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53 results for “simulation input files”
Input files for the simulation of KcsA-K+-LAB-TEA, when LAB-TEA is placed in the cytoplasmic region with K+-ion in the channel cavity
<p>Input files for the simulation of KcsA-K<sup>+</sup>-LAB-TEA, when LAB-TEA is placed in the cytoplasmic region with K<sup>+</sup>-ion in the channel cavity. The inputs include,<br> 1. Input files for minimization (*min.in)<br> 2. Input files for heating (*h1.in, *h2.in, and *h3.in)<br> 3. Input files for equilibration (*eq*.in) and production runs (*prd*.in)<br> 4. Input files for the first trajectories start with file name, 1-lab-tea-k-entra*<br> 5. Input files for the remaining different trajectories start with file name, lab-tea-k-entra*<br> 6. Input files for the trajectories with restraint weight on K<sup>+</sup>-ion starting with file name, lab-tea-entra-k-restraint*</p>
Input files for the simulation of KcsA-LAB-TEA, when LAB-TEA is placed in the channel cavity with no K+-ion
<p>Input files for the simulation of KcsA-LAB-TEA, when LAB-TEA is placed in the channel cavity. The simulation is performed without K<sup>+</sup>-ion. The inputs include,<br> 1. Input files for minimization (*min.in)<br> 2. Input files for heating (*h1.in, *h2.in, and *h3.in)<br> 3. Input files for equilibration (*eq*.in) and production runs (*prd*.in)<br> 4. Input files for the first trajectories start with file name, 1-lab-tea*<br> 5. Input files for the remaining different trajectories start with file name, lab-tea*</p>
Input files for the simulation of KcsA-K+-LAB-TEA, when both LAB-TEA and K+-ion are placed inside the channel cavity.
<p>Input files for the simulation of KcsA-K<sup>+</sup>-LAB-TEA, when both LAB-TEA and K+-ion are placed inside the channel cavity. The inputs include,<br> 1. Input files for minimization (*min.in)<br> 2. Input files for heating (*h1.in, *h2.in, and *h3.in)<br> 3. Input files for equilibration (*eq*.in) and production runs (*prd*.in)<br> 4. Input files for the first trajectories start with file name, 1-lab-tea-k<sup>+</sup>*<br> 5. Input files for the remaining different trajectories start with the file name, lab-tea-k<sup>+</sup>*</p>
Introduction to HPC: molecular dynamics simulations with GROMACS: input files
<p>Introduction to HPC: molecular dynamics simulations with GROMACS: input files</p>
Wildland-urban interface fire dynamics simulator input files for pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests, California, USA
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Input files for WRF simulations Across the the iCMV
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HemeLB input files for areteriovenous fistula simulation
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Input and output files for WRF urban simulations for the metropolitan area of Tel-Aviv
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Input files and scripts for Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered proteins using a software GROMACS patched with PLUMED
<p>Here we share the necessary files and scripts to run Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered protein studied in the preprint uploaded to bioRxiv (doi: https://doi.org/10.1101/2020.06.16.155374). It requires software GROMACS patched with PLUMED.</p>
Hdf5 input files for FICOS simulator
<p>This resource contains the hdf5 input files needed by the FICOS water quality simulator. To use them with the ficosUQ package, download the files below and place them in the ficosUQ/data folder:</p> <ul> <li>hd_files.hdf5 : Boundary conditions.</li> <li>hd_files_ma_5.hdf5 : Boundary conditions with moving average smoothing for solar radiation.</li> <li>loading.hdf5 : Nutrient loadings.</li> <li>loading_Aurajoki.hdf5 : Nutrient loadings based on the Aurajoki basin.</li> </ul>
Input data files for RSS-NET analysis of simulated GWAS summary statistics and B cell regulatory network
<p>Details of these data files are provided in https://suwonglab.github.io/rss-net/wtccc_bcell.</p> <p>Contact:<code> xiangzhu[at]psu.edu </code></p>
Towed chain datasets and input files for simulations used in the manuscript "Increased mixing and turbulence in the wake of offshore wind farm foundations"
<p><strong>Contents</strong></p> <p>1. File S01_S12 Input files for simulations (precursor runs and main runs)</p> <p>2. File S13 Topography file for simulations with monopile</p> <p>2. Data sets ds01 to ds06 (towed chain data collected in May 25, 2015)</p> <p>3. Data sets ds07 to ds14 (towed chain data collected in July 19, 2017)</p> <p>4. Data sets d15 to ds16 (ADCP data collected in May 25, 2015 and July 19, 2017)</p> <p><strong>Introduction </strong></p> <p>This package contains the input parameters used in each of the precursor (S01 - S04) and main runs (S05 - S12) presented in the manuscript “Increased mixing and turbulence in the wake of offshore wind farm foundations”. These input files are found in the PDF file "S01_S12".</p> <p>The main runs, in which the wake of a monopile was simulated (S05, S07, S09, S11), require a topography file, which is a NETCDF-file that has been uploaded separately (S13). All simulations were run using the Parallelized Large-Eddy Simulation Model for atmospheric and oceanic flows (PALM, version 4.0, revision 2504).</p> <p>Further, this package contains the data sets collected using the towed chain in 2015 (ds01-ds06, ds15) and 2017 (ds07-ds14, ds16), which have been uploaded as separate NETCDF-files.</p>
Run input files for the simulation of a C. jejuni inner membrane model
<p>Run input files for the simulation of a C. jejuni inner membrane model (Chapter 5 of Kahlan Newman's Doctoral Thesis). Full trajectories can be shared on request. </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.