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1,726 results for “simulation data”
Data from 666 earthquake/tsunami scenario simulations targeting Nankai subduction
<p><strong>Summary: </strong></p> <ul> <li>Data from 666 earthquake/tsunami scenario simulations targeting Nankai subduction</li> <li>Tsunami simulation solver: TUNAMI-N2</li> <li>Fault rupture model: Okada model(Okada, 1985)</li> <li>Each scenario data consists of 71 ASCII files containing the simulated wave sequences at the synthetic gauges </li> <li>Each single scenario is tagged as "Nankai-XYZE", where XYZW would be the number from <strong>0003</strong> to <strong>1470</strong>.</li> <li>Some of the synthetic gauges are located based on the real ocean gauge points (e.g., DONET2, NOPHAS) nearby Shikoku region, Japan.</li> </ul> <p> </p> <p><strong>Details of each file:</strong></p> <ul> <li><strong>wave_sequenses.tar.gz</strong>: A series of wave sequences (4-hour wave history-data, recorded every 5 seconds) at 71 synthetic gauges are provided in ascii type format. <br> Note that <strong>5.8GB additional storage would be required</strong> to fully unzip this archive file with the following command. <pre><code>tar xzvf wave_sequences.tar.gz</code></pre> <p>You can get all scenario data as follows:</p> <pre><code>wave_sequences ├ Nankai-0003 ├ Nankai-0004 ├… ├ Nankai-1467 └ Nankai-1470 </code></pre> <p>Each directory contains the 71 files, head with 'pntX_Y.asc',</p> <pre><code>Nankai-0003 ├ pnt1_01.asc ├ pnt1_02.asc ├... ├ pnt5_46.asc └ pnt5_47.asc</code></pre> <p>which contains the wave sequence data. The ASCII file, the time (minute) elapsed from the fault rupture is aligned in the left column, and the wave displacements \eta (meter) from the original surface location are in the right column.</p> </li> </ul> <ul> <li> <p><strong>quake_params.csv</strong>: The parameter used to generate 666 earthquake scenarios caused by the rupture of rectangular fault, by means of Okada model. (Okada 1985)</p> </li> </ul> <ul> <li><strong>synthetic_gauges.csv</strong>: The locations of 71 synthetic gauges. </li> </ul>
Cerebellum spiking data during simulated saccade control
<p>This repository contains data generated by simulating the cerebellum spiking neural network for saccade motor control. Please refer to the article at https://doi.org/10.1101/2022.03.14.483471.</p> <p>Please check the journal of PLOS computational biology for the published version of this article (inpress).</p> <p>The python scripts will generate plots from the simulation datasets. In order to do so, please unzip the datasets and put each of the data subfolders into the current folder along with the plotting scripts.</p> <p>The spiking neuronal circuit datasets have been generated using the NEST spiking neural network library (https://www.nest-simulator.org/), in .gdf format. Users can refer to the presented python scripts to understand how to read from and plot the data. Additionally, for interested users, the trained PF-PC synaptic weights from saccade simulations are also available as EXCEL files in the same dataset folders.</p> <p>In case of queries or any problems, please email me at the email id given in the article linked above.</p>
Simulation of Fire Propagation in Cable Tray Installations - Data Set
<p>This repository contains simulation data used for a conference paper at ISTSS 2018, with the title "<a href="https://www.researchgate.net/publication/323999819_Simulation_of_Fire_Propagation_in_Cable_Tray_Installations_for_Particle_Accelerator_Facility_Tunnels?ev=auth_pub">Simulation of Fire Propagation in Cable Tray Installations for Particle Accelerator Facility Tunnels</a>". Furthermore, the plots are provided, including the Python 3 scripts to create the plots, used in this paper.</p> <p>With the Fire Dynamics Simulator FDS, in the versions 6.3.2 and 6.5.3, simulations of cable fire tests have been performed. Experimental data from micro-combustion calorimetry and Cone Calorimeter tests were used to calibrate a material parameter set, aming to predict the fire spread in a cable tray installation. The simulations are based on experimental data from the CHRISTIFIRE Phase 1 campaign.</p> <p>The authors want to thank Kevin B. McGrattan for providing access to the CHRISTIFIRE data.</p> <p> </p> <p><strong>Some remarks on the usage:</strong></p> <p>Unfortunately, for some unclear reason, Zenodo does right now not support the creation of folders within the repository. In an effort to maintain the structure of the data, ZIP archives have been created. Note that specifically the MT-3 simulations are quite large and take about 3.5 GB of space after extraction.</p> <p>It is only necessary to reproduce the file structure, if the user wants to utilise the provided Python scripts "as is". It is, of course, also possible to adjust the file pathes in the scripts to the users desire.</p> <p>To recreate the original file structure, one needs to copy all files of this repository into a single directory. The ZIP archives are sub-directories within that basic directory. The names of the archives contain the information of how the sub-directory structure looks like. Triple underscores '___' are placeholders indicating the file path, thus need basically changed to '/'. For example, the ZIP archive ''Cone___CoarseCone___ArrCHRISTIFIRE.zip' translates to the path 'Cone\CoarseCone\ArrCHRISTIFIRE\'.</p> <p> </p>
Data for: Impact of SO2 injection profiles on simulated volcanic forcing for the Sarychev 2009 eruptions - investigating the importance of using high vertical resolution methods when compiling SO2 data
<p>The files are data assosicated with the study High-resolution stratospheric volcanic SO2 injections in WACCM. The files are associated with four differnt simulaions described in the paper: M16, S21-1D, S21-3D and No-Volc. The files with "input" in the name are the SO2 input files used in the WACCM (Whole Atmosphere Community Climate Model) simulations in the paper. The files with "monthly_averages" in the filenames are monthly averages of model output data the variables used in the paper. </p> <p>The CALIOP_monthly_averages.nc file is monthly average of the CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) satellite data used in the study to evaluate the WACCM simulations. </p> <p> </p>
A large data-set of CASP protein refinement simulations for machine-learning
<p>The uploaded trajectory data originates from our own laboratory's refinement method in CASP11 and CASP12 for which the reference crystal structure is available in the PDB. In total the trajectory data consists of 904 trajectories with 3419 ns cumulative simulation time and 1,709,704 snapshots with a delta t =2 ps from 42 different protein systems.</p> <p><strong>File Overview</strong></p> <ul> <li><strong>trajectory_data_pdbs.tar.gz :</strong> contains the PDB files of the different trajectories as well as the starting model and reference crystal structure for each target</li> <li><strong>casp_normalized_all_data_final.csv.gz : </strong>contains the trajectory features calculated for each snapshot from the trajectory PDBs</li> <li><strong>cv_folds.csv : </strong>contains the 7 fold cross-validation assignment used to assess the performance of the model<br> </li> </ul> <p> </p> <p> </p> <p> </p>
Data for the 'Evaluation of global simulations of aerosol particle and cloud condensation nuclei number, with implications for cloud droplet formation'
<p>All numerical data used in the manuscript <strong>“Evaluation of global simulations of aerosol particle number and cloud condensation nuclei, and implications for cloud droplet formation” </strong>by G. S. Fanourgakis et al. ACP (2019) are categorized and provided in a number of files. All files are in the hdf format. A readme file is also provided.</p> <p>These data files have been created by G. S. Fanourgakis (fanourg@uoc.gr)</p> <p>Details on the data are provided in Fanourgakis et al. Atmos. Chem. Phys. 2019 https://doi.org/10.5194/acp-2018-1340 (e-mail to <a href="mailto:mariak@uoc.gr">mariak@uoc.gr</a> ; <a href="mailto:athanasios.nenes@epfl.ch">athanasios.nenes@epfl.ch</a> )</p> <p>For an in-depth understanding of the description below, a study of the above mentioned manuscript is required.</p> <p>(A) Station model results</p> <p>The station results can be found in files with filenames of the form:</p> <p>station $MODEL.nc</p> <p>The “$MODEL” (as well as all names starting with “$”) indicates a variable, and more specifically one of the models participated in the present study. The values of this variable are tabulated in Table 1 in the readme file.</p> <p>In each file a number of computational results are provided by the specified model for all nine (9) stations that provided observational data. The name of the variable is formed as:</p> <p>st $STATION $FIELDhour st $STATION $FIELD month</p> <p>where all possible values of the variables $STATION and $FIELD are tabulated in Tables 2 and 3 in the readme file, respectively. The extension _hour denotes that hourly values for the field are provided, while the extension _month the monthly average of this quantity. For example, the variable</p> <p>st Finokalia CCN02 hour</p> <p>found in the file station_TM4-ECPL.nc, contains the hourly values of the CCN<sub>0<em>.</em>2 </sub>at the Finokalia station as computed by the TM4-ECPL model. In a similar way, in the file station_EMAC.nc, the variable below gives the monthly values of dust at Vavihill as computed with the EMAC model.</p> <p>st Vavihill DU month</p> <p>Notice also that in all files hourly and monthly data are provided for the time period from 1-1-2011 up to 31-12-2015 (60 months and 43,824 hours)</p> <p>(B) Station observational results</p> <p>There is one file that contains all observational data from Schmale et al., SCIENTIFIC DATA | 4:170003 | DOI: 10.1038/sdata.2017.3, 2017 (<a href="mailto:julia.schmale@psi.ch">julia.schmale@psi.ch</a>) and the data that were computed based on the observations (i.e. number of cloud droplets) (contact person: athanasios.nenes@epfl.ch). The file is</p> <p>station observations.nc</p> <p>while the following fields are contained in there:</p> <p>st $STATION $FIELDhour</p> <p>st $STATION $FIELD month</p> <p>The values of variables are given in the Tables 2 and 3 in the readme file. The time period covered is from 1-1-2011 up to 31-12-2015. Notice that due to the lack of observations a lot of data are missing. For missing observational data the value -9999.999 is given. Contact person for the observational data is Julia Schmale (julia.schmale@psi.ch).</p> <p>(C) Station Multi-model Median</p> <p>Monthly averages of the models can be found in the file</p> <p>station MMM.nc</p> <p>The following fields can be found in the file</p> <p>st $STATION $FIELD month median</p> <p>st $STATION$FIELD month quart25</p> <p>st $STATION$FIELD month quart75</p> <p>where the values of the variables $STATION and $FIELD can be found in Tables 2 and 3, respectively. The extension median corresponds to the multi-model median, while the quart25 and quart75 to the 25 % and 75 % quartiles, respectively.</p> <p>(D) Global model results</p> <p>In the following single file can be found for each of the models the surface distribution of various fields.</p> <p>results global models year2011.nc</p> <p>They correspond to the annual mean of the year 2011. The resolution of the grid is 1<sup>◦ </sup>× 1<sup>◦</sup>. The file contains the following variables:</p> <p>$FIELD $MODEL</p> <p>The $FIELD and $MODEL can be found in Tables 3 and 1, respectively.</p> <p>(E) Global average results</p> <p>In the file</p> <p>surface_ global_average_year2011.nc</p> <p>can be found in 5<sup>◦</sup>×5<sup>◦ </sup>resolution, the Multi-model median of surface distribution of the various fields denoted in Table 3 and their corresponding diversity. The names of the variables are formed as:</p> <p>med $FIELD</p> <p>div $FIELD</p> <p>where, ‘med’ stands for median and ‘div’ for diversity calculated as standard deviation divided by the mean of the model results.</p> <p>Tables and details on the fields provided are given in the readme file.</p>
Coherent vortex dynamics in a strongly-interacting superfluid on a silicon chip: Experimental and simulation data sets
<p>This data set collates the experimental and simulation data for the research paper "Coherent vortex dynamics in a strongly-interacting superfluid on a silicon chip".</p>
The data that support the findings of a review paper "From urban data to city-scale models: A review of traffic simulation case studies"
<p>This dataset contains the data that were used in a review paper "From urban data to city-scale models: A review of traffic simulation case studies". It contains the following files:</p> <ul> <li>keywords with counts.txt - list of keywords and their counts in the considered corpus of traffic simulation case studies. The data were used to produce Figure 2 and Figure 3 in the paper.</li> <li>Papers analysis.xlsx - Excel file containing the data on the reviewed studies. The document has the following sheets: <ul> <li> Appendix A - contains a table short reference, location, simulation period, spatial scale, simulated units and marked categories for a paper;</li> <li>Geography - contains data on geographical distribution of simulated areas between world regions and countries, these data were used to produce Figure 4 in the paper;</li> <li>Software tools - contains data on simulation tools used in the studies. </li> <li>Journals and conferences - contains data on where the reviewed papers were published.</li> </ul> </li> </ul>
Data from simulations done in Hydrolight calculating annular irradiances 2021-06-28
<p>This publication contains a dataset of 3024 simulations of irradiances and diffuse attenuation coefficients obtained and calculated with Hydolight software in CSV (.csv) and Python 3.8.0 DataFrame (.pkl) format.</p> <p>Each simulation has its condition of solar zenith angle, cloud coverage and water type (represented by the concentration of chlorophyll, mineral and CDOM absorption), at PAR band (400-700 nm wavelength) and several depths.</p> <p>On the one hand, this data shows the downwelling irradiances obtained by Hydrolight. On the other hand, it shows the annular irradiances and the downwelling and annular diffuse attenuation coefficients calculated from this data.</p> <p>Data contains the following variables:</p> <ul> <li>Ed (Wm<sup>-2</sup>)</li> <li>calculated_Ed (Wm<sup>-2</sup>)</li> <li>calculated_Ea_10 (Wm<sup>-2</sup>)</li> <li>calculated_Ea_20 (Wm<sup>-2</sup>)</li> <li>calculated_Ea_30 (Wm<sup>-2</sup>)</li> <li>calculated_Ea_40 (Wm<sup>-2</sup>)</li> <li>calculated_Ea_50 (Wm<sup>-2</sup>)</li> <li>calculated_Ea_60 (Wm<sup>-2</sup>)</li> <li>calculated_Ea_70 (Wm<sup>-2</sup>)</li> <li>calculated_Ea_80 (Wm<sup>-2</sup>)</li> <li>calculated_Kd (m<sup>-1</sup>)</li> <li>calculated_Ka_10 (m<sup>-1</sup>)</li> <li>calculated_Ka_20 (m<sup>-1</sup>)</li> <li>calculated_Ka_30 (m<sup>-1</sup>)</li> <li>calculated_Ka_40 (m<sup>-1</sup>)</li> <li>calculated_Ka_50 (m<sup>-1</sup>)</li> <li>calculated_Ka_60 (m<sup>-1</sup>)</li> <li>calculated_Ka_70 (m<sup>-1</sup>)</li> <li>calculated_Ka_80 (m<sup>-1</sup>)</li> </ul> <p>Data contains the following index:</p> <ul> <li>wavelength: "PAR" band (400-700 nm)</li> <li>depth: 0.2, 0.5, 1.0, 1.5, 5.0 and 10.0 m.</li> <li>SZA (solar zenith angle): 0, 10, 20, 30, 40, 50, 60, 70 and 80 degrees</li> <li>cloud: 0, 20, 40, 60, 80 and 100 %</li> <li>num: from 0 to 3023</li> <li>water_type: ultra clear, very clear, clear, moderate, turbid, very turbid and brown</li> <li>chl: from 0 to 67.6 mg m<sup>-3</sup></li> <li>cdom: from 0 to 22.5 absoption 380 m<sup>-1</sup></li> <li>mineral: from 0 to 38.7 g m<sup>-3</sup></li> </ul>
MEDIATOR Driving Simulator Study Germany: Questionnaire Data User Evaluation HMI
<p>The dataset provided resulted from a driving simulator study conducted by Chemnitz University of Technology (TUC) within work package 3 of the MEDIATOR project. The study focused on the user evaluation of the Mediator system and its functionalities, including the innovative Human Machine interface (HMI). The user evaluation centred on acceptance, trust, usability, comfort and the experience of Transitions of Control (TOCs). The core idea of the Mediator system is to mediate between the human driver and the automated system. Thereby, the Mediator system aims at establishing both as a team that is aware of each other’s strengths, limitations as well as current states in order to achieve safe TOCs, which are actively proposed by the HMI. The main focus of the driving simulator study was on comfort TOCs from manual to automated driving, simulated automation degradation and related TOCs by the human driver, comfort critical situations (i.e., close approach to the rear-end of a traffic jam) as well as the influence of driver characteristics. The provided dataset contains the questionnaire data of 74 German-speaking participants.</p> <p> </p> <p>This document contains information about the study methodology and coding of the variables. For a detailed description, please consult Mediator deliverable D3.3 ‘Results of the MEDIATOR driving simulator evaluation studies’ (Part II – Driving simulator study Germany). Please note that selected passages of this deliverable were adopted (partly in a slightly modified manner) in this document.</p> <p> </p> <p>This dataset is licensed under a <a href="https://spdx.org/licenses/CC-BY-4.0.html">Creative Commons Attribution 4.0 International</a> License.</p> <p> </p> <p>The research leading to this dataset received funding from the European Commission Horizon 2020 programme under the project MEDIATOR (<a href="https://mediatorproject.eu/">https://mediatorproject.eu/</a>), grant agreement number 814735.</p> <p> </p> <p>If you use the dataset, please cite it as: MEDIATOR (2023). MEDIATOR Driving Simulator Study Germany: Questionnaire Data User Evaluation HMI. <a href="https://doi.org/10.5281/zenodo.7638299">https://doi.org/10.5281/zenodo.7638299</a></p> <p> </p> <p>For further information, please contact: <a href="mailto:cornelia.hollander@psychologie.tu-chemnitz.de">cornelia.hollander@psychologie.tu-chemnitz.de</a>.</p>
Sampled and simulated benthic invertebrate body-mass data from the Porcupine Abyssal Plain Sustained Observatory (4850 m, 48.83° N 16.50 °W, NE Atlantic)
<p>A dataset of sampled and simulated benthic invertebrate body-mass data from the Porcupine Abyssal Plain Sustained Observatory (4850 m, 48.83° N 16.50 °W, NE Atlantic) has been produced. It includes data on macro- and megabenthos derived from a randomly sampled power law distribution, seabed core samples, large-scale seabed photography, and seabed trawls.</p>
Application of two-step clustering algorithm to QuaLiKiz-v2.6.2 turbulent transport simulation data
<p>QuaLiKiz simulation data in support of the two-step clustering algorithm, developed by Bart J. J. Kremers.</p> <p>The NETCDF file, generated via NETCDF4, contains the raw QuaLiKiz output for the 3-dimensional (2-input, 1-output) toy case used to develop the algorithm. Within the NETCDF file, the coordinates represent the code inputs and various vector indices and the data variables represent the code outputs.</p> <p>There are also 4 HDF5 files, containing the results from the two-step clustering reduction algorithm, where the data is saved under 2 keys: "/input" and "/flattened". The file names indicate the reduction algorithm settings used to produce the results within.</p> <p>The algorithm is available open-source at <a href="https://gitlab.com/BartKremers/two-step-clustering">https://gitlab.com/BartKremers/two-step-clustering</a>.</p>
Data and simulation files for "Constraints on the intergalactic magnetic field using Fermi-LAT and H.E.S.S. blazar observations"
<p>In this repository, we provide data files in connection to our paper “Constraints on the intergalactic magnetic field using Fermi-LAT and H.E.S.S. blazar observations” accepted for publication in the Astrophysical Journals and soon available on Arxiv.</p> <p>In the publication, we perform a joint analysis of observations of five blazars with the Fermi Large Area Telescope (LAT) and the High Energy Stereoscopic System (H.E.S.S.) in order to search for signatures of a gamma-ray halo around these sources. The non-detection of such extended emission allows us to place lower limits on the intergalactic magnetic field (IGMF).</p> <p>In this repository, we provide our data analysis products of both H.E.S.S. and LAT data for the case when a template for the halo flux is <em>not</em> included in the data. Furthermore, we provide files that contain the log likelihood profiles as functions of the IGMF in case the halo emission <em>is</em> included. Lastly, we also provide our template files for the halo, generated with <a href="https://crpropa.github.io/CRPropa3/">CRPropa 3</a>.</p> <p>Below, we provide minimal code examples to demonstrate how to read in the specific files.</p> <p><strong>H.E.S.S. observational results</strong></p> <p>We provide the best-fit spectral parameters as well as the flux points (spectral energy distribution; SED) for the H.E.S.S. observations of the five blazars under consideration. The corresponding files are:</p> <ul> <li>hess_fit_result_*.fits which contain the best-fit parameters,</li> <li>hess_sed_file_*.fits which contain the flux points.</li> </ul> <p>In the file names above, the '*' should be replaced with a the corresponding source name, e.g. 1ES0229+200. The files can be read in using astropy:</p> <pre><code class="language-python">from astropy.table import Table src = "1ES0229+200" best_fit_pars = Table.read("hess_fit_result_1ES0229+200.fits") sed = Table.read("hess_sed_file_1ES0229+200.fits")</code></pre> <p><strong>Fermi observational results</strong></p> <p>For Fermi-LAT, we provide the SED files as well as the best-fit models for the region of interests. These files are called:</p> <ul> <li>fermi_avg_file_*.npy provides the best-fit ROI model</li> <li>fermi_sed_file_*.npy provides the SED.</li> </ul> <p>Both of these files are generated with <a href="https://fermipy.readthedocs.io/en/latest/">fermipy</a> and can be read-in the following way:</p> <pre><code class="language-python">import numpy as np # first a little helper function since the # fermipy analysis was run under python 2.7 def convert(data): if isinstance(data, bytes): return data.decode('ascii') if isinstance(data, dict): return dict(map(convert, data.items())) if isinstance(data, tuple): return map(convert, data) return data # Load the ROI fit roi_fit_file = "fermi_avg_file_1ES0229+200.npy" roi_fit = np.load(avg_file, allow_pickle=True, encoding="latin1").flat[0] # if you want to inspect the dictionaries in python 3, you need to run the convert function. # For example, to inspect the central source of the ROI # you would first get the source name src_fgl_name = roi_fit['config']['selection']['target'] # and then you can get the dictionary for the central source src_dict = convert(roi_fit['sources'])[src_fgl_name] # Load the SED sed_file = "fermi_sed_file_1ES0229+200.npy" sed = np.load(sed_file, allow_pickle=True, encoding='latin1').flat[0] # to plot the SED, you can use the SEDPlotter class from fermipy from fermipy.plotting import SEDPlotter SEDPlotter.plot_sed(sed)</code></pre> <p><strong>Likelihood profiles</strong></p> <p>The likelihood profiles as function of the IGMF strengths are provided in the files logl_profile_*_*yr.npz. Their are provided for all five sources and all tested blazar activity times of 10, 10<sup>4</sup>, and 10<sup>7</sup> years. They can be read in with the following code snippet:</p> <pre><code class="language-python">import numpy as np logl = dict(np.load("logl_profile_1ES0229+200_1.0e+07yr.npz")) b_fields = np.array([1.00000e-16, 3.16228e-16, 1.00000e-15, 3.16228e-15, 1.00000e-14, 3.16228e-14, 1.00000e-13]) for k, v in logl.items(): print(k,v)</code></pre> <p>As the print command shows, the python dictionary contains 3 entries: "fermi_only" are the likelihood values for the Fermi data as a function of magnetic field, "combined" are the likelihood values from Fermi and H.E.S.S. combined, and "ps" is the likelihood value of the Fit without halo to the H.E.S.S. data only.</p> <p><strong>Halo simulations</strong></p> <p>Lastly, we also provide the output simulations files from CRPropa. For details how the simulations were run, please consult the accompanying paper, in particular Section 3.1 and Appendix C. For each source redshift, a tar file is provided, which in itself contains 7 hdf5 files with the simulation outputs for each tested magnetic field strength. The name of the files is casc_file_z*.tar.gz. After unpacking the files, they can be read in with your favorite hdf5 library; in python you would need to install h5py. We recommend that you check out <a href="https://github.com/me-manu/simCRpropa">this github repository</a> which provides an advanced python wrapper for CRPropa and functions to read in the files. In particular, you can use <a href="https://github.com/me-manu/simCRpropa/blob/b3f39b5c77c6b97d19f7db387427d857690444d2/simCRpropa/cascmaps.py#L28">this function</a> to read in the files. It also writes a new hdf5 file with parallel transport applied. The written data is also returned together with the configuration dictionary.</p> <pre><code class="language-python">from simCRpropa.cascmaps import stack_results_lso data, config = stack_results_lso("casc_file_z0.140_B1.00e-16.hdf5", "casc_file_z0.140_B1.00e-16_theta_obs0.0.hdf5" )</code></pre> <p>You can provide arbitrary angles between the observer and the jet angles using the theta_obs keyword. Note, however, that the simulations used a jet opening angle of 3 degrees and going beyond that value will return zero halo photons.</p>
Data from Simulations of a Magnetic Shielding System to Deflect Background-Inducing Secondary Electrons away from Space-Based X-ray Detectors
<p>Data from simulations examining the effect of cosmic rays and secondary particles generated by them on background induced in an X-ray astronomy space telescope, and the effectiveness of a surrounding magnetic field at reducing this background.</p> <p>These simulations were performed for the paper “Effectiveness of a dual solenoid magnetic shield at reducing X-ray-like background in silicon-based X-ray detectors” (2023) published in the Journal of Astronomical Telescopes Instruments and Systems. The paper can also be found at https://openresearch.surrey.ac.uk/esploro/outputs/journalArticle/The-Effectiveness-of-a-Dual-Solenoid/99777566602346/filesAndLinks?forceView=true&mode=quickaccess&index=0 .</p> <p>This data was also used for the simulations and analysis described in the thesis "The Simulation, Composition and Shielding of Radiation-Induced X-ray-like Background in Space-Based X-ray Astronomy Missions" (2021), which can be found at <a href="https://doi.org/10.21954/ou.ro.00012e1f">https://doi.org/10.21954/ou.ro.00012e1f</a> .</p>
Soil and meteorological data, and finite element simulation framework for heat transfer through shrubs in winter near Lautaret pass, French Alps
<p>The data allow the calculation using finite element modeling of heat transfer through shrub branches and snow between the atmosphere and the soil. The shrubs are green alders (Alnus viridis). The site where they are found is called Alnus-Nivus (45.034750°N, 6.413630°E, 2034 m asl) near Col du Lautaret, French Alps. The soil data consist in temperature and volumetric liquid water content at 5 and 15 cm depths. One spot is near the alder collar (ALNUS), the other spot is 6 m away, under grass (GRASS).</p> <p>The meteorological data were obtained from the FR-Clt station, 750 m away (45.041278°N, 6.410611°E, 2046 m asl). See (Gupta et al., 2023) for details. Only the data relevant for heat transfer simulations are given.</p> <p>The simulation framework gives the alder mesh used in the heat transfer simulations. Typical simulations use a wood thermal conductivity of 1 W m<sup>-1</sup> K<sup>-1</sup> and a snow thermal conductivity of 0.1 W m<sup>-1</sup> K<sup>-1</sup>. Based on observations, the snow height at Alnus-Nivus is likely to be at least twice the value at FR-Clt. Forcing uses the snow surface temperature, derived from upwelling longwave radiation using an emissivity of 1. The data allow testing thermal bridging through shrub branches. These data are used in a publication in preparation: Domine, Fourteau, Choler, Exploration of Thermal Bridging Through Shrub Branches in Alpine Snow.</p> <p>Reference</p> <p>Gupta, A., Reverdy, A., Cohard, J. M., Hector, B., Descloitres, M., Vandervaere, J. P., Coulaud, C., Biron, R., Liger, L., Maxwell, R., Valay, J. G., and Voisin, D.: Impact of distributed meteorological forcing on simulated snow cover and hydrological fluxes over a mid-elevation alpine micro-scale catchment, Hydrol. Earth Syst. Sci., 27, 191-212, 2023.</p>
Data from 1564 earthquake/tsunami scenario simulations targeting the Nankai Trough subduction zone
<p><strong>Summary:</strong></p> <ul> <li>Data from 1564 earthquake/tsunami scenario simulations targeting the Nankai Trough subduction zone</li> <li>Tsunami simulation solver: TUNAMI-N2</li> <li>Fault rupture model: Okada model (Okada, 1985)</li> <li>Each scenario data comprises 247 ASCII files storing the simulated wave sequences at synthetic gauges.</li> <li>Every single scenario is tagged as "JNan_X.X_YYY", where X.X indicates the magnitude and YYY is a serial number.</li> <li>Some synthetic gauges are in identical locations to actual ocean gauges (e.g., DONET2, NOWPHAS) near Shikoku, Japan.</li> </ul> <p><strong>Details of each file:</strong></p> <ul> <li><strong>data.tar.gz:</strong> A series of wave sequences (6-hour wave historical data, recorded every 5 seconds) at the 247 virtual gauges. Note that 52 GB of additional storage would be required to fully unzip this archive file with the following command. <pre><code>tar xzvf data.tar.gz</code></pre> <p>The unzipped directory contains all scenario data as follows:</p> <pre><code>data ├── JNan_7.6_001 ├── JNan_7.6_002 ├── JNan_7.6_003 ├── ├── ├── JNan_8.8_326 ├── JNan_8.8_327 └── JNan_8.8_328</code></pre> <p>Each directory contains 247 files named 'pntX_YY.asc'.</p> <pre><code>JNan_X.X_YYY ├── pnt1_01.asc ├── pnt1_02.asc ├── pnt1_03.asc ├── ├── ├── pnt5_46.asc ├── pnt5_47.asc └── pnt5_48.asc</code></pre> <p>In each ASCII file, the time (minute) elapsed from the fault rupture is aligned in the left column, and the wave displacements (meter) from the original sea level are in the right column.</p> </li> <li> <p><strong>quake_params.csv:</strong> The parameter used to generate 1564 earthquake scenarios caused by the rupture of rectangular fault, by means of the Okada model (Okada 1985)</p> </li> <li> <p><strong>synthetic_gauges.csv:</strong> The locations of the 247 synthetic gauges</p> </li> </ul>
GR4SP Suite: Additional Data and Simulation Results
<p>This entry is for the GR4SP's Suite, a model and simulation tool used to analyse the Victorian electricity system's history and potential future transition pathways. It includes additional input data and simulation results. Most of these files were used or generated with Jupyter Notebook scripts shared in the author's <a href="https://github.com/gr4sp/simulationEngine">GitHub repository</a>. </p> <p>Input data in YAML files include VIC.yaml with input settings for the business-as-usual scenario. Some of these inputs can be changed to achieve different future trajectories. For example, try increasing 25% the <em>basePrice </em>of Brown Coal and check how this could impact future emission trajectories, electricity production from renewable energy, and spot prices.</p> <p>This entry includes Sobol's sensitivity indices, the Elementary Effects Test (EET) mu* and sigma. The Morris and Sobol sampling results are saved as .tar.gz files with corresponding names. </p> <p>The input data and results for the Energy Vulnerability (EV) assessment quantifying the LIHC indicator and the data used for the Sectoral Network Analysis (SNA) (i.e. ActorActorRelV0.8.csv). </p> <p>This also includes the results from exploring future pathways of the electricity system using EMA workbench's PRIM, FS and other tools for open exploration (https://emaworkbench.readthedocs.io/en/latest/). The exploration was guided by three scenarios: Low-Carbon Transition (LCT), Just Transition (JT), and Sustainability Transition (ST). Any additional file with BAU in the name includes the results for the Business-as-usual scenario.</p> <p>This version of the dataset includes a few results of policy mixes to achieve any of the three transition scenarios generated in the Jupyter Notebook <a href="https://github.com/gr4sp/experiments/blob/main/notebooksGr4sp/ScenariosAnalysis.ipynb">ScenariosAnalysis</a>. The zip file "policyMixesResults" contains the .csv file with the outputs for different input changes. These details of the input changes for each file are in the "ScenarioAnalysisOutputDetailsv0.2.xlsx". The outputs of the model for these policy mixes can be found in the zip file "policyMixesFigs".</p>
Transmission ultrasound data simulated using the k-Wave toolbox as a benchmark for biomedical quantitative ultrasound tomography using a ray approximation to Green's function
<p><strong>Transmission ultrasound data simulated using the k-Wave toolbox as a benchmark for biomedical quantitative ultrasound tomography using a ray approximation to Green's function </strong></p> <p> </p> <p>The folder ‘’simulation<em>’’ </em>includes the transmission ultrasound data sets used in the project:<a href="https://github.com/Ash1362/ray-based-quantitative-ultrasound-tomography">https://github.com/Ash1362/ray-based-quantitative-ultrasound-tomography</a>. In the Github link, the associated project can be found in the branch master in the folder r-Wave #V1.1. (The folder ‘’data_ust_kWave_transmission.zip<em>’’ </em>is deprecated.)</p> <p>...........................................................................................</p> <p>The ultrasound data were simulated using the k-Wave toolbox (version 1.3.) [5] and using a digital breast phantom [4]. In k-Wave version 1.4., no changes have been reported that affects the simulations. The simulations were done assuming isotropic point sources.</p> <p>The folder ‘’simulation<em>’’ </em> must be added to the path:</p> <p><em>''…r-Wave/data/simulation/…''</em></p> <p>For running the Matlab example scripts in the project in the github, the user has two choices: </p> <ol> <li>Simulate the k-Wave ultrasound data by setting <em>data_sim=true;</em> in the examples in the project.</li> <li>Upload the already simulated k-Wave ultrasound data according to the description below and load them by setting <em>data_sim=false;</em> in the examples in the project.</li> </ol> <p>Please read the description in the example scripts!</p> <p>…………………………………………………………………………………</p> <p>The folder simulation includes 2 subfolders, ‘’phantom<em>’’ </em>and ‘’data_ust_kWave_transmission<em>’’.</em></p> <p>1) The subfolder ‘’simulation/phantom<em>’’ </em> includes ‘’OA-BREAST<em>’’. </em></p> <p>In the project: https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/,</p> <p>the user must upload the folder ‘’Neg_47_Left<em>’’ </em>, and add it as ‘’r-wave/data/simulation/phantom/OA-BREAST/Neg_47_Left/<em>’’.</em></p> <p><em>.......................................................................................................................................................................</em></p> <p>2) The subfolder ‘’simulation/data_ust_kWave_transmission’<em>’ </em>includes 2 subfolders, ‘’2D<em>’’ </em> and ‘’3D<em>’’ </em>.</p> <p>The subfolder ‘’2D<em>’’ </em> includes:</p> <p><strong>data_ust_kWave_transmission/2D/PulsePammoth_1_dx4_cfl1_Nr256_Ne64_Interpoffgrid_Transgeompoint_Absorption1_CodeMatlab/data4_sphere_nonsmooth.mat</strong></p> <p>Two transmission ultrasound data sets were simulated using the k-wave for only water and breast in water according to section <em>‘’6.1. data simulation’’</em> in [1]. 64 emitters and 256 receivers are simulated as off-grid points which are placed on a 2D circular ring. (The characters ‘’_sphere_’’ are added to indicate that the transducers are placed on a ring.) To simulate the data, each emitter was individually driven by an excitation pulse, and the induced acoustic pressure time series were recorded on all the receivers. The k-Wave simulation was performed on a grid with grid spacing 0.4 mm, and the time spacing was set using a CFL number 0.1. The acoustic absorption and dispersion were accounted for based on the frequency power law. This data set is used for the purpose of image reconstruction, and therefore, the sound speed and absorption coefficients maps are not smoothed, i.e., the original maps are used for simulations. This data set can be used for image reconstruction using the time-of-flight-based approach and then the Green's approach.</p> <p><strong>data_ust_kWave_transmission/2D/PulsePammoth_1_dx4_cfl1_Nr256_Ne64_Interpoffgrid_Transgeompoint_Absorption1_CodeMatlab/data4_plane_nonsmooth.mat</strong></p> <p>Two transmission ultrasound data sets were simulated using the k-wave for only water and breast in water. 64 emitters and 256 receivers are simulated as off-grid points which are placed on 16 planar arrays which are all aligned with a circle. Each planar array includes 4 emitters and 16 receivers. Therefore, in contrast with the data mentioned above, the ray linking is performed using the line equations defining the 2D geometry of the linear arrays. (The characters ‘’_plane_’’ are added to indicate that the transducers are placed on line.) To simulate the data, each emitter was individually driven by an excitation pulse, and the induced acoustic pressure time series were recorded on all the receivers. The k-Wave simulation was performed on a grid with grid spacing 0.4 mm, and the time spacing was set using a CFL number 0.1. The acoustic absorption and dispersion were accounted for based on the frequency power law. This data set is used for the purpose of image reconstruction, and therefore, the sound speed and absorption coefficients maps are not smoothed, i.e., the original maps are used for simulations. This data set can be used for image reconstruction using the time-of-flight-based approach, but ahs not been extended to the Green's approach yet. The image reconstruction should be slower than the circular array. the reason is for circular array, for each emitter, the raylinking problem is solved for all receivers once using the equation of circle. However, for this data set, for each emitter, the ray linking problem is solved for each receiver array separately, because receiver arrays are defined with different line equations.</p> <p><strong>data_ust_kWave_transmission/2D/PulsePammoth_1_dx4_cfl1_Nr256_Ne64_Interpoffgrid_Transgeompoint_Absorption1_CodeMatlab/data4_sphere_smooth_17_1.mat</strong></p> <p>Two transmission ultrasound data sets were simulated using the k-Wave for only water and breast in water as the benchmark for validation of ray approximation to Green’s function in homogeneous and heterogenous media, respectively. The simulation was performed according to section <em>‘’6.2. Numerical validation of the ray approximation to the Green’s function’’</em> in [1].</p> <p>64 emitters and 256 receivers are simulated as off-grid points which are placed on a 2D circular ring. (The characters ‘’_sphere_’’ are added to indicate that the transducers are placed on a ring.) The pressure field was produced by emitter 1 (of the 64 emitters) and was recorded in time on all 256 receivers. The k-Wave simulation was performed on a grid with grid spacing 0.4 mm, and the time spacing was set using a CFL number 0.1. The acoustic absorption and dispersion were accounted for based on the frequency power law. The sound speed and absorption coefficient maps were smoothed by an averaging window of size 17 grid points. This data set is used as the benchmark for measuring accuracy of ray approximation to Green’s function for computing phase and amplitude of the pressure field on the receivers.</p> <p><strong>data_ust_kWave_transmission/2D/PulsePammoth_1_dx4_cfl1_Nr256_Ne64_Interpoffgrid_Transgeompoint_Absorption1_CodeMatlab/data4_sphere_smooth_17_20.mat</strong></p> <p> This data set is the same as data4_smooth_17_1 except the pressure field is produced by emitter 20.</p> <p>………………………………………………………………………………………………………………….</p> <p>The subfolder ‘’3D<em>’’ </em> includes:</p> <p><strong>data_ust_kWave_transmission/3D/PulsePammoth_1_dx5_cfl1_Nr4096_Ne1024_Interpnearest_Transgeompoint_Absorption0_CodeCUDA/data5_sphere_nonsmooth_tof_singram.mat</strong></p> <p>The discrepancy of time-of-flight data for two transmission ultrasound data sets simulated by the k-wave for breast in water and only water according to section 5.2 in [3]. The pressure fields were produced by 1024 emitters separately and were recorded on 4096 receivers. The emitters and receivers were simulated as points which are placed on a 3D hemispherical surface, and are interpolated onto the grid using a neighboring interpolation. The k-Wave simulations were performed on a grid with grid spacing 0.5 mm, and the time spacing was set using a CFL number 0.1. The time-of-flight data were computed and will be used for a refraction-corrected image reconstruction of the sound speed based on the inversion approach proposed in [3].</p> <p><strong>References</strong></p> <p>1 - A. Javaherian, ❝Hessian-inversion-free ray-born inversion for high-resolution quantitative ultrasound tomography❞, 2022, <a href="https://arxiv.org/abs/2211.00316/">https://arxiv.org/abs/2211.00316/</a> .</p> <p>2 - A. Javaherian and B. Cox, ❝Ray-based inversion accounting for scattering for biomedical ultrasound tomography❞, Inverse Problems vol. 37, no.11, 115003, 2021. <a href="https://iopscience.iop.org/article/10.1088/1361-6420/ac28ed/">https://iopscience.iop.org/article/10.1088/1361-6420/ac28ed/</a></p> <p>3- A. Javaherian, F. Lucka and B. T. Cox, ❝Refraction-corrected ray-based inversion for three-dimensional ultrasound tomography of the breast❞, Inverse Problems, 36 125010. <a href="https://iopscience.iop.org/article/10.1088/1361-6420/abc0fc/">https://iopscience.iop.org/article/10.1088/1361-6420/abc0fc/</a> </p> <p>4- Y. Lou, W. Zhou, T. P. Matthews, C. M. Appleton and M. A. Anastasio, ❝Generation of anatomically realistic numerical phantoms for photoacoustic and ultrasonic breast imaging❞, J. Biomed. Opt., vol. 22, no. 4, pp. 041015, 2017. <a href="https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/">https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/</a></p> <p>5 - B. E. Treeby and B. T. Cox, ❝k-Wave: MATLAB toolbox for the simulation and reconstruction of photoacoustic wave fields❞, J. Biomed. Opt. vol. 15, no. 2, 021314, 2010. <a href="http://www.k-wave.org/">http://www.k-wave.org/</a></p>
Plot-level field data and model simulation results, archived to accompany Turner et al. manuscript; reports data from summer 2017 sampling of short-interval fires that burned during summer 2016 in Greater Yellowstone.
Subalpine forests in the northern Rocky Mountains have been resilient to stand-replacing fires that historically burned at 100–300-yr intervals. Fire intervals are projected to decline drastically as climate warms, and forests that reburn before recovering from previous fire may lose their ability to rebound. We studied recent fires in Greater Yellowstone (Wyoming, USA) and asked whether short-interval (less than 30 yrs) stand-replacing fires can erode lodgepole pine (Pinus contorta var. latifolia) forest resilience via increased burn severity, reduced early postfire tree regeneration, reduced carbon stocks, and slower carbon recovery. During 2016, fires reburned young lodgepole pine forests that regenerated after wildfires in 1988 and 2000. During 2017, we sampled 0.25-ha plots in stand-replacing reburns (n=18) and nearby young forests that did not reburn (n=9). We also simulated stand development with and without reburns to assess carbon recovery trajectories. Nearly all prefire biomass was combusted ("crown fire plus") in some reburns in which prefire trees were dense and small (≤ 4 cm basal diameter). Postfire tree seedling density was reduced six-fold relative to the previous (long-interval) fire, and high-density stands (greater than 40,000 stems ha-1) were converted to sparse stands (less than 1,000 stems ha-1). In reburns, coarse wood biomass and aboveground carbon stocks were reduced by 65% and 62%, respectively, relative to areas that did not reburn. Increased carbon loss plus sparse tree regeneration delayed simulated carbon recovery by greater than 150 yrs. Forests did not transition to nonforest, but extreme burn severity and reduced tree recovery foreshadow an erosion of forest resilience.
MACREL software benchmark data set: Simulated metagenomes with sequencing quality, errors profile and abundance distributions derived from real samples
<p>These metagenomes were used in the benchmarking of FACS pipeline, and were designed after NGLess benchmark dataset (doi.org/10.5281/zenodo.2560288). Metagenomes were simulated with <a href="https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm">ART-bin-MountRainier-2016.06.05</a> using real abundance profiles (.abund files) available <a href="https://doi.org/10.5281/zenodo.2560288">elsewhere</a>, and <a href="http://progenomes1.embl.de/data/repGenomes/representatives.contigs.fasta.gz">proGenomes' representative contigs</a> as reference genomes. There are available metagenomes with 40, 60 and 80 M (million of reads) based in the reference genomes and abundances of the following samples:</p> <pre><code>SAMEA2466916 SAMEA2466953 SAMEA2466965 SAMEA2621107 SAMEA2621229 SAMEA2621247</code></pre> <p>To convert them from the CRAM format back to fastq files:</p> <pre><code> ## 1. converting from cram to bam format: samtools view -b -T refgenome.fa -o file.bam file.cram ## 2. sorting the bam file: samtools sort -n file.bam -o input_sorted.bam # sort reads by identifier-name (-n) ## 3. converting from bam to fastq format: bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq </code></pre> <p> </p>
ScienceDex guides
Understand access before you commit
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.