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1,726 results for “simulated data”
Dynamic Albedo of Neutrons (DAN) Simulated and Observed Die-Away Data
<p>These datasets provide the data associated with the article, "Analysis of active neutron measurements from the Mars Science Laboratory Dynamic Albedo of Neutrons instrument: Intrinsic variability, outliers, and implications for future investigations" by H. R. Kerner et al. (full citation below). The Dynamic Albedo of Neutrons (DAN) is a nuclear spectroscopy investigation onboard the Mars Science Laboratory (Curiosity) rover.</p> <p>If you use this dataset, please use the following citation: Kerner, H. R., Hardgrove, C. J., Czarnecki, S., Gabriel, T. S. J., Mitrofanov, I. G., Litvak, M. L., Sanin, A. B., and Lisov, D. I. Analysis of active neutron measurements from the Mars Science Laboratory Dynamic Albedo of Neutrons instrument: Intrinsic variability, outliers, and implications for future investigations. Under review. </p>
Underlying data for "Interpretation of Hydrogen-Deuterium Exchange Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles"
<p>This dataset contains code, data, and figures used in the article "Interpretation of Hydrogen-Deuterium Exchange Data<br> by Maximum-Entropy Reweighting of Simulated Structural Ensembles".</p> <p>Contents:</p> <p>code/* - Underlying code used to analyze molecular dynamics trajectories and calculate predicted HDX-MS data, used to reweight structural ensembles to best fit target HDX-MS data, and used to structurally cluster simulation frames after reweighting</p> <p>data/* - Simulation trajectories of the TeaA protein, along with two sub-trajectories corresponding to only 'closed' or 'open' TeaA frames, and predicted HDX-MS deuterated fractions used as target data in simulation reweighting. Also simulation trajectories of the LeuT protein, in either 'outward-facing' or 'inward-facing' conformational states embedded in a DMPC bilayer, and experimental HDX-MS deuterated fractions used as target data in simulation reweighting</p> <p>figures/* - Underlying data and scripts used to create all figures and movies used in the article.</p> <p>Where appropriate, README files include instructions for regenerating data used in the article, and details of the Python packages used to run Python scripts are available in conda_environment.yml</p>
Eddy Kinetic Energy in the Arctic Ocean from a High-resolution Global Simulation with 1-km Arctic (data).
<p>Data for the "Eddy Kinetic Energy in the Arctic Ocean from a High-resolution Global Simulation with 1-km Arctic".</p>
Thermodynamics data of Alkali Feldspars from FPMD simulations
<p>We computed the thermodynamic properties (pressure, temperature, internal energy, heat capacity) and thermoelastic coefficients (isobaric expansivity, isothermal compressibility, thermal pressure coefficient) on the two alkali feldspars end-members using <em>ab initio</em> molecular dynamics simulation in the 2000-20000 K temperature range and in the 0.5-6 g.cm<sup>-3</sup> density range.</p> <p>Simulations are performed using the Vienna Ab Initio Simulation Package (VASP) (Kresse and Furthmuller, 1996) in the canonical (NVT) ensemble with a timestep of 0.5-2 fs for 5-20 ps depending on the temperature and density. We model the feldspar end-members in a cubic cell containing 208 atoms (16 formula units) and 1024 or 1152 electrons for the Na- and K-feldspars respectively. For simulations at low density we used pseudopotentials which require a lower plane wave energy cutoff, set to 370 eV. For Na-end-member, we also used hard pseudopotentials at high density in order to reduce the overlap of electronic spheres, in particular for Na-Na pairs. The energy cutoff for this set of pseudopotentials is 950 eV. Additional details can be found in the manuscript.</p> <p> </p> <p>There is one dataset for each different composition and set of pseudopotentials used:</p> <ol> <li>kobsch-ds01.txt --> NaAlSi<sub>3</sub>O<sub>8</sub></li> <li>kobsch-ds02.txt --> NaAlSi<sub>3</sub>O<sub>8 </sub>and set of pseudopotentials with a lower plane wave energy cutoff than in 01</li> <li>kobsch-ds03.txt --> NaAlSi<sub>3</sub>O<sub>8</sub> and harder pseudopotentials than in 01</li> <li>kobsch-ds04.txt --> KAlSi<sub>3</sub>O<sub>8</sub></li> <li>kobsch-ds05.txt --> KAlSi<sub>3</sub>O<sub>8</sub> and set of pseudopotentials with a lower plane wave energy cutoff than in 04</li> </ol> <p> </p> <p>Each file present the arithmetic time averages of the pressure (P), temperature (T) and internal energy (E). The standard deviation of the data to the mean is indicated by stdev_X, where X is P, T or E. The statistical error to the mean (err_X) is computed using the blocking method as described by Flyvbjerg and Petersen (1989). The sign '>' is indicated before the value of the statistical error when no convergence was reached during the estimation of this error. The heat capacity Cv is computed using fluctuations on both potential and kinetic energies (Allen and Tildesley, 1989) and its statistical error stdev_Cv is computed using the bootstrap method. </p> <p>We computed the thermoelastic coefficients only for densities (<span class="math-tex">\(\rho\)</span>) above 1.5 g.cm<sup>-3</sup>. The thermal pressure coefficient (TPC = <span class="math-tex">\(\frac{\partial P}{\partial T}\big|_V\)</span>) is the slope of linear fit of P vs. T isochores. The isothermal compressibility (<span class="math-tex">\(\beta = -\frac{1}{\rho} \frac{\partial \rho}{\partial P}\big|_T\)</span>) is computed using central finite differences on our P vs. <span class="math-tex">\(\rho\)</span> isotherms. The isobaric expansivity (<span class="math-tex">\(\alpha = \frac{1}{\rho} \frac{\partial \rho}{\partial T}\big|_P\)</span>) is computed using the previously computed <span class="math-tex">\(\beta\)</span> and TPC.</p>
Effect of changing ocean circulation on deep ocean temperature in the last millennium: simulation output data
<ul> <li>This dataset contains the output of model simulations used in the paper:<br> Scheen, Jeemijn and Stocker, Thomas F., "Effect of changing ocean circulation on deep ocean temperature in the last millennium", Earth System Dynamics Discussions, https://doi.org/10.5194/esd-11-925-2020, 2020 </li> <li>All figures can be reproduced when combining this dataset with the published analysis code. <br> </li> <li>In addition this dataset contains the data behind Fig. 2 of the paper:<br> Gebbie, G. and Huybers, P. : "The Little Ice Age and 20th-century deep Pacific cooling", Science, 363, 70-74, https://doi.org/10.1126/science.aar8413, 2019<br> </li> <li>Download either the small (unzipped 5 Gb) or large (unzipped 22 Gb) version of the dataset. <strong>Warning: this needs to be loaded into memory when running the notebook.</strong> You only need the small version to run the github notebook and reproduce the figures, but you are free to explore additional variables in the large version.</li> </ul> <p>Overview of doi's:</p> <ul> <li>paper: <a href="https://doi.org/10.5194/esd-11-925-2020">https://doi.org/10.5194/esd-11-925-2020</a></li> <li>code (analysis and figures): <a href="https://doi.org/10.5281/zenodo.4022947">https://doi.org/10.5281/zenodo.4022947</a></li> <li>data (simulation output): <a href="https://doi.org/10.5281/zenodo.4022927">https://doi.org/10.5281/zenodo.4022927</a></li> </ul>
Datasets For "Estimating Maximum Extent of Auroral Equatorward Boundary using Historical and Simulated Surface Magnetic Field Data", Blake et al. (2020), JGR
<p>Datasets and sample Python codes for the 2020 paper <em>"Estimating Maximum Extent of Auroral Equatorward Boundary using Historical and Simulated Surface Magnetic Field Data"</em>, by Blake et al., submitted to the Journal of Gephysical Research, Space Physics. </p> <p>Up-to-date Python codes can be found at <a href="https://github.com/TerminusEst/Auroral_Boundary_Geomag">https://github.com/TerminusEst/Auroral_Boundary_Geomag</a></p> <p>The complete SWMF simulation folders (including parameter and log files etc.) can be requested from <a href="https://ccmc.gsfc.nasa.gov/index.php">NASA's Community Coordinated Modeling Center</a>.</p> <p>#########</p> <p><strong>Data/ </strong>contains the following:</p> <p><strong>Data/HIST_DATA.txt </strong>contains the minimum Dst values and calculated maximum extents of the auroral equatorward boundaries for 25 years of INTERMAGNET data (1991-2016). The fourth column is the standard deviation of the calculated auroral boundary in degrees. </p> <p><strong>Data/Boundary_Fits.csv </strong>contains the calculated minimum Dst values, and calculated auroral boundaries using Method 1 and Method 2 (see main paper's ttext), for each of the 15 SWMF simulations. Also included are the uncertainties for each calculation.</p> <p><strong>Data/SWMF_outputs/ </strong>contains 15<strong> </strong>.txt files,<strong> </strong>each of which correspond to an SWMF simulation of the same name given in Table 1 in the main text. These data are for the magnetic longitude, magnetic latitude and maximum calculated <em>E<sub>H</sub> </em>(V/km) for each simulation.</p> <p>#########</p> <p><strong>Codes/ </strong>contains two python scripts, and some sample data. These scripts correspond to Section 2 in the main text:</p> <p>1) <strong>Boundary_Calc.py</strong> calculates the extent of the auroral boundary using magnetic latitudes and maximum calculated <em>E<sub>H</sub></em> values from multiple INTERMAGNET sites. </p> <p>2) <strong>Efield_Calc.py </strong>calculates the E-field for a single INTERMAGNET site using the Quebec 1-D resistivity model.</p> <p>A more detailed description of these codes can be found here: <a href="https://github.com/TerminusEst/Auroral_Boundary_Geomag">https://github.com/TerminusEst/Auroral_Boundary_Geomag</a></p> <p> </p>
Mechanical data of rotary shear experiments and temperature measurements for the manuscript: "Fast and localized temperature measurements during simulated earthquakes in carbonate rocks"
<p>Mechanical data of rotary shear experiments and temperature measurements</p> <p>Each experiment is presented in a file with the experiment name (mechanical data of rotary shear experiment) and a file with the experiment name and _Temp (temperature measurement with the optical fiber).</p> <p>Mechanical data are presented in a tab-delimited file with calibrated measurements of:</p> <ul> <li>Time (milliseconds)</li> <li>Normal stress: Normal (MPa) </li> <li>Fault displacement: Slip (mm)</li> <li>Fault velocity: Velocity (mm/s)</li> <li>Shear stress: Shearstress (MPa)</li> <li>Axial shortening: Shortening (mm).</li> </ul> <p> In a separate file, temperature data are presented as tab-delimited file with calibrated measurements of:</p> <ul> <li>Time (milliseconds)</li> <li>Temperature from optical fiber in the channel at 1.5 µm : Temperature_1,5 (°C) </li> </ul>
MD simulation data: An Entropic Safety Catch Controls Hepatitis C Virus Entry and Antibody Resistance
<p><strong>Background</strong></p> <p>Equilibration, relaxation and production runs were performed on GPUs using the CUDA version of PMEMD in AMBER 16 and AMBER ff14SB force field. Minimisation steps were performed on a CPU using PMEMD in AMBER 16 and the AMBER ff14SB force field. All software is available from http://ambermd.org/. </p> <p><strong>Contents</strong></p> <p>There are three tarball (<strong>.tar.gz</strong>) files containing the <strong>core simulation data</strong>: one for wild type (WT), the second for the I438V A524T mutant and the third for the S449P mutant. Each contains:</p> <p>1. a source PDB (<strong>.pdb</strong>) file</p> <p>2. Five AMBER trajectory (<strong>.nc</strong>) files for five independent MD simulations, numbered 1 to 5. <strong>Note: </strong>each of these files is over 2GB.</p> <p>There is an additional tarball containing the <strong>control files</strong> <strong>and scripts</strong> used for running the MD simulations:</p> <p>1. Multiple control (<strong>.ctl</strong>) files numbered 1 to 10 that are used to minimize (<strong>min</strong> prefix), relax (<strong>rel</strong> prefix) and equilibrate (<strong>equ</strong> prefix) the model</p> <p>2. Executable <strong>do_md</strong> that performed all the minimisation, relaxation and equilibration steps</p> <p>3. control file <strong>prod.ctl</strong> used for the production run </p> <p>4. Executable <strong>run_prod</strong> that was used to perform the production run</p> <p>5. Two control files (<strong>prod_short.ctl </strong>and <strong>prod_short_2.ctl</strong>) for the short runs used to de-correlate the simulation for the independent runs</p> <p>6. Executable <strong>run_short</strong> and <strong>run_short_2</strong> used to carry out the de-correlated production runs.</p>
Ionization rate simulation data for "Standing Shock Prevents Propagation of Sparks in Supersonic Explosive Flows"
<p><strong>Background</strong></p> <p>This is a set of 3d data containing ionization rates computed from Hyburn hydrodynamic simulations contained in a Matlab .mat file, along with a plot in both .png and Matlab .fig format, and a Matlab script for plotting.</p> <p>This data is used in figure 5 of the paper "Standing Shock Prevents Propagation of Sparks in Supersonic Explosive Flows".</p> <p>Electric sparks and explosive flows have long been associated with each other. Flowing dust particles originate charge through contact and separate based on inertia, resulting in strong electric fields supporting sparks. These sparks can cause explosions in dusty environments, especially those rich in carbon, such as coal mines and grain elevators. Recent observations of explosive events in nature and decompression experiments indicate that supersonic flows of explosions may alter the electrical discharge process. Shocks may suppress parts of the hierarchy of the discharge phenomena, such as leaders. In our decompression experiments, a shock tube ejects a flow of gas and particles into an expansion chamber. We imaged an illuminated plume from the decompression of a mixture of argon and <100 mg of diamond particles and observe sparks occurring below the sharp boundary of a condensation cloud. We also performed hydrodynamics simulations of the decompression event that provide insight into the conditions supporting the observed behavior. Simulation results agree closely with the experimentally observed Mach disk shock shape and height. This represents direct evidence that the sparks are sculpted by the outflow. The spatial and temporal scale of the sparks transmit an impression of the shock tube flow, a connection that could enable novel instrumentation to diagnose currently inaccessible supersonic granular phenomena.</p> <p><strong>Accessing Data</strong></p> <p>The .mat file can be opened in Matlab to examine data. The 3d arrays contained therein can be viewed in various ways, including using the enclosed script with syntax like plot_isosurfaces(xg,yg,zg,density,max(density(:)),pressure,max(pressure(:))) to produce the included isosurface plot.</p> <p>The data arrays contained are:</p> <p>e: electric field magnitude</p> <p>alpha: ionization rate lengths: ionization lengths (equal to 1/alpha)</p> <p>eOverN: electric field divided by gas number density</p> <p>alphaOverN: ionization rate divided by gas number</p> <p>density density: gas mass density</p> <p>pressure: gas pressure</p> <p>x,y,z: spatial coordinates</p> <p>xg,yg,zg: spatial coordinates in 3d meshgrid format, for Matlab plotting</p> <p>The electric field e was artificially generated from velocities in Hyburn output; alpha was computed from BOLSIG+ with Hyburn input; density and pressure data were from Hyburn.</p> <p> </p>
Supplementary material for "Song et al., Modelling Simul. Mater. Sci. Eng., 2021: Data-mining of dislocation microstructures: concepts for coarse-graining of internal energies"
<p>This zip archive contains supplementary material in the form of datasets and jupyter notebooks that are used in the following publication:</p> <ul> <li>authors: Hengxu Song, Nina Gunkelmann, Giacomo Po, and Stefan Sandfeld</li> <li>journal: Modelling Simul. Mater. Sci. Eng.</li> <li>year: 2021</li> <li>title: Data-mining of dislocation microstructures: concepts for coarse-graining of internal energies</li> </ul>
Transcript quantification data from Varabyou et al. 2020 simulations
<p>Transcript quantification data from different methods and configurations and simulated counts for simulated samples. The quantification results are in quants.tar.gz, and the true transcript fragment counts are in true_counts.tar.gz.</p>
Three-dimensional magnetic reconnection in particle-in-cell simulations of anisotropic plasma turbulence (Simulation Data)
<p>This folder contains the output of the following simulation: </p> <p>We use the explicit Plasma Simulation Code (PSC, Germaschewski et al.2016) to simulate eight anisotropic counter-propagating Alfvén waves in an ion-electron plasma. The anisotropy of the initial fluctuation is set up according to the theory of critical balance by Sridhar & Goldreich (1994) and Goldreich & Sridhar (1995) at the small scale end of the inertial range: <span class="math-tex">\(k_{\parallel} d_{i} = C (|k_{\perp}|d_{i})^{2/3}\)</span>, where <span class="math-tex">\(C= 10^{-4/3}\)</span>. The normalization parameters are the speed of light <span class="math-tex">\(c = 1\)</span>, the vacuum permittivity <span class="math-tex">\(\epsilon_{0} = 1\)</span>, the magnetic permeability <span class="math-tex">\(\mu_{0} = 1\)</span>, the Boltzmann constant <span class="math-tex">\(k_{b}=1\)</span>, the elementary charge <span class="math-tex">\(q=1\)</span>, the ion mass <span class="math-tex">\(m_{i}=1\)</span>, the density of ions and electrons <span class="math-tex">\(n_{i}=n_{e}=1\)</span> and the ion inertial length <span class="math-tex">\(d_{i}=c/\omega_{pi}\)</span> where <span class="math-tex">\(\omega_{pi}=\sqrt{n_{i}q^{2}/m_{i}\epsilon_{0}}\)</span> is the ion plasma frequency. We set <span class="math-tex">\(\beta_{s,\parallel}=1\)</span> and <span class="math-tex">\(T_{s,\parallel}/T_{s,\perp}=1\)</span>, where <span class="math-tex">\(\beta_{s,\parallel}=2 n_s \mu_{0} k_{B}T_{s,\parallel}/B_{0}^{2}\)</span> is the ratio between the plasma pressure parallel to the background magnetic field <span class="math-tex">\(\mathbf{B}_{0}\)</span> and the magnetic pressure and $T_{s,\parallel}$ is the parallel temperature. The magnetic field is normalised to <span class="math-tex">\(B_{0}=V_{A}/c\)</span>, where <span class="math-tex">\(V_{A}=B_{0} / \sqrt{\mu_{0}n_{i}m_{i}}\)</span> is the ion Alfvén speed. We use 100 particles per cell (100 ions and 100 electrons), a mass ratio of <span class="math-tex">\(m_{i}/m_{e} = 100\)</span> so that <span class="math-tex">\(d_e = 0.1 d_{i}\)</span> where <span class="math-tex">\(m_{e}\)</span> is the electron mass and <span class="math-tex">\(d_{e}\)</span> is the electron inertial length. The simulation box size is <span class="math-tex">\(L_{x} \times L_{y} \times L_{z} = 24d_{i}\times24d_{i}\times125d_{i}\)</span> and the spatial resolution is <span class="math-tex">\(\Delta x =\Delta y = \Delta z = 0.06d_{i}\)</span>. We use a time step <span class="math-tex">\(\Delta t =0.06/ \omega_{pi}\)</span>. In our normalisation, the Debye length <span class="math-tex">\(\lambda_{D}=d_{i}\sqrt{\beta_{i}/2}V_{A}/c\)</span> defines the minimum spatial distance that needs to be resolve in the simulation and <span class="math-tex">\(\lambda_D=0.07d_i\)</span>.</p> <p>This output corresponds to <span class="math-tex">\(t=120 \omega_{pi}\)</span>. </p> <p>These data were produced using the Data Intensive at Leicester (DIaL) facility provided by the DiRAC project<br> dp126 "Identifying and Quantifying the Role of Magnetic Reconnection in Space Plasma Turbulence".</p>
Simulated RNA-seq data
<p>Simulated RNA-seq data shows that histograms from p value sets with around one hundred true effects out of 20,000 features can be classified as 'uniform'. RNA-seq data was simulated with polyester R package <a href="https://doi.org/10.1093/bioinformatics/btv272">(Frazee, 2015)</a> on 20,000 transcripts from human transcriptome using grid of 3, 6, and 10 replicates and 100, 200, 400, and 800 effects for two groups. Fold changes were set to 0.5 and 2. Differential expression was assessed using DESeq2 R package <a href="https://doi.org/10.1186/s13059-014-0550-8">(Love, 2014)</a> using default settings and group 1 versus group 2 contrast. Effects denotes in facet labels the number of true effects and N denotes number of replicates. Red line denotes QC threshold used for dividing p histograms into discrete classes. Workflow and code used to run this simulation is available on <a href="https://github.com/rstats-tartu/simulate-rnaseq">rstats-tartu/simulate-rnaseq</a>.</p> <p> </p> <p>Files</p> <ul> <li>de_simulation_results.csv -- merged and processed DE analysis results of simulated data.</li> <li>simulate-reads-2021-01-25.tar.gz -- raw DE analysis results on 20,000 transcripts from human transcriptome using grid of 3, 6, and 10 replicates and 100, 200, 400, and 800 effects for two groups. Fold changes were set to 0.5, 1, and 2. Differential expression was assessed using DESeq2 with default settings.</li> <li>simulate-rnaseq.tar.gz -- snakemake workflow and input fasta file to simulate RNA-seq data with polyester and analyse results with DESeq2. Adjust settings in config.yaml to customise simulation. Includes software to run workflow on Linux, given that <a href="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh">Conda</a> and <a href="https://snakemake.readthedocs.io/en/stable/index.html">snakemake</a> are installed.</li> </ul> <p>The simulate-rnaseq.tar.gz archive can be re-executed on a vanilla machine that only has Conda and Snakemake installed via:</p> <pre><code class="language-bash">tar -xf simulate-rnaseq.tar.gz snakemake --use-conda -n</code></pre> <p> </p> <p> </p>
DCSsim (simulated) and DCSsub (sub-sampled) ChIP-seq data for benchmarking DCS tools.
<p>These data are the results from five independent runs of DCSsim and DCSsub for TF, sharp and broad mark signals in 50:50 and 100:0 regulation scenarios.</p> <p> </p> <p>Simulated data from DCSsim: simulated_ChIP-seq_data.zip</p> <ul> <li>Set1: TF 50:50</li> <li>Set2: TF 100:0</li> <li>Set3: Sharp mark 50:50</li> <li>Set4: Sharp mark 100:0</li> <li>Set5: Broad mark 50:50</li> <li>Set6: Broad mark 100:0</li> </ul> <p> </p> <p>Sub-sampled data from DCSsub: sub-sampled_ChIP-seq_data.zip</p> <ul> <li>Set1: Cebpa-ChIP-seq 50:50</li> <li>Set2: Cebpa-ChIP-seq 100:0</li> <li>Set3: H3K27ac-ChIP-seq 50:50</li> <li>Set4: H3K27ac-ChIP-seq 100:0</li> <li>Set5: H3K36me3-ChIP-seq 50:50</li> <li>Set6: H3K36me3-ChIP-seq 100:0</li> </ul>
HUMANE Wikipedia simulation modelling bootstrapping data
<p>This data set has been derived from the Simple English Wikipedia data publicly available and post-processed in the WikiWarMonitor project. The data set this is derived from is available from: http://wwm.phy.bme.hu/light.html</p> <p>The data set comprises a collection of 15 CSV files with summary statistics of the contributors to Wikipedia (Simple English only) in the period of 18/05/2001 to 17/10/2012. The files cover:</p> <ul> <li>Statistics of registered users, anonymous users and bots.</li> <li>History of revert activity</li> <li>History of edit wars</li> <li>Activity statistics broken down into weekly snapshots</li> </ul> <p>Each CSV file has a descriptive header that is generally self-explanatory, so the data is not further described here. However, note that in the activity_snapshots_aggregated.csv file, the edit war conditions are as follows:</p> <ul> <li>Condition 1: ongoing (started before the snapshot and continues)</li> <li>Condition 2: started and finished within the snapshot</li> <li>Condition 3: started within the snapshot, but did not finish yet</li> <li>Condition 4: started before the snapshot, but finished within the snapshot</li> </ul>
Moisture-Precipitation Couplings for Mesoscale Convective Systems in Tracking Data and Idealized Simulations
<p>Morphological properties, collocated synoptic conditions, and collocated rainfall for mesoscale convective systems in 1) the ISCCP Convective Tracking (CT) dataset with coincident data from the ERA-Interim (ERA-I) reanalysis and the Multi-Source Weighted-Ensemble Precipitation (MSWEP) product and 2) long-channel radiative-convective equilibrium (RCE) simulations in the System for Atmospheric Modeling (SAM).</p> <p><strong>ISCCP_tracking_colloc.tar.gz </strong>- NetCDF files by year from 2000 to 2004 inclusive including ISCCP-CT morphological properties of MCSs, a series of collocated synoptic variables from ERA-5 (including specific humidity, temperature, vertical velocity, and cloud condensate profiles), and collocated precipitation intensity and accumulation from MSWEP.</p> <p><strong>RCE_colloc_execution1.tar.gz</strong> - NetCDF files including RCE-SAM extent of MCSs (RCE_COL_cluster-sizes_*.nc), as well as collocated synoptic variables. Collocation of synoptic variables is performed for these files by extracting and averaging the variables over grid cells where the precipitation is greater than either its mean (RCE_COL_MEAN_*.nc) or its 99th percentile (RCE_COL_99_*.nc).</p> <p><strong>RCE_colloc_execution2.tar.gz</strong> - NetCDF files including RCE-SAM extent of MCSs (RCE_COL_cluster-sizes_*.nc), as well as collocated synoptic variables. Collocation of synoptic variables is performed for these files by taking either the mean (RCE_COL_MEAN_*.nc) or the 99th percentile (RCE_COL_99_*.nc) value over all grid cells within the MCS.<br><br>For the NetCDF files from RCE output, the numeric value in the file name is the corresponding sea surface temperature from 280 to 310 K.</p>
Data archive for journal paper "Assimilation of Sentinel-1 Backscatter into a Land Surface Model with River Routing and Its Impact on Streamflow Simulations in Two Belgian Catchments"
<p>The datasets archived here include data assimilation results presented in the journal paper, "Assimilation of Sentinel-1 Backscatter into a Land Surface Model with River Routing and Its Impact on Streamflow Simulations in Two Belgian Catchments" (https://doi.org/10.1175/JHM-D-22-0198.1). The output was produced by combining land surface modeling (Noah-MP with HYMAP river routing) and Sentinel-1 backscatter data, applying a 1D Ensemble Kalman Filter using the NASA Land Information System. We provide Netcdf daily output files for 6 different experiments</p><p>- OLfd and OLgw: model-only (open-loop, OL) for two different model settings (fd: free drainage and gw: SIMTOP groundwater option) <br>- DASMfd and DASMgw: data assimilation (DA) with soil moisture (SM) updating for two different model settings (fd: free drainage and gw: SIMTOP groundwater option) <br>- DASMLAIfd and DASMLAIgw: data assimilation (DA) with soil moisture (SM) and leaf area index (LAI) updating for two different model settings (fd: free drainage and gw: SIMTOP groundwater option) </p><p>Each experiment directory contains five subdirectories (DAOBS, EnKF, ROUTING, RTM, SURFACEMODEL) with corresponding outputs as described in https://nasa-lis.github.io/LISF/LIS_users_guide/LIS_users_guide.html</p>
Data for: Bayesian Analysis for Remote Biosignature Identification on exoEarths (BARBIE) 2: Using Grid-Based Nested Sampling in Coronagraphy Observation Simulations for O2 and O3
<p>We present all of the data across our SNR and abundance study for the molecules O2 and O3 for an exoEarth twin. The wavelength range is from 0.515-1 micron, with 25 evenly spaced 20% bandpasses in this range. The SNR ranges from 3-20, and the abundance values range in log space in steps of 0.5 and/or 0.25 (all presented in VMR in the associated table). We present the lower and upper wavelength per bandpass, the input O2 and O3 values (abundance case), the retrieved O2 and O3 values (presented as the log10(VMR)), the lower and upper limits of the 68% credible region (presented as the log10(VMR)), and the log-Bayes factor for O2 and O3. For more information about how these were calculated, please see Bayesian Analysis for Remote Biosignature Identification on exoEarths (BARBIE) 2: Using Grid-Based Nested Sampling in Coronagraphy Observation Simulations for O2 and O3, accepted and currently available on arXiv. </p> <p>To open this csv as a Pandas dataframe, use the following command:</p> <p>your_dataframe_name = pd.read_csv(f'zenodo_table.csv', dtype={'Input O2': str, {'Input O3': str}})</p>
Data for: Machine-learning-accelerated simulations enable heuristic-free surface reconstruction
<p>This is the dataset for the publication "Machine-learning-accelerated simulations to enable automatic surface reconstruction", by X. Du, J.K. Damewood, J.R. Lunger, R. Millan, B. Yildiz, L. Li, and R. Gómez-Bombarelli. The repository contains the density-functional theory (DFT) data used to train the neural network force fields (NFF), selected results from our GaN(0001), Si(111), and SrTiO3(001) Virtual Surface Site Relaxation-Monte Carlo (VSSR-MC) runs, and Jupyter notebooks used for analysis and plots. To run the .ipynb's, you will need to install <a href="https://github.com/learningmatter-mit/surface-sampling">surface-sampling</a> (tested up to commit 02820d339eed6291b6af6ccb809f154ad6244110 on master) and <a href="https://github.com/learningmatter-mit/NeuralForceField">NeuralForceField</a> (tested up to commit 72d1f32f43f202c1a466116beeed15845a6456e7 on master) from the <a href="https://github.com/learningmatter-mit">Rafael Gómez-Bombarelli Group @ MIT</a>.</p>
Bubble/Foam Simulations for Malej et al. 2023, source codes, input files, matlab files, data files
<p><i>.F are source codes, *.m are matlab scripts for analysis and postprocessing, .txt are data files including bathymetry and data from sensitivity tests</i></p>
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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.