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2,617 results for “next generation”
Compact continuum source finding for next generation radio surveys
<p>This is a data set that accompanies the paper "Compact continuum source finding for next generation radio surveys" (2012MNRAS.422.1812H)</p> <p>The image files and source catalogues contained here were used to test the completeness and false detection rate of a number of source finding algorithms including: Aegean, Selavy, Sfind, SExtractor, and IMSAD. These data can be used to assess the performance of future source finding codes, and to verify the the performance of code during development.</p>
Next generation global ice-ocean-biogeochemistry coupled model with 13C-cycling (GFDL MOM5-BLING13C)
<p> </p> <p>======= DESCRIPTION =======</p> <p>This is the model output supporting our paper <em>A next generation ocean carbon isotope model for climate studies I: Steady state controls on ocean <sup>13</sup>C</em> (2021 Global Biogeochemical Cycles).</p> <p>This model output simulates the transient response of ocean carbon biogeochemistry to anthropogenic CO<sub>2</sub> and <sup>13</sup>CO<sub>2</sub> atmospheric emissions with a nominal lateral resolution of 1° and 50 vertical levels. The model uses the NOAA's Geophysical Fluid Dynamics Laboratory (GFDL) MOM5 coupled to the NOAA-GFDL Biogeochemistry with Light Iron Nutrients and Gas (BLING) with <sup>13</sup>C-cycling. Atmospheric forcing is prescribed using the repeating annual cycle of the Common Ocean Reference Experiment version 2 normal year forcing dataset (COREv2-NYF). The implementation of <sup>13</sup>C-cycling applies isotopic fractionations during air-sea gas exchange, photosynthetic production of organic matter, and formation of calcium carbonate. The sensitivity of dissolved inorganic <sup>13</sup>C in the ocean to the CO<sub>2</sub> gas exchange rate is explored by repeating the simulation twice, once using the latest OMIP-CMIP6 protocol for the k-U<sub>10 </sub>parameterization (standard) and once using the previous OCMIP2 protocol (fast-gas-exchange).</p> <p> </p> <p>Files information:</p> <ul> <li><strong>ocean_static.nc</strong>: Static fields (longitude, latitude, area).</li> <li><strong>1990-2002.ocean_month.nc</strong>: Monthly output between 1990 and 2002 of ocean physical variables (temperature, salinity, averaged mixed layer depth, maximum mixed layer depth).</li> <li><strong>1990-2002.ocean_bling_trc_month_CMIP6.nc</strong>: Monthly output between 1990 and 2002 of biogeochemical variables* for the simulation using the OMIP-CMIP6 air-sea gas exchange protocol.</li> <li><strong>1970_1989_d13c_org_mldave_CMIP6.nc</strong>: Monthly output between 1970 and 1989 of d<sup>13</sup>C of organic matter averaged over the mixed layer.</li> <li><strong>1990-2002.ocean_bling_trc_month_OCMIP2.nc</strong>: Monthly output between 1990 and 2002 of biogeochemical variables* for the simulation using the OCMIP2 air-sea gas exchange protocol.</li> </ul> <p>* Biogeochemical variables are dissolved inorganic carbon, dissolved inorganic carbon-13, oxygen, and dissolved inorganic phosphate.</p> <p> </p> <p>======= HOW TO CITE =======</p> <p>This model output can be freely distributed, but please cite it using the following paper:</p> <p>Claret, M., Sonnerup, R. E., & Quay, P. D. (2021). A next generation ocean carbon isotope model for climate studies I: Steady state controls on ocean <sup>13</sup>C. <em>Global Biogeochemical Cycles</em>, 35, e2020GB006757. <a href="https://doi.org/10.1029/2020GB006757">https://doi.org/10.1029/2020GB006757</a></p> <p> </p> <p>======= ACKNOWLEDGEMENTS =======</p> <p>This work was funded by the National Science Foundation (NSF-OCE 1356756 and NSF-OCE 1829796). We would also like to acknowledge high-performance computing support from Cheyenne (<a href="https://doi.org/10.5065/D6RX99HX">doi:10.5065/D6RX99HX</a>) provided by NCAR's Computational and Information Systems Laboratory, sponsored by the NSF.</p> <p> </p> <p>======= QUESTIONS AND REQUESTS? =======</p> <p>Please contact Mariona Claret (mclaret@uw.edu) or Rolf Sonnerup (rolf@uw.edu).</p> <p> </p>
SNP and indel discovery and genotyping in next-generation sequencing data
<p>Code, logs and data for discovery and genotyping of SNPs and indels, in the the D.melanogaster genome, using GATK HaplotypeCaller. Code is in the zipped folder named code.zip. Run logs for this code as in the zipped folder named logs.zip. The unfiltered vcf genotypes file is named lhm_rg_HC_2015-09-15.vcf.gz. The filtered vcf genotypes file is named f1.lhm_rg_HC_raw.vcf.gz. The vcf submitted to NCBI dbSNP (filtered, and with indels >50bp and variants with null alternate alleles both removed) is named dbSNP.lhm_rg_HC_raw.vcf.gz. The folder local_reference.zip contains the reference assembly files against which genotypes were called against, and includes the code used to format the data prior to use. Also included is genotypes data from the two in-house reference line samples sequenced (BDGP6+ISO1 mito/dm6, Bloomington <em>Drosophila</em> Stock Center no. 2057)</p> <p>Samples are 220 Sussex-LH<sub>M</sub> hemiclones, and 2 RG. The first run did not include chromosome 4 and the mitochondrial genome, so these were genotyped separately, and then added to the rest of the results.</p> <p>The link for the NCBI dbSNP record is currently https://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewBatch.cgi?sbid=1062461and the submitter handle is MORROW_EBE_SUSSEX.</p> <p>At the time of writting, the NCBI D.melanogaster build is still being updated, and therefore ss identifiers, but not rs identifers are available.</p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p>
Structural variant discovery and genotyping in next-generation sequencing data
<p>Code, logs, data, and summaries for detection and genotyping of genomic structural variants in the D.melanogaster Sussex LHM hemiclones (and one in-house reference line individual), using Genomestrip/2.0</p> <p>The unfiltered CNV pipleline results are lhm_gs.cnvs.raw.vcf.gz</p> <p>Filtered CNV results (including removal of bad samples) are filtered.goodS.lhm_gs.cnvs.raw.vcf.gz</p> <p>The file uploaded to NCBI dbVAR (which comprises of the filtered CNVs and indels >50bp from the HaplotypeCaller method) is lhm_sx16.dbVAR.vcf.gz</p> <p>The NCBI dbVAR accession number is nstd134. Code, logs and summary data are in the zipped archives, named accordingly. The archive reference_data.zip contains additional input files required for Genomestrip, including a shell script for making some of them. The file gstrip_lhm_RG_bams.list is also an input for Genomestrip, indicating bam file names and paths.</p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p> <p> </p>
End-user's survey results on needs and expectations for next- generation Energy Performance Certificates (H2020 X-tendo project)
<p>The SPSS data file consists of survey data from the X-tendo project on the end-user needs and expectations from next-generation energy performance certificates.</p>
Proposal for a Next-Generation Metadata framework
<p>This figure illustrates a Next-generation Metadata framework and how it will provide the community a composable collection of metadata schemas to remove barriers to re-use and collaboration. </p>
Outputs of the next generation sea ice model (neXtSIM) for winter 2006 - 2007 saved for comparison with RGPS.
<p>NeXtSIM was run from 1 December 2006 to 15 April 2007 with the following parameters:</p> <p><code>[mesh]</code><br><code>filename=small_arctic_10km.msh</code></p> <p><code>[simul]</code><br><code>duration=150</code><br><code>time_init=2006-11-15</code><br><code>timestep=900</code></p> <p><code>[dynamics]</code><br><code>compression_factor=13800</code><br><code>C_lab=2675000</code><br><code>nu0=0.301</code><br><code>tan_phi=0.624</code><br><code>substeps=90</code><br><code>time_relaxation_damage=15</code><br><code>use_temperature_dependent_healing=true</code></p> <p><code>[output]</code><br><code>exporter_path=/cluster/work/users/akorosov/music/sa10free_mat00</code><br><code>output_per_day=4</code><br><code>variables=M_VT</code><br><code>variables=Concentration</code><br><code>variables=Thickness</code></p> <p><code>[setup]</code><br><code>atmosphere-type=era5</code><br><code>ice-type=topaz_osisaf_icesat</code><br><code>ocean-type=topaz</code><br><code>bathymetry-type=etopo</code><br><code>dynamics-type=bbm</code></p> <p><code>[thermo]</code><br><code>diffusivity_sss=0</code><br><code>diffusivity_sst=0</code><br><code>h_young_max=0.3</code><br><code>newice_type=1</code><br><code>hnull=0.5</code></p> <p><code>[debugging]</code><br><code>check_fields_fast=false</code></p> <p>The outputs (binary snapshots at every 3 hours) were then merged with RGPS data from the same period using this notebook:</p> <p>https://github.com/nansencenter/music_nextsim_tuning_paper/blob/main/02_process_nextsim.ipynb</p> <p> </p>
From Ridge 2 Reef: An Interdisciplinary Model for Training the Next Generation of Environmental Problem Solvers
<p>This dataset contains the raw data from the evaluation instruments and accompanies the manuscript: "From Ridge 2 Reef: An Interdisciplinary Model for Training the Next Generation of Environmental Problem Solvers". It contains all trainee and advisor interviews from 2018 - 2022, as well as a select few partner interviews. It also contains pre and post-annual trainee survey data and the codebook to decipher the survey data. Rubric criteria and scores are included for trainees enrolled in the R2R Communication Skills course. The R script contains the statistical analyses reported in the manuscript and code used to generate figures.</p>
Dataset of "Advancing Logic Circuits with Halide Perovskite Memristors for Next-Generation Digital Systems"
<p><span>This dataset supports the article "Advancing Logic Circuits with Halide Perovskite Memristors for Next-Generation Digital Systems" </span></p> <p> </p> <p><span>Raw data for the article "<span>Advancing Logic Circuits with Halide Perovskite Memristors for Next-Generation Digital Systems</span>". For further details see the readme.txt file.</span></p>
Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method
<p>The data set comprises 164 FASTQ files generated with an Ion AmpliSeq-based genotyping method for <em>Toxoplasma gondii </em>and<em> </em>a BED file used for the design of the Ion AmpliSeq primer panel. The FASTA file named as "AmpliSeq-ME49-Reference" was used as a reference for mapping and data analysis of the FASTQ files. The GZ file named as "Tgondii_IonAmpliSeq_Results_SNPs_VCF" is a VCF file, which contains all SNPs identified within the 164 FASTQ files relative to the AmpliSeq-ME49-Reference. The VCF file was converted into a FASTA file named as "Tgondii_IonAmpliSeq_Results_SNPs", which also contains the SNPs identified within the 164 FASTQ files relative to the AmpliSeq-ME49-Reference.</p> <p>The work is published in the European Journal of Clinical Microbiology & Infectious Diseases with the title "Genotyping of European <em>Toxoplasma gondii</em> strains by a new high‑resolution next‑generation sequencing‑based method"; https://doi.org/10.1007/s10096-023-04721-7</p>
NEXT GENERATION OPTICAL ENCODER
<p>Linear encoders provide direct position feedback to various machine tool and automation systems. Working in a linear format allows extreme length position measurement and control. José Luis de la Peña from <a href="https://www.fagorautomation.com/en/">Fagor Automation</a> explains how <a href="https://www.laser4surf.eu">Laser4Surf</a> technology will make linear encoders even more precise with the help of lasered nano strucures on the tape.</p>
Dataset: On the Properties of Next Generation Wireless Backhaul
<p>This dataset contains all the data used in the Paper: "On the Properties of Next Generation Wireless Backhaul" sent to Transaction of Network Science and Engineering.</p> <p>It is divided into three main archives:</p> <ul> <li>The first archive, called <strong>geodata.zip</strong>, contains the Data Surface Model (DSM) and the topographical maps used to generate the intervisibility graphs. These maps have been aggregated from different sources and they are all released under a CC-BY-SA 4.0 license. It is divided into two folders: 'dsm' and 'topo_maps': <ul> <li> 'dsm' contains the Data Surface Model (DSM) of the nine areas used in our research. Each area is saved in a separate .tif file and can be used directly from the tool. The projection system is EPSG:3003.</li> <li>'topo_mapsì contains the PostGIS dump of the tables containing the topographical maps of the cities. In order to use them, you have to import those in PostGIS and connect our tool to the PostGIS DB.<br> The CTR files (technical region maps) are divided by region, while the openstreetmap file (osm.tar) contains the whole Italian peninsula. All the geographical data are projected in the reference system EPSG:3003. The CTR of Campania is unavailable due to licensing incompatibilities.</li> </ul> </li> <li>The second archive, called <strong>visibility_graphs.zip</strong>, contains the visibility graph we have generated using our tool. It is released as a CC-BY-SA 4.0 license. It is divided into folders, one for each area of the analysis. Each folder contains two files: <ul> <li>best_p.csv : contains the ids of the nodes associated with their coordinates on a cartesian projection. The projection is EPSG:3003</li> <li>intervisibility.adj : contains the intervisibility graph represented as an adjacency matrix. It can be read by common libraries such as networkx or igraph. The intervisibility has been calculated 2m above the building.</li> </ul> </li> <li>The third folder, called <strong>network_topologies.zip</strong>, contains the network topologies we have computed using a State-of-the-Art algorithm from Polese et Al. The folder is divided into two folders: '30gNB' and '60gNB', corresponding to the density of base stations for square km. It s further divided in 9 folders (one for each area), then divided on the basis of the model we use for the visibility graph. You can find more information about these models in section V of the paper. In this last folder we have two sets of 50 files, which are the intervisibility graph of that set of Base Stations and the topology produced. This dataset has been released under a CC-BY-SA 4.0 license.</li> </ul> <p>All the results can be replicated using our code which will be released with an open-source license as soon as the article is published.</p>
Raw NGS data for the study 'Spouse-to-spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untraslated Region of Hepatitis C Virus Analyzed by Next-generation Sequencing'
<p>This file contains the original next-generation sequencing data (raw sequences in fastq format) which were analyzed in the study titled: "Spouse-to-spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untraslated Region of Hepatitis C Virus Analyzed by Next-generation Sequencing".</p> <p> </p> <p> </p>
Graphing and tabulating next-generation sequencing and genotyping data
<p>Making figures and tables for publication. Each zip archive contains input data, shell script to initiate and log R script, one R script for generating several graphs and tables, and the output graphs and tables themselves.</p> <p>Data was generated by whole-genome resequencing of 22 individual D.melanogaster from Sussex-LHM population and 2 from the Sussex RG line, followed by read-mapping, then genotyping with Haplotype Caller and Genomestrip.</p> <p>Locations for raw data, code, logs, extended QC data:</p> <p>Sequence reads NCBI SRA268956</p> <p>NCBI dbSNP https://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewBatch.cgi?sbid=1062461</p> <p>NCBI dbVar accession number pre-release nstd134</p> <p> </p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p> <p> </p>
Read-mapping for next-generation sequencing data (Drosophila melanogaster)
<p>Code, logs and quality-control data for whole-genome resequencing of Sussex-LH<sub>M</sub> and RG <em>Drosophila melanogaster</em>.</p> <p>Mapping code is in the archive lhm_mapping_scripts.zip</p> <p>Mapping logs are in the in the archive lhm_mapping_logs.zip</p> <p>Other zip archives contain the quality control data.</p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p>
Read-mapping for next-generation sequencing data (Wolbachia)
<p>Code, log files and QC data. NCBI SRA accession number SRP091004. Note that sequencing Wolbachia was not a central aim of the project, and was undertaken in order to maximise the amount of information that could be extracted from the raw genome sequence data targetted at the fruit-fly host.</p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p>
Genotype reproducibility testing in next-generation sequencing data
<p>Code, log and results summary for testing the reproducibility of genotypes with three pairs of hemiclones in the Sussex LH<sub>M </sub><em>D.melanogaster </em>population sample. Discovery and genotyping of genomic sequence variants was done using GATK HaplotypeCaller, and Genomestrip. Numerical comparison of genotype calls within each pairs of hemiclone individuals was performed using GATK GenotypeConcordance.</p> <p> </p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p>
Next-generation 3D object detection and tracking for self-driving vehicles using object velocity
<p>The synthetic dataset was generated using KITTI-like specifications and annotations format. It is comprised by the training and testing sets, that include KITTI standard folders: label_2, image_2 and calib. Furthermore, there is a velodyne file for each of the following use cases:</p><ul><li>Point cloud 1: (x,y,z, (Float)Radial_Velocity): this point cloud has the relative radial velocity as an additional feature for each point. File: velodyne_radial_velocity;</li><li>Point cloud 2: (x,y,z,(Float)Absolute_Speed): in this point cloud, every point has the absolute speed of the object as the additional feature. File: velodyne_abs_speed;</li><li>Point cloud 3: (x,y,z,(Bool)Is_Moving): the additional feature of this point cloud is a Boolean value that is set to 1.0 if the object is moving; contrariwise, it is set to 0.0 for static objects. File: velodyne_is_moving;</li><li>Point cloud 4: (x,y,z,0): no additional feature information. If desired, requires post-processing to convert to (x,y,z) or changing the toolbox point cloud configuration to not consider the additional feature. File: velodyne_xyz;</li></ul><p>Additionally, the detections generated with the OpenPCDet toolbox and Second-IoU model are provided.</p><p>This work was made as part of a master thesis of Informatics Engineering in the University of Aveiro.</p>
The NGDEEP NIRIS calibration files for 'The Next Generation Deep Extragalactic Exploratory Public Near-Infrared Slitless Survey Epoch 1 (NGDEEP-NISS1): Extra-Galactic Star-formation and Active Galactic Nuclei at 0.5 < z < 3.6
<p>GRISMCONF configurations files used in Pirzkal et al. 2024. These contain the full field calibrated solution for the dispersion solution, trace as well as wavelength calibration. They provide a mean to extract NIRISS WFSS spectra obtained using the F115W, F150W, or F200W to within an acccuracy better than 0.25 pixel over most of the field of view. Wavelength calibration of both grism was verified to be accurate to within 15A over most of the field of view. Details can be found in Appendix A of Pirzkal et al. 2024.</p>
Next-Generation Sequencing Dataset of Adult Pilocytic Astrocytomas
<p>Next-Generation Sequencing Dataset of Adult Pilocytic Astrocytomas</p> <p>Pilocytic astrocytoma (PA) is a benign grade 1 glioma according to the World Health Organization (WHO), common in children but rare in adults, where it may have a worse prognosis. Pediatric PA is usually associated with dysregulation of the MAPK pathway, often involving BRAF alterations such as the KIAA1549::BRAF (K-B) fusion or the V600E mutation. This dataset contains molecular data of 28 cases of adult PA obtained by using gene-targeted next-generation sequencing (NGS).</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.