Efficient ensemble data assimilation for coupled models with the Parallel Data Assimilation Framework: Example of AWI-CM" submitted to GMD (gmd-2019-167). Further the scripts to extract timing information from the raw output files and plot scripts are included.</p> <p>The archive SST-DA_plotting.zip contains the scripts to compute RMS errors for the free ensemble run (output file in gmd_N46_free.zip) and the SST assimilation run (gmd_N46_sst.zip) and to plot these. The two output files contain each a Netcdf file with the ensemble mean state information and the stdout file from the model run.</p>
Supplementary Information for Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS
<p>Supplementary information for<br> Páll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B, & Lindahl, E.. (2020). Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. The Journal of Chemical Physics, 2020</p> <p>Contains benchmark methodology description as well as all inputs used in the application performance benchmarks included the paper.</p>
Massively parallel coherent laser ranging using soliton microcomb
<p>Available data for "Massively parallel coherent laser ranging using soliton microcomb", published in Nature 561, 164-170 on May 14th. </p> <p>DOI of original paper: https://doi.org/10.1038/s41586-020-2239-3</p> <p>URL of original paper: <a href="https://www.nature.com/articles/s41586-020-2239-3">https://www.nature.com/articles/s41586-020-2239-3</a></p> <p><br> Execution tested with Matlab 2019a or newer on Windows. Unzip folder to access files.</p> <p>For Figures and extended data Figures execute "Figure*.m" and "ExtDataFigure*.mat" files in corresponding subfolders.<br> Contact johann.riemensberger@epfl.ch or johann.riemensberger@gmail.com if problems with matlab code arise. <br> All matlab code remains under copyright by the authors: Johann Riemensberger and Wenle Weng and is provided solely to be used to reproduce the figures of the aforementioned paper.</p> <p>Raw data for the figures is stored in folder .\Data, preprocessed data is stored in folder .\ProcessedData. GDS file of Si3N4 photonic damascene waveguide resonators is stored in folder: GDS_design. </p>
Data from: Parallel evolution of bower-building behavior in two groups of bowerbirds suggested by phylogenomics
<p>The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that <em>Scenopoeetes dentirostris</em>, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. </p>
Application of spectral library prediction for parallel reaction monitoring of viral peptides_DDA_data
<p><strong>Project description: </strong></p> <p>A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1,529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Additionally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab.</p> <p> </p> <p><strong>Sample processing protocol:</strong></p> <p>A total of 1,569 crude synthetic viral peptides were ordered in six pools from JPT (Berlin, Germany). Synthetic peptides were separated on a 200 cm μPAC™ column (PharmaFluidics) by using an EASY-nLC1200 system (Thermo Fisher Scientific) equipped with a μPAC™ trapping column (PharmaFluidics). The flow rate was set to 300 nL/min and a stepped linear 160 min gradient was applied: 3-10% B in 22 min, 10-33%B in 95 min, 33-49% B in 23 min, 49-80% B in 10 min and 80% B for 10 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive Plus (Thermo Fisher Scientific) operated in Full MS/dd-MS2 or unscheduled PRM mode. For MS/dd-MS2 the following parameters were used. MS1 resolution was 70.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z. The analysis parameters in PRM mode were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 17.500 with an AGC target of 10<sup>6</sup>, max. injection time of 55 ms and an isolation window of 1.4 m/z.</p> <p>Potential SARS-CoV-2 target peptides belonging to the N protein were identified by DDA of SARS-CoV-2 infected Calu-3 cells. Peptides were diluted in 0.1% TFA (0.2 µg/µL) and 5 µL were separated on a 50 cm μPAC™ column (PharmaFluidics) using an EASY-nLC1200 system (Thermo Fisher Scientific). The flow rate was set to 800 nL/min and a stepped 30 min gradient was applied: 6-11% B in 2:58 min, 11-30% B in 17:10 min, 30-35% B in 2:41 min, 35-47% B in 3:11 min, 47-80% B for 0:10 min, 80% B for 1:50 min, 80-0% B in 0:10 min and 100% A for 1:50 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive HF (Thermo Fisher Scientific) operated in Full MS/dd-MS2 (Top20) using the following parameters. MS1 resolution was 60.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z.</p> <p> </p> <p>To simulate a SARS-CoV-2 positive patient sample, we spiked cell-culture derived virus in a negative oropharyngeal swab and targeted the N protein by PRM. LC parameters were identical to DDA analysis of SARS-CoV-2 infected Calu-3 cells. The PRM parameters of the The Q Exactive HF (Thermo Fisher Scientific) were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 45.000 with an AGC target of 10<sup>6</sup>, max. injection time of 100 ms and an isolation window of 1.4 m/z.</p> <p> </p> <p> </p> <p><strong>Data processing protocol:</strong></p> <p>DDA Raw files were searched with MaxQuant against the respective virus database (UniProt) with a peptide FDR of 1%. Detailed MaxQuant parameters can be found in the parameters.txt files of the according results. MaxQuant .msms output files were used to generate spectral libraries with BiblioSpec implemented in the Skyline environment using a cut-off score of 0.95. Peptide identification of PRM runs was done in Skyline using the top 6 fragment ions of the DDA spectral library or according Prosit derived library (Prosit_2020_intensity_model).</p>
Application of spectral library prediction for parallel reaction monitoring of viral peptides_PRM_NCE_data
<p><strong>Project description: </strong></p> <p>A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1,529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Additionally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab.</p> <p> </p> <p><strong>Sample processing protocol:</strong></p> <p>A total of 1,569 crude synthetic viral peptides were ordered in six pools from JPT (Berlin, Germany). Synthetic peptides were separated on a 200 cm μPAC™ column (PharmaFluidics) by using an EASY-nLC1200 system (Thermo Fisher Scientific) equipped with a μPAC™ trapping column (PharmaFluidics). The flow rate was set to 300 nL/min and a stepped linear 160 min gradient was applied: 3-10% B in 22 min, 10-33%B in 95 min, 33-49% B in 23 min, 49-80% B in 10 min and 80% B for 10 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive Plus (Thermo Fisher Scientific) operated in Full MS/dd-MS2 or unscheduled PRM mode. For MS/dd-MS2 the following parameters were used. MS1 resolution was 70.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z. The analysis parameters in PRM mode were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 17.500 with an AGC target of 10<sup>6</sup>, max. injection time of 55 ms and an isolation window of 1.4 m/z.</p> <p>Potential SARS-CoV-2 target peptides belonging to the N protein were identified by DDA of SARS-CoV-2 infected Calu-3 cells. Peptides were diluted in 0.1% TFA (0.2 µg/µL) and 5 µL were separated on a 50 cm μPAC™ column (PharmaFluidics) using an EASY-nLC1200 system (Thermo Fisher Scientific). The flow rate was set to 800 nL/min and a stepped 30 min gradient was applied: 6-11% B in 2:58 min, 11-30% B in 17:10 min, 30-35% B in 2:41 min, 35-47% B in 3:11 min, 47-80% B for 0:10 min, 80% B for 1:50 min, 80-0% B in 0:10 min and 100% A for 1:50 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive HF (Thermo Fisher Scientific) operated in Full MS/dd-MS2 (Top20) using the following parameters. MS1 resolution was 60.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z.</p> <p> </p> <p>To simulate a SARS-CoV-2 positive patient sample, we spiked cell-culture derived virus in a negative oropharyngeal swab and targeted the N protein by PRM. LC parameters were identical to DDA analysis of SARS-CoV-2 infected Calu-3 cells. The PRM parameters of the The Q Exactive HF (Thermo Fisher Scientific) were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 45.000 with an AGC target of 10<sup>6</sup>, max. injection time of 100 ms and an isolation window of 1.4 m/z.</p> <p> </p> <p> </p> <p><strong>Data processing protocol:</strong></p> <p>DDA Raw files were searched with MaxQuant against the respective virus database (UniProt) with a peptide FDR of 1%. Detailed MaxQuant parameters can be found in the parameters.txt files of the according results. MaxQuant .msms output files were used to generate spectral libraries with BiblioSpec implemented in the Skyline environment using a cut-off score of 0.95. Peptide identification of PRM runs was done in Skyline using the top 6 fragment ions of the DDA spectral library or according Prosit derived library (Prosit_2020_intensity_model).</p>
Repeated parallel losses of inflexed stamens in Moraceae: phylogenomics and generic revision of the tribe Moreae and the reinstatement of the tribe Olmedieae (Moraceae)
<p><span><span><span><span><span><span><span><span><span><span><span>We present a densely-sampled phylogenomic study of the mulberry tribe (Moreae, Moraceae), an economically important clade with a global distribution, revealing multiple losses of inflexed stamens, a character traditionally used to circumscribe Moreae. Inflexed stamens facilitate ballistic pollen release and are associated with wind pollination, and the results presented here suggest that losses of this character state may have evolved repeatedly in Moraceae. Neither Moreae nor several of its major genera (<i>Morus</i>, <i>Streblus</i>, <i>Trophis</i>) were found to be monophyletic. A revised system for a monophyletic Moreae is presented, including the reinstatement of the genera <i>Ampalis, Maillardia, Taxotrophis, </i>and <i>Paratrophis</i>, and the recognition of the new genus <i>Afromorus</i>. <i>Pseudostreblus </i>is reinstated and transferred to the Parartocarpeae, and <i>Sloetiopsis </i>is reinstated and transferred to the Dorstenieae. The tribe Olmediae is reinstated, replacing the Castilleae, owing to the reinstatement of the type genus <i>Olmedia, </i>and its exclusion from Moreae. <i>Streblus </i>s.s. is excluded from Moreae and transferred to the Olmediae, which is characterized primarily by involucrate inflorescences without regard to stamen position. Eight new combinations are made.</span></span></span></span></span></span></span></span></span></span></span></p>
On the causes of geographically heterogeneous parallel evolution in sticklebacks
<p>The three-spined stickleback (<i>Gasterosteus aculeatus</i>) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Most signatures of parallel evolution were unique to the Eastern Pacific and trans-oceanic marine–freshwater differentiation was restricted to a limited number of shared genomic regions, including three chromosomal inversions. On the basis of simulations and empirical data, we demonstrate that this could result from the stochastic loss of freshwater-adapted alleles during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which can reduce standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the elevated linkage disequilibrium associated with marine–freshwater differentiation in the Eastern Pacific is consistent with secondary contact between marine and freshwater populations that evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies from the Eastern Pacific region have led us to believe, parallel marine–freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.</p>
Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (Salvelinus alpinus)
<p>The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (<i>Salvelinus alpinus</i>) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation are largely unknown despite the cultural and economic importance of the anadromous morph. We used a newly designed 87k SNP chip to investigate the character and consistency of the genomic differences among sympatric morphs within three recently deglaciated and geographically proximate lakes in Labrador, Canada. We found genetically distinct small and large morph Arctic Charr in all three lakes consistent with resident and anadromous morphs, respectively. A degree of reproductive isolation among sympatric morphs is likely given genome-wide distributions of outlier SNPs and high genome-wide <i>F</i><sub>ST</sub>s. Across all lakes, outlier SNPs were largely non-overlapping suggesting a lack of genetic parallelism driving morph differentiation. Alternatively, several genes and paralogous copies of the same gene consistently differentiated morphs across multiple lakes suggesting their importance to the manifestation of morphs. Our results confirm the utility of Arctic Charr as a model for investigating the predictability of evolution and support the importance of both genetic parallelism and non-parallelism to the incipient speciation of Arctic Charr morphs.</p>
Pre-introduction introgression contributes to parallel differentiation and contrasting hybridisation outcomes between invasive and native marine mussels
<p class="CxSpFirst">Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, <i>Mytilus galloprovincialis</i>, in the absence (South Africa and California) and presence of hybridisation with a native congener (<i>Mytilus planulatus</i> in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (<i>maxFST</i>>0.4) and parallelism at outlier loci. Identification of long non-coding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of <i>M. galloprovincialis</i> ancestry and resistance to introgression at loci differentiating parental lineages (<i>M. planulatus</i> and Atlantic <i>M. galloprovincialis</i>)<i>. </i>Additionally, contigs putatively introgressed with divergent alleles from a closely related species, <i>Mytilus edulis, </i>showed stronger introgression asymmetries compared to genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influences contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonising populations and their hybridisation with native congeners.</p>
Data from: Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation
<p>The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.</p>
Data from: Divergent trait and environment relationships among parallel radiations in Pelargonium (Geraniaceae): a role for evolutionary legacy?
Functional traits in closely related lineages are expected to vary similarly along common environmental gradients due to shared evolutionary and biogeographic history, or legacy effects, and due to biophysical tradeoffs in construction. We test these predictions in Pelargonium, a relatively recent evolutionary radiation. Bayesian phylogenetic mixed effects models assessed, at the subclade level, associations between plant height, leaf area, leaf nitrogen content and leaf mass per area (LMA), and five environmental variables capturing temperature and rainfall gradients across the Greater Cape Floristic Region of South Africa. Trait-trait integration was assessed via pairwise-correlations within subclades. Of 20 trait-environment associations, 17 differed among subclades. Signs of regression coefficients diverged for height, leaf area and leaf nitrogen content, but not for LMA. Subclades also differed in trait-trait relationships and these differences were modulated by rainfall seasonality. Leave-one-out cross-validation revealed that whether trait variation was better predicted by environmental predictors or trait-trait integration depended on the clade and trait in question. Legacy signals in trait-environment and trait-trait relationships were apparently lost during the earliest diversification of Pelargonium, but then retained during subsequent subclade evolution. Overall, we demonstrate that global-scale patterns are poor predictors of patterns of trait variation at finer geographic and taxonomic scales.
Data from: Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity
Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests.
Concentric parallel ribbed striations - 15.6B
Part of a pot produced by experimental archaeologist Caroline Jeffra with the wheel-coiling technique. 3D scanning performed by archaeologist Kelly Papastergiou with the DAVID SLS-3 structured light scanner. Texture is recorded with the native DAVID-camera. The original fusion resolution is 0.026mm and the exported OBJ is 1.7GB and consisted of 9384292 vertices. It was decimated to 536518 vertices (160MB) in order to publish the file online. Source: Objaverse 1.0 / Sketchfab
High frequency of X4/DM-tropic viruses in PBMC samples from HIV-1 recently infected blood donors by massively parallel sequencing: the REDS II Study
<p>Here is a sub-library of the <em>env</em> V3 massively parallel sequencing proviral data generated (by Illumina MiSeq platform) during the early phase of HIV-1 infection in a group of first-time blood donors. Only paired-end reads that encompass the complete V3 region from each dataset were extracted, uploaded and considered for the analysis to avoid artificial generation of <em>in silico</em> chimeras through assembly and to evade inflating the diversity estimates of the V3 region</p>
Parallel reverse genetic screening in mutant human cells using transcriptomics - Data and analyses
<p>This dataset contains data files and analysis code associated with manuscript entitled "Parallel reverse genetic screening in mutant human cells using transcriptomics".</p> <p>Data files include expression profiles for over 1800 RNA-seq samples and annotations.</p> <p>Analysis files include R scripts to generate summary figures.</p>
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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.