Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
11,506
datasets available to search
ShareScore release 0.9.0
Dataset results
11,506 results for “Dynamics”
The Set Increment with Limited Views Encoding Ratio (SILVER) Method for Optimizing Radial Sampling of Dynamic MRI: Supporting Data
<p>This data was created to perform the first experiments with the SILVER method of optimizing radial MRI acquisition. The files are mainly .mat files containing the numerical data used to assess the SILVER method using MATLAB (Version R2018b). Instructions on how to use the data and how to reproduce the experiments are available on https://github.com/SophieSchau/SILVER</p>
Dataset to "Applied Research of the Hygrothermal Behaviour of an Internally Insulated Historic Wall without Vapour Barrier: In Situ Measurements and Dynamic Simulations"
<p>This record contains raw data of a 3-month monitoring period of the HeLLo project.</p> <p>The datafiles titled MeasLog_YYYY-MM-DD.dat correspond to the raw data used for the data analysis presented in “Hygrothermal analysis at critical points of an internally insulated historic wall without vapour barrier: in situ measurements and dynamic simulation”, submitted for publication in journal <em>energies</em>.</p> <p>Each file, format MeasLog_YYYY-MM-DD.dat, corresponds to daily registered data monitored every minute.</p> <p>Each file, format MeasLog_YYYY-MM-DD.dat, contains temperature (T) and relative humidity (RH) values, monitored through T-RH sensors (Telaire T9602; Amphenol). The general architecture of the acquisition system is based on a Master Slave configuratio, as described in “Development of a Compatible, Low Cost and High Accurate Conservation Remote Sensing Technology for the Hygrothermal Assessment of Historic Walls” (doi:10.3390/electronics8060643).</p> <p>Each file, format MeasLog_YYYY-MM-DD.dat is a text-based DAT file and can be opened with a standard text editor.</p>
Molecular dynamics trajectories for SARS-CoV-2 Mpro with 7 HIV inhibitors
<p>Raw trajectory data (GROMACS format) of all atom molecular dynamics simulation of COVID-19 related SARS-CoV-2 dimeric main protease (based on PDB 6LU7) with 7 kinds of HIV inhibitors (darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir) were calculated on massively parallel supercomputer HOKUSAI Big Waterfall at RIKEN ISC, and a special-purpose computer, MDGRAPE-4A, at RIKEN BDR, JAPAN. For each ligand, 200ns length 28 trajectories were calculated. Some of these trajectories were calculated further longer. We can observe formation of encounter complex and investigate potential binding sites on the surface of the dimeric protease. We hope that these raw data are valuable for further drug repurposing/development research targeting the SARS-CoV-2 main protease. We will submit analysis of these data to refereed journal.</p> <p>Molecular dynamics simulations were performed under NVT at 310K, with the time step 2.5fs. The starting structure was prepared based on PDB 6LU7, with amber14sb force field in about 10nm cubic box with periodic boundary conditions. The ligands were initially placed apart from the active sites of the dimeric main protease.</p> <p>We have also already deposited 10 microseconds trajectories of the dimeric protease without ligand (with amber99sb-ildn force field) in the repository https://data.mendeley.com/datasets/vpps4vhryg/1 (DOI:10.17632/vpps4vhryg.1).</p> <p>Files:</p> <ul> <li><strong><em>LIG</em></strong>_28traj200ns_every200ps.zip (28trajectories for each ligand) <ul> <li>traj200ns_every200ps/<strong><em>LIG</em></strong>/<strong><em>a</em></strong>/traj200ns_every200ps_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>.xtc <ul> <li>(trajectory in GROMACS XTC)</li> </ul> </li> <li>traj200ns_every200ps/<strong><em>LIG</em></strong>/<strong><em>a</em></strong>/conf.gro <ul> <li>(initial condition in GROMACS GRO)</li> </ul> </li> <li>traj200ns_every200ps/<em><strong>LIG</strong></em>/topology/ <ul> <li>(contains topology files)</li> </ul> </li> <li>traj200ns_every200ps/<strong><em>LIG</em></strong>/mdp/ <ul> <li>(contains run paramter files)</li> </ul> </li> </ul> </li> <li>ZZZ_20traj1us_every200ps.zip (20trajectories extended to 1microsecond) <ul> <li>traj1us_every200ps/traj1us_every200ps_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>.xtc <ul> <li>DAR-C-06, DAR-D-07</li> <li>IND-C-05, IND-C-06, IND-D-06</li> <li>LOP-A-02, LOP-D-03</li> <li>NEL-B-01, NEL-C-07, NEL-D-02</li> <li>RIT-B-07, RIT-C-07</li> <li>SAQ-B-01, SAQ-C-04, SAQ-D-03</li> <li>TPR-A-07, TPR-B-04, TPR-B-06, TPR-C-05, TPR-D-02</li> </ul> </li> </ul> </li> <li>ZZZ_3traj6us_every1ns.zip (3trajectories extended to 6microseconds or more) <ul> <li>traj6us_every1ns/traj6us_every1ns_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>.xtc <ul> <li>IND-D-06, NEL-B-01, TPR-B-04</li> </ul> </li> </ul> </li> </ul> <p> </p> <ul> <li>ZZZ_LigandBindingPosePDBs.zip (pickup 3 snapshots for each ligand) <ul> <li>LigandBindingPosePDBs/<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>_frame.pdb</li> </ul> </li> </ul> <p> </p> <ul> <li>movies_overlooking_28traj200ns.zip (7x2movies) <ul> <li>movies_28traj200ns/movie_overlooking_<strong><em>LIG</em></strong>_28traj200ns-viewA.mp4 <ul> <li>inspecting 28traj at once</li> </ul> </li> <li>movies_28traj200ns/movie_overlooking_<strong><em>LIG</em></strong>_28traj200ns-viewB.mp4 <ul> <li>from the opposite angle</li> </ul> </li> </ul> </li> <li>movies_1us.zip (17movies) <ul> <li>movies_1us/movie_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>_1us.mp4</li> </ul> </li> <li>movies_6us.zip (3movies) <ul> <li>movies_6us/movie_<em><strong>LIG</strong>-<strong>a</strong>-<strong>n</strong></em>_6us.mp4</li> </ul> </li> </ul> <p> where</p> <p> <em><strong>LIG</strong></em>={DAR,IND,LOP,NEL,RIT,SAQ,TPR}<br> DAR:darunavir<br> IND:indinavir<br> NEL:nelfinavir<br> RIT:ritonavir<br> SAQ:saquinavir<br> TPR:tipranavir<br> <em><strong>a</strong></em>={A,B,C,D}<br> <em><strong>n</strong></em>={01,02,03,04,05,06,07}</p> <p> </p> <ul> <li>ZZZz_3traj1us_every200ps_unbinding.zip (3trajectories extended to 1microsecond exhibiting unbinding)</li> <li>ZZZz_56traj200ns_every200ps_negative_control.zip (56trajectories as a negative control)</li> <li>ZZZz_LigandBindingPosePDBsRevised.zip (pickuped 3 snapshots for each ligand)</li> </ul> <p> </p>
Figure 3 in Temporal dynamics of invertebrate and aquatic plant communities at three intermittent ponds in livestock grazed Patagonian wetlands
Figure 3. Seasonal variation of total taxa richness (A), mean density (A), and relative contribution of biomass (B) of most abundant groups of aquatic invertebrates at three ponds in a Patagonian wetland (Mallín Crespo) during the study period (May 2008 to April 2009). Livestock stocking period is indicated by the black bar.
Figure 3 in Investigating the influence of habitat type and weather conditions on the population dynamics of land snails Vertigo angustior Jeffreys, 1830 and Vertigo moulinsiana (Dupuy, 1849). A case study from western Poland
Figure 3. Diagram of one-way analysis of covariance test comparing a logarithmized number of individuals of Vertigo angustior (F = 92.16; p <0.01) and Vertigo moulinsiana (F = 8.165; p <0.01) in the Ilanka and Pliszka sites in 2009. Middle line: mean; box range: standard error; whiskers: standard deviation.
Figure 2 in Investigating the influence of habitat type and weather conditions on the population dynamics of land snails Vertigo angustior Jeffreys, 1830 and Vertigo moulinsiana (Dupuy, 1849). A case study from western Poland
Figure 2. Precipitation in the studied sites in consecutive months of 2009; dashed bars – sampling months. (B) and (C) Abundance of individuals: juveniles (white bars) and adults (black bars) of Vertigo angustior (B) and Vertigo moulinsiana (C) in each sampling event in the Ilanka and Pliszka sites in 2009.
Structural dynamics of DNA depending on methylation pattern: Simulation dataset
<p>Dataset of molecular dynamics simulations of double-stranded DNA<br> (repeats of CpG dinucleotides with regular patterns of methylation).</p> <p>- Input: Parameters and initial structures<br> - Output: Trajectories</p> <p>NAMD 2.13 (multi-core with CUDA) was used for the simulations.</p>
Figure 1 in Terrestrial isopods and myriapods in a forested scree slope: subterranean biodiversity, depth gradient and annual dynamics
Figure 1. Distribution of Isopoda, Diplopoda and Chilopoda along the depth gradient of the scree slope expressed as the total number of individuals trapped in two sampling periods (November 2008–November 2009; November 2009–July 2010).
Data from: Dynamics of diet-egg transfer of fatty acids in the teleost fish, red drum (Sciaenops ocellatus)
<p>Eggs of marine organisms are increasingly being recognized as important components of marine food webs. The degree to which egg fatty acid profiles reflect maternal diet fatty acid profiles, and therefore the value of fatty acids in eggs as trophic biomarkers, depends on the species' reproductive strategy and the extent of modification of ingested fatty acids. We measured the dynamics of transfer of recently ingested fatty acids to spawned eggs in a batch-spawning teleost, red drum (<em>Sciaenops ocellatus</em>). Results of 21 dietshift experiments, from which the fatty acid profiles of the diets and eggs were compared, showed that 15 of 27 fatty acids measured (one saturated, two monounsaturated and 12 polyunsaturated fatty acids) in eggs were correlated with their levels in the recent diet, and the rate of incorporation into eggs was proportional to the magnitude of the diet shift. Large shifts in diet might occur naturally during spawningmigrations or when prey communities vary over time. Results of this study indicate that fatty acids in red drum eggs can be useful for studying adult diet and exploring trophic linkages in marine systems.</p> <p>This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.</p>
Figure 5 in Population dynamics of the gall inducer Eriogallococcus isaias (Hemiptera: Coccoidea: Eriococcidae) on Pseudobombax grandiflorum (Malvaceae)
Figure 5. Phenological cycle of the galls induced by Eriogallococcus isaias on Pseudobombax grandiflorum from August to December 2008.
Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å
<p>These are the molecular dynamics (MD) data that are analyzed, in Flores et al. 2020. Each trajectory file (.dcd) has an associated structure file (.psf), which can be analyzed in VMD. Each gap junction system, Cx46 & Cx50, were simulated with either KCl or NaCl in the intracellular space: Cx46_KCl/NaCl, Cx50_KCl/NaCl. All four systems were equilibrated for 30ns and then followed up with 2 separate 100ns production runs.</p> <p>For MD lipid-densities the Cx50_KCl system was used as the representative dataset. Lipid densities from all other systems can be calculated with the provided TCL script <em>calc-density.tcl</em>. </p> <p><strong>In VMD TK-Console:</strong></p> <p>> mol new <system>.psf<br> > mol addfile <system>.dcd waitfor all<br> > source /path/to/scripts/LipNetwork.tcl<br> > align<br> > source /path/to/scripts/calc-density.tcl<br> > dmpcdensity <outname><br> [output] outname_ltailden.dx<br> <br> Convert from .dx to .mrc using <em>UCSF-Chimera Volume_Viewer</em> plugin.<br> [output] outname_ltailden.mrc<br> <br> <strong>Using Relion:</strong><br> <br> $ relion_image_handler --i outname_ltailden.mrc --o outname_ltailden_D6-Sym.mrc --sym D6<br> [output] outname_ltailden_D6-Sym.mrc</p> <p> </p> <p>All trajectory files (.dcd) are 100ns longs (1,000 frames x 100ps/frame).</p> <p>For questions regarding MD-data analysis and full trajectory files (2ps/frame), please contact Dr. Steve Reichow (reichow@pdx.edu).</p>
Investigation of Dynamic Fracture of Elastomers - I
<p>Dynamic fracture of a Poly Urethane elastomer has been investigated. Pure shear samples made of Poly Urethane have been used for this experimental work. The samples are 200 mm long, 40 mm tall and 3 mm thick.</p> <p>The test protocol involves stretching the sample first to the required strain level and then introducing a seed crack into the specimen. The seed crack then propagates through the specimen thereby breaking it into two pieces. The two steps are recorded by two cameras - a High Resolution (HR) camera to record the initial stretching and a High Speed (HS) camera to record the fracture process.</p> <p>The data set contains the initial loading (stretching) and fracture images of the experiment. The experiments have been performed by Thomas Corre and Michel Coret.</p> <p>The compressed folder consists of folders named according to the initial stretch level. For example L17 would indicate an initial stretch ratio (\lambda_y) of 1.7.</p>
Coarse-grained Near-global Aqua-planet Simulation with Computed Dynamical Tendencies
<p>This dataset includes the coarse-grained 3D state of the near-global CRM simulations (NG-Aqua). The simulation is run at a 4km resolution using the System for Atmospheric Modeling (SAM)</p> <p>A dataset derived from the same simulation is included at the <a href="https://dx.doi.org/10.5281/zenodo.1226370">10.5281/zenodo.1226370</a>. This current posting supplements this dataset with the dynamical tendencies for total water and liquid-ice potential temperature, respectively given by FQT and FSLI. These are computed by initializing SAM run at a 160km resolution with the coarse-grained fields from NG-Aqua; evolving the state forward for 10 30 second time steps; saving the output; and finally computing the difference with the initial condition.</p> <p>This netCDF dataset is split into several part files for more robust uploading/downloading. To download this data, download each "part" file, and combine them with the "cat" linux command:</p> <pre><code>cat noBlur.nc.part?? > noBlur.nc</code></pre> <p>If using this with the uwnet code repository, you should then move this file to "data/processed/training/noBlur.nc", creating that folder if necessary.</p>
An introduction to the use of Extended Petri Nets to represent Hydrological Dynamical Systems
<p>The video tries to be a quiet introduction to the Extended Petri Nets (EPN), a graphical representations designed to describe Earth Science and Environmental models that results is systems of ordinary differential equations. The video uses an example to exemplify the mechanics of EPN and constitute ancillary material for a paper submitted to Hydrological Processes (https://osf.io/fpx7y/). The main reference for the EPN is: Bancheri,M., Serafin,F. and Rigon, R (2019), "The representation of hydrological dynamical systems using the extended petri nets." Water Resources Research, 8(01), 159–27. In our opinion, EPN improve models representation and help to understand the feedbacks among the various processes.</p> <p> </p>
H.I.D.R.A.: A Hierarchical, Interactive and Dynamic Recognition Architecture for Product Categorization
<p>The Hierarchical, Interactive and Dynamic Recognition Architecture (H.I.D.R.A.) for Product Categorization is a new intelligent system architecture developed by Elo7 to easily evolve its category tree and automatically classify millions of products, thus improving the page ranking of our marketplace.</p>
Vortex input files -- Ashe et al., "Minding the data-gap trap: predicting the dynamics of abundant dolphin species under uncertainty"
<p>Vortex input file used for analyses presented in:<br> "Minding the data-gap trap: predicting the dynamics of abundant dolphin species under uncertainty", <br> by Erin Ashe, Rob Williams, Christopher Clark, Christine Erbe, Leah Gerber, Ailsa Hall, Philip Hammond, Robert C. Lacy, Randall Reeves, & Nicole Vollmer<br> </p>
Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite"
<p>Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite", by Paulina Szymoniak, Brian R. Pauw, Xintong Qu, and Andreas Schönhals.</p> <p>Datasets are in three-column ascii (processed and azimuthally averaged data) from a Xenocs NanoInXider SW instrument. Monte-Carlo analyses were performed using McSAS 1.3.1, other analyses are in the Python 3.7 worksheet. Graphics and result tables are output by the worksheet. </p>
Holocene regional population dynamics and climatic trends in the Near East: a first comparison using archaeo-demographic proxies (dataset and R scripts)
<p>The present digital archive is the outcome of the paper: <strong>Palmisano, A., Lawrence, D., de Gruchy, M.W., Bevan, A., and Shennan, S., 2021. <a href="https://doi.org/10.1016/j.quascirev.2020.106739">Holocene regional population dynamics and climatic trends in the Near East: a first comparison using archaeo-demographic proxies</a>. <em>Quaternary Science Reviews</em>, <em>252</em></strong>.</p> <p>The dataset included here provides a collection of <strong>10,606</strong> radiocarbon dates, <strong>1884</strong> sites from archaeological surveys (1336 from Central Anatolia and 478 from Upper Mesopotamia) and <strong>16</strong> palaeoclimatic records for a period spanning between 14,000 and 2500 BP. In addition, the digital archive related to this paper provides reproducible analyses in the form of four scripts written in R statistical computing language.</p> <p>List of versions:</p> <ul> <li><strong>2.0.</strong> 15 December 2020 — Includes a few minor error corrections (the files 'References.txt' within the folder csv and the script 'radiocarbon.R').</li> <li><strong>1.0</strong> 28 November 2020 — First public release of the dataset on Zenodo.</li> </ul>
Cyclone tracks from 1901 to 2010 in dynamically downscaled ERA-20C reanalysis (COSMO-CLM+NEMO)
<p>The database contains two files: one with all cyclone trajectories from 1901 to 2010, and another one only with the so-called Vb-cyclones that propagate from the Mediterranean Sea north-eastward to Central Europe.</p> <p>We detected the cyclone trajectories with the method of Wernli and Schwierz (2006) and Sprenger et al. (2017) and classified all cyclone trajectories that crossed the 47°N latitude between 12°E and 22°E as Vb-cyclones following Hofstätter and Blöschl (2019). The cyclone tracking was based on mean sea level pressure data of dynamically downscaled ERA-20C reanalysis. The downscaling was performed over Europe [including MED-CORDEX (Somot et al. 2018) and EURO-CORDEX (Giorgi et al. 2009)] from 1901 to 2010 with an interactively coupled high-resolution atmosphere-ocean model (COSMO-CLM+NEMO) by Cristina Primo. More details on the data basis can be found in Primo et al. (2019) and Krug et al. (2020).</p> <p> </p> <p>Giorgi, F., Jones, C. & Asrar, G. Addressing climate information needs at the regional level: the CORDEX framework.<em> WMO Bulletin</em> <strong>58</strong>, 175–183 (2009).</p> <p>Hofstätter, M. & Blöschl, G. Vb Cyclones Synchronized With the Arctic-/North Atlantic Oscillation. <em>J. Geophys. Res. Atmos.</em> <strong>124</strong>, 3259–3278 (2019).</p> <p>Krug, A., Primo, C., Fischer, S., Schumann, A. & Ahrens, B. On the temporal variability of widespread rain-on-snow floods. <em>Meteorol. Zeitschrift</em> <strong>29</strong>, 147–163 (2020).</p> <p>Primo, C., Kelemen, F. D., Feldmann, H., Akhtar, N. & Ahrens, B. A regional atmosphere-ocean climate system model (CCLMv5.0clm7-NEMOv3.3-NEMOv3.6) over Europe including three marginal seas: on its stability and performance. <em>Geosci. Model Dev.</em> <strong>12</strong>, 5077–5095 (2019).</p> <p>Somot, S. <em>et al.</em> Editorial for the Med-CORDEX special issue. <em>Clim. Dyn.</em> <strong>51</strong>, 771–777 (2018). doi: 10.1007/s00382-018-4325-x</p> <p>Sprenger, M. <em>et al.</em> Global climatologies of Eulerian and Lagrangian flow features based on ERA-Interim. <em>Bull. Am. Meteorol. Soc.</em> (2017). doi:10.1175/BAMS-D-15-00299.1</p> <p>Wernli, H. & Schwierz, C. Surface Cyclones in the ERA-40 Dataset (1958–2001). Part I: Novel Identification Method and Global Climatology. <em>J. Atmos. Sci.</em> <strong>63</strong>, 2486–2507 (2006).</p>
The Complex Geometry and Dynamical Role of Stellar Wind Bubbles in Turbulent Molecular Clouds
<p>Research Data Management Package for paper in Monthly Notices of the Royal Astronomical Society with same title and author list</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.