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2,152 results for “outputs”
200 Synthetic Epilepsy Clinic letters Markup annotation outputs as CSV files
<p>We have produced 200 synthetic epilepsy clinic letters which were annotated using Markup Annotation Tool with the annotation files (.ann and JSON formats) uploded previously : https://doi.org/10.5281/zenodo.8356494. Here we are making available annotation outputs for each entity extracted as a separate CSV file. These outputs can be directly compared with outputs created by ExECTv2 when processing the 200 synthetic letters. </p>
Outputs from fitted models across the cross-validation scenarios for 'Space-time species distribution modeling with opportunistic presence-only data: a case study of passerines in a protected area'
<p>Three Zenodo repositories are linked to the preprint <em>Space-time Species Distribution Modeling for Opportunistic Presence-Only Data: A Case Study of Passerines in a Protected Area </em>(Lasgorceux et al., unpublished, <a href="https://hal.science/hal-04616332">https://hal.science/hal-04616332</a>):</p> <ul> <li>Data, scripts and, code (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12545052">https://doi.org/10.5281/zenodo.12545052</a>)</li> <li>Outputs from fitted models across the cross-validation scenarios (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12544212">https://doi.org/10.5281/zenodo.12544212</a>)</li> <li>Supplementary information at (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12541412">https://doi.org/10.5281/zenodo.12541412</a>)</li> </ul> <p>This repository contains the outputs from fitted models across the cross-validation scenarios.</p> <p>In the folder <em>Ouputs_cross_validation</em>, each species is represented by a .RData file, numbered from 1 to 77 (excluding 7, which corresponds to <em>Bombycilla garrulus</em>; see the preprint for details). This dataset is specifically used to generate Figure 1, which shows the AUC of various cross-validation scenarios. To reproduce this figure in R, place all the files in the <em>Results/Fitted_models</em> folder and run the <em>Models_Outputs.R</em> script located in the <em>Results</em> folder of Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12545052">https://doi.org/10.5281/zenodo.12545052.</a></p> <p>Note: These data have been separated due to memory requirements (23.14GB).</p>
DYAMOND-II Model Outputs for "Boundary-Layer-Coupled and Decoupled Clouds in Global Storm-Resolving Models: Comparisons with the ARM Observations"
<p>This dataset contains outputs from the DYAMOND Phase-II simulations, focusing on Global Storm-Resolving Models (GSRMs) at various Atmospheric Radiation Measurement (ARM) sites. The dataset supports the analysis presented in the manuscript "Boundary-Layer-Coupled and Decoupled Clouds in Global Storm-Resolving Models: Comparisons with the ARM Observations."</p> <p>Included are high-resolution model outputs from nine GSRMs, detailing simulations of atmospheric processes at six ARM sites, including variables of clouds, temperature, humidity, wind, and surface fluxes. This dataset allows for a direct comparison between GSRM simulations and ARM field observations, facilitating the evaluation of PBL-coupled and decoupled clouds. For further inquiries or assistance regarding the dataset, please contact the corresponding author at su10@llnl.gov.</p>
MITgcm code output for TGT and TEIS
<p>TGT_case.zip: The output of the MITgcm simulation for an Ice Grounding Zone (IGZ) length of 15km and a Thermal Forcing (TF) of 3.75 C is provided.</p> <p>TEIS_case.zip: The output of the MITgcm simulation for an IGZ length of 14km and TF of 3.2 C is provided.</p> <p>The Matlab codes, data, and binary files that serve as input for the MITgcm model are also provided, along with a compiled MITgcm model.</p>
Post-transition state trajectories and transition state structures of 4+2/6+4 cycloadditions | BGAN-EPS outputs
<p>dataset.zip and log.zip are the dataset and outputs for the bidirectional generative adversarial network - entropic path sampling (BGAN-EPS). The source code can be found at https://github.com/rshin1209/bgan_eps.</p> <p>dataset.zip includes post-TS trajectories (xyz format) and transition state structures (pdb format) for the following 4+2/6+4 cycloadditions:</p> <ul> <li>Diene/triene cycloaddition (i.e., dta)</li> <li>Tethered-diene/triene cycloaddition (i.e., dtb)</li> <li>NgnD-catalyzed Diels–Alder reaction (i.e., ngnd)</li> <li>SpnF-catalyzed Diels–Alder reaction (i.e., spnf)</li> </ul> <p>dataset.zip can be unzipped and directly used for the BGAN-EPS method.</p> <p>XXX_r2p_1 refers to 4+2-adduct and XXX_r2p_2 refers to 6+4-adduct.</p> <p>log.zip includes outputs of the BGAN-EPS for the above 4+2/6+4 cycloadditions. The graphing for entropic profiles and entropy decomposition analysis can also be found at Git Hub link.</p>
Model outputs used in "Drivers of cross-shelf exchange in the East Auckland Current system"
<p>These simulations were developed during the work published in in Santana et al. (2023) (https://gmd.copernicus.org/articles/16/3675/2023/). The DA run is refeered as ASFUVTS (7-day assimilation window) and the NoDA run is the non-assimilative run in Santana et al., (2023). The DA run assimilates observations presented and analysed in Santana et al. (2020) (https://www.nature.com/articles/s41598-021-89222-3).</p> <p>We used the Regional Ocean Modeling System (ROMS), a primitive-equation, hydrostatic, and free-surface ocean model that solves the Reynolds-averaged form of the Navier–Stokes equations. ROMS is a fully nonlinear, finite-difference model that uses terrain-following (sigma) vertical coordinates and horizontal orthogonal or curvilinear Arakawa C grid (Shchepetkin and McWilliams, 2003, 2005; Haidvogel et al., 2008). The model domain (290 x 150) is rotated 52.14° clockwise to better resolve the NZNES and spans 332 km offshore at the widest point (near North Cape). The domain has horizontal resolution of approximately 2 km, which roughly captures coastline variability and still resolves the continental shelf and slope without large computational cost. The model has 30 vertical sigma layers and model bathymetry was interpolated from the 250 m resolution bathymetric data set built by the National Institute of Water and Atmospheric Research (NIWA - https://niwa.co.nz/our-science/oceans/bathymetry). We use a vertical discretisation scheme that increases the resolution near the surface and bottom by applying stretching function type 4 and transformation equation option 2 (Shchepetkin and McWilliams, 2005, 2009). The vertical resolution is higher at the upper 200 m (from 4 to 30 layers). On the slope (depth<1000 m), the vertical resolution is higher than 66 m and in the open ocean the thickest level is 233 m (3838.6 m depth). Baroclinic modes are resolved using a time step of 180 s, while the barotropic time step is 6 s.</p> <p>Model surface forcing is from the Japanese atmospheric 55-year reanalysis for driving ocean models (JRA55-do, Tsujino et al., 2018). A previous study demonstrated that JRA55-do had the highest correlation with observed winds in comparison to other atmospheric forcing datasets in the Southwest Pacific (Taboada et al., 2019). Atmospheric forcing fields of wind speed, net shortwave radiation, downward longwave radiation, relative humidity, temperature, rain, and pressure are specified every 3 h and used to compute the surface fluxes of stress, heat and freshwater using the bulk flux parameterisation of Fairall et al., (2003). The model uses initial and boundary conditions of SSH, temperature, salinity, and velocities from HYCOM-NCODA (Chassignet et al., 2009) versions 91.1 and 91.2 which cover period of simulations generated here. de Souza et al., (2021) analysed the performance of four global reanalysis that assimilate SSH, SST and Argo data on the New Zealand waters. The authors found that HYCOM-NCODA (8 km resolution) had higher SSH and SST variability than low-resolution (25 km) satellite surface observations and other reanalyses with similar grid-spacing. HYCOM-NCODA had velocity standard deviation similar to that observed at M4 and M5, even though GLORYS (8 km global ocean reanalysis, Lellouche et al., 2018) better represented temperature and salinity profiles in the region. Annual average discharge from several rivers are included as lateral forcing in the model. The boundary forcing is applied daily using Chapman (1985) condition for free surface, Shchepetkin condition (Mason et al., 2010) for barotropic velocities and mixed radiation-nudging (Marchesiello et al., 2001) for baroclinic velocities, temperature and salinity. A 5-day nudging coefficient is applied towards the lateral boundaries. The model aims to simulate continental shelf, slope and rise regions, including the offshore extent of the EAuC and its eddy variability. This and the upcoming studies using the simulations analysed here focus on intra-annual variability and tides are not included as forcing.</p>
Model simulation output for New Configuration for Impact of microphysics and convection schemes on the mean-state and variability of clouds and precipitation in the E3SM Atmosphere Model
<p>Simulation output from the new configuration model used in the manuscript Impact of microphysics and convection schemes on the mean-state and variability of clouds and precipitation in the E3SM Atmosphere Model</p>
Raw model output presented and analyzed in: "Ancient Stratified Thermochemical Piles due to High Intrinsic Viscosity"
<h3>Summary</h3> <p>This archive contains the raw model output for all cases presented in the manuscript titled "Ancient Stratified Thermochemical Piles due to High Intrinsic Viscosity".</p> <p>The output files are archived in hdf5 file format. The content of these files (one for each case) is as follows:</p> <ul> <li>Temperature, viscosity and compositional fields, as well as the time-series of the lower heat-flux (from 4 billion years of model evolution onwards)</li> <li>Age field at 5 billion years of model evolution</li> <li>Time</li> </ul> <p>The file mesh.h5 contains the x and y meshes of the models (called 'xmesh' and 'ymesh', respectively).</p> <p>All data provided can be used to reproduce the results and figures in the manuscript, as detailed in the main and supplementary text. </p> <p> </p> <p> </p>
MOM6 Model Output from "Improved Upper Ocean Vertical Mixing in the Equatorial Oceans in NOAA/GFDL's OM4 Model"
<p>Datasets produced during the MOM6 experiments described by "Improved Upper Ocean Vertical Mixing in the Equatorial Oceans in NOAA/GFDL's OM4 Model".</p> <p>These datasets are needed to reproduce the figures in the version of this manuscript as submitted to ESS.</p> <p>The location of the notebooks for creating figures from these datasets is indicated in the manuscript.</p>
SOSE output analyzed in "Evaluation of MITgcm-based ocean reanalysis for the Southern Ocean" (Part 2-6)
Open the record for dataset details and reuse information.
SOSE output analyzed in "Evaluation of MITgcm-based ocean reanalysis for the Southern Ocean" (Part 2-4)
Open the record for dataset details and reuse information.
WRF Model Output for a Simulation of Hurricane Laura (2020), 2.25km grid, 2020-08-26-00Z through 2020-08-26-10Z
<p>This is WRF model output for a simulation of Hurricane Laura (2020). The tar file contains gzipped netcdf files each with 6 model outputs at 20 minute intervals.</p>
WRF Model Output for a Simulation of Hurricane Laura (2020), 2.25 km grid, 2020-08-26-12Z to 2020-08-26-22Z
<p>This is WRF model output for a simulation of Hurricane Laura (2020). The tar file contains gzipped netcdf files each with 6 model outputs at 20 minute intervals.</p>
Removal of developmentally regulated microexons has a minimal impact on larval zebrafish brain morphology and function - behavior data output
<p>Graphs and quantification of larval zebrafish behavioral data from mutants with microexons removed. All genes are grouped by their beginning letter, and two runs are included for most mutants.</p>
Scherrenberg et al. (2024) supplement (Climate of the past): Ice-sheet model code, and output of Northern Hemisphere ice-sheet evolution of the past 800 kyr
<p>Supplement to Scherrenberg et al. (2024), article in Climate of the Past.</p> <p>This data-set contains ice-sheet model (IMAU-ICE) code (see IMAU_ICE_Code.zip; see https://github.com/IMAU-paleo/IMAU-ICE/tree/main for the most recent version of the model), the model output and configuration files (see Data_output.zip), and scripts to create figures (see Scripts_and_Figures.zip).</p> <p>Please note that additional input fields are required to run IMAU-ICE and to produce the figures. See Scherrenberg et al., (2024) for more information or contact the corresponding author.</p> <p>Citation: M.D.W. Scherrenberg, C.J. Berends, R.S.W. van de Wal: Late Pleistocene glacial terminations accelerated by proglacial lakes, climate of the past, special issue "icy landscapes of the past", 2024</p>
OpenFoam model output for "A Fuel Cell Power Supply System Equipped with Artificial Gill Membranes for Underwater Applications"
<p>Dataset of numerical experiments carried out with OpenFOAM v 10 as used in the manuscript "A Fuel Cell Power Supply System Equipped with Artificial Gill Membranes for Underwater Applications" by Lucas Merckelbach and Prokopios Georgopanos.</p> <p> </p>
Full TMM outputs for all iterations for cell lines
<p>The archive contains the full TMM outputs, including input and output PSF files, and summary TMM reports in PDF and tabular formats, for each of the 68 iterations performed on cell lines. </p>
Simulation data output used in test-particle simulations of linear and nonlinear interactions between a 2D whistler-mode wave packet and radiation belt electrons
<p><strong>Dataset</strong></p> <p>The zip file contains the data used in the paper "Test-particle simulations of linear and nonlinear interactions between a 2D whistler-mode wave packet and radiation belt electrons" submitted for publication in Geophysical Research Letters (GRL) by da Silva et al. See the GRL paper and Supporting Information for details about the simulations. This data has been uploaded to Zenodo to comply with AGU's data policy.</p> <p>To load the data please run the self-explanatory script load_hyb_test_part.m in Matlab. See README.txt for further instructions.</p> <p>C. L. da Silva, Mar/21/2018</p> <p> </p> <p><strong>Corresponding Article</strong></p> <p>C. L. da Silva, R. E. Denton, M. K. Hudson, R. M. Millan, K. Liu, J. Bortnik (2018) Test-particle simulations of linear and nonlinear interactions between a 2D whistler-mode wave packet and radiation belt electrons, Submitted for publication, <em>Geophys. Res. Lett.</em>, doi:10.1002/2018GL077877.</p> <p> </p> <p><strong>Article Abstract</strong></p> <p>Using test-particle simulations, we describe (in 2D) the interaction of an ensemble of electrons with a discrete whistler-mode wave packet, which propagates with a moderate wave-normal angle with respect to the background magnetic field. We evaluate both the average transport coefficients used in quasi-linear diffusion transport, and also the full nonlinear wave-particle interactions. The magnitude of the calculated diffusion coefficients is found to increase proportionally to the wave amplitude squared, in agreement with quasi-linear diffusion theory. Cyclotron resonance of counterstreaming electrons (n=1 harmonic number) is more important for pitch-angle scattering than Landau resonance. Landau resonance of costreaming electrons (n=0) is comparable to cyclotron resonance for energy diffusion and advection. Strong acceleration of high-pitch-angle, costreaming electrons arises in nonlinear wave-particle interactions with high amplitude waves. In our simulations with zero parallel electric field, the energy source for electron acceleration is the wave's perpendicular electric field, in both the cyclotron and Landau resonances. The Landau resonance can happen even with zero parallel electric field, if the wave packet propagates with a finite wave-normal angle. This resonance between the particle's azimuthal velocity and the wave fields leads to trapping and substantial parallel acceleration.</p> <p> </p> <p><strong>Article key points</strong></p> <p>Cyclotron resonance of counterstreaming electrons is dominant for pitch-angle scattering, consistent with quasi-linear theory</p> <p>Landau and cyclotron resonances are comparable for acceleration; here the energy source is the wave perpendicular electric field in both</p> <p>Substantial Landau parallel acceleration occurs with a finite wave-normal angle, even with zero parallel electric field</p> <p> </p> <p><strong>Acknowledgments</strong></p> <p>These simulations were performed at Dartmouth's Discovery computer cluster. We would like to thank all the supporting staff for their assistance and for their splendid maintenance of Discovery.</p> <p> </p> <p> </p> <p> </p>
Rationalizing Systems Analysis for the Evaluation of Adaptation Strategies in Complex Human-Water Systems - Outputs Dataset
<p>Dataset containing the outputs of the paper entitled Rationalizing Systems Analysis for the Evaluation of Adaptation Strategies in Complex Human-Water Systems. Outputs are subdivided into PMAUP and SWAT-PMAUP folders. Scenario runs are available in the folder scenario, inside SWAT-PMAUP, together with the SWAT model setup used throughout the manuscript.</p>
Simulation data output used in Griffiths and Phelps lightning initiation model, revisited
<p>Simulation data output used in the paper titled "Griffiths and Phelps Lightning Initiation Model, Revisited" submitted for publication in JGR by A. Attanasio, P. R. Krehbiel, and C. L. da Silva.</p> <p>The model simulates the collective dynamics of a system of positive streamers using the framework first proposed by Griffiths and Phelps [1976]. The README.txt file contains details about the data structure.</p> <p>C. L. da Silva, Jan/29/2019</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.