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3,688 results for “Computer”
Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD
<p>Set of data and scripts for the analysis of RAMD dissociation trajectories generated for BN-NS and BT/BCT-BPTI mutants, reported in the manuscript:</p> <p><br>"Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD"</p> <p>by Giulia D'Arrigo, Daria B. Kokh, Ariane Nunes-Alves and Rebecca C. Wade</p> <p> </p> <ol> <li>RAMD movies of WT Bn-Bs and D35Abn mutant dissociation pathway (WT-diss.mp4 and D35Abn-diss.mp4)</li> <li>Protein-Protein.zip contains:</li> </ol> <ul> <li>README - set of instructions to go through files and for the use of the scripts</li> <li>Jupyter notebooks: tauRAMD_PP_Residence_time.ipynb and tauRAMD_PP_Unbinding_pathways.ipynb</li> <li>Scripts used for analysis and postprocessing RAMD simulations - for the correct usage of the scripts check the corresponding file header</li> <li>System input files in BN-BS/ and BT_BCT-BPTI/</li> <li>Experimental data used</li> <li>2 RAMD movies (.mp4) showing dissociation of WT Bn-Bs and D35Abn mutant</li> </ul>
Data files and computer code scripts for reproducing the results of a manuscript on the measurement and ranking of cotton drought tolerance capacity
<p>This upload contains the data files and computer code scripts for reproducing the main results, esp. figures, of the manuscript entitled<br>"Rapid measurement and statistical ranking of leaf drought tolerance capacity in cotton," by X. Dong, D. A. Mott, J. Garg, Q. Zhou, J. Sunoj V. S., and B. M. McKnight. The manuscriptt is currently under peer review.</p>
Chondritic reactivity under H2-rich atmospheres: Formation of H2S. Computational Data.
<p>This supporting material includes:</p> <ul> <li>Cartesian coordinates of the PBE-optimized minima and transition states for the studied reactions, provided in both XYZ and CIF formats.</li> <li>Examples of input and output files used with the <a href="https://www.cp2k.org/">CP2K</a> package.</li> <li>Vibrational analysis, including all calculated frequencies.</li> </ul>
Neural pathways and computations that achieve stable contrast processing tuned to natural scenes
<h1>Gur et al. 2024 database</h1> <p>Source data of the paper Gür et al. 2024, “Neural pathways and computations that achieve stable contrast processing tuned to natural scenes”, Nature Communications. This work contains an analysis of post-receptor luminance gain in the Drosophila visual system, focusing on the circuitry and algorithms for implementation of rapid luminance gain control.</p> <p>All data can be analyzed using the code provided in the Github repository: <a href="https://github.com/silieslab/Gur-etal-2024">https://github.com/silieslab/Gur-etal-2024</a>. Please go to the “Readme” file in the repository for how to use the code.</p> <h2>Raw data</h2> <p>All raw data is located in the folder “raw_data”. "Readme" file located in the code repository will guide you on how to analyze all data.</p> <h2>Processed data</h2> <p>All processed data is located in the folder “processed_data”. "Readme" file located in the code repository will guide you on how to analyze all data.</p> <p>- 2p_imaging_python_pickle: Processed data stored as .pickle files. <br>- Dm12_Figure7_Mat_files: Processed data for Dm12 imaging and optogenetics experiments presented in Figure 7 stored as .mat files.<br>- EM_data: Processed data for EM analysis done in Figure 7.<br>- Figure 6 Tm9 flpSTOP: tdTomato expression data for Figure 6 Tm9 flpSTOP experiments.<br>- Figure S5 Tm1 flpSTOP: tdTomato expression data for FigureS5 Tm1 flpSTOP experiments.</p>
Rapid portabilization of elasto-chemical evolution data for dental Ti-Cr alloy microstructure through sparsification and tensor computation
<ol> <li><strong>c_theta_interpolation_function_data.csv</strong>: Interpolation function is utilized in phase field model to interpolate the material properties along the interface region. In this work, the corresponding material property that has been interpolated is the elasticity tensor. The csv file (c_theta_interpolation_function_data.csv) consists of the data of the interpolation function <strong>h(theta,c)</strong> given by the expression <em><strong>h = 1/(1+ exp(-theta(2c-1)))</strong></em>. The input feature "c" in the weighted input feature for the sigmoidal function is the mole fraction of Chromium in the two metastable phase regions in the binary Ti-Cr alloy undergoing phase decomposition. The "c" column in the table represents the data of Chromium composition. For the present study, the value of weighted parameter in the input feature is taken as equal to 10 i.e. theta = 10 . Hence, the column h(10,c) represents the data of the interpolation function used by the phase field simulation (Eq. 8 in the paper). To illustrate on how the choice of theta alters the values of h, this csv file also presents four additional columns of h corresponding to different constant values of theta (theta = 5, 15, 20 and 50). The steepness of the sigmoidal interpolation function increases as theta increases, and the graphical representation of the table can be accessed at <a title="c-theta-interpolation-function" href="https://interpolationfunction.streamlit.app/" target="_blank" rel="noopener">https://interpolationfunction.streamlit.app/</a>. </li> <li><strong>spatial-coordinates_composition_data_Figure4c.csv</strong>: This file contains the data of Fig. 4(c) which is the result of the microstructure reconstruction after Tucker decomposition with 10 % sparsification for t = 1 h 23 min 20s. The spatial distribution of Cr composition is sufficient to represent the microstructural information for the binary Ti-Cr alloy. That is the data of spatial coordinates and mole fraction of Cu at each coordinate is sufficient to represent this microstructure. Thus, the csv file consists of the following three columns : X-Coordinate (nm), Y-Coordinate (nm) and Cr_MoleFraction. The unit for the values of X and Y coordinates is nm. The mole fraction is unitless. </li> <li><strong>bulk_free_energy.csv</strong>: The file contains the data of the coefficients alpha, beta, gamma, delta, epsilon and ceq in the equation for bulk thermodynamic free energy ( F_{chem}) at T = 700.15 K. Mathematically, F_{chem} = f_{chem}* Vmol where Vmol is the molar volume of a phase. The expression for molar bulk chemical free energy is: <em><strong>F_{chem} = alpha*(epsilon*c - ceq)^2 + beta*(epsilon*c - ceq) + beta*(epsilon*c - ceq)^6 + delta</strong></em>. </li> <li><strong>statistical_metrics_comparison.zip</strong>:This folder consists of three files that compares the outcome of tensor impainting results of Canonical Polyadic (CP) and Tucker methods for three sparsity values ( 10 %, 15 % and 25%). Each of the files corresponds to the sparsity value, and so the names of of the files are statistical_metrics_10percent.csv, statistical_metrics_15percent.csv and statistical_metrics_20percent.csv. Four types of statistical techniques are considered: <strong>root mean square error (RMSE)</strong>, microstructural similarity (micro sim), blob detection via deviation quantified from <strong>Determinant of Hessian (DoH)</strong>, and Shape Index. The first three methods: RMSE, microstructural similarity and blob detection via DoH are used quantitatively to compare the tensor inpainted images with the benchmark image from phase field method. Shape index is used to perform qualitative analysis, and it has been inferred that both CP and Tucker methods based decomposition and subsequent reconstruction/inpainting are in the acceptable from the viewpoint of tracking the curvature of interfaces. For 10% sparsity, the Tucker method is found to produce better results even if both CP and Tucker produce acceptable ones.</li> </ol>
Computational data for Structure of G protein-coupled receptor GPR1 bound to full-length chemerin adipokine reveals a chemokine-like reverse binding mode
<p>MD simulation data for the research article titled "Structure of G protein-coupled receptor GPR1 bound to full-length chemerin adipokine reveals a chemokine-like reverse binding mode".</p>
The Effects of Computational Resources on Flaky Tests (Artifact)
<p>This artifact contains resources for reproducing and extending the work "The Effects of Computational Resources on Flaky Tests"</p><p>Contents:</p><ul><li> Analysis and Processed Test Results.tgz: An archive that contains information about the projects analyzed, summarized test results per-throttling configuration per-run, and a Jupyter notebook that detects RAFT (generating all tables and figures in the article). A README in this archive provides further guidance on its contents</li><li>js-results.tar, java-results.tar, python-results.tar: The raw results produced by the test runner when executing each JavaScript, Java and Python project 300 times in each of the throttling configurations.</li></ul><p>See also:</p><p>We have published docker containers that include each project that we studied, along with all of the dependenices for running the tests. These containers can be used to reproduce our results, or to extend our work by running additional tests. The containers are available at <a href="https://hub.docker.com/r/jonbell/raft/tags">https://hub.docker.com/r/jonbell/raft/tags</a></p>
Computational Dataset for Iminobispyrazole (IBP) Photoswitches: Two Pyrazole Rings Can Be Better Than One
<p>The computational data for the publication "<span>Iminobispyrazole (IBP) Photoswitches: Two Pyrazole Rings Can Be Better Than One". Additional data can be found in the papers supporting information.</span></p>
Data and code for "Programmable Trans-splicing Riboregulators for Complex Cellular Logic Computation"
<p>Split-intron ENabled Trans-splicing Riboregulators (SENTR) is a class of programmable riboregulators based on group I intron mediated trans-splicing. SENTR functions by seperating target mRNA into two strands, 5'RNA and 3'RNA, and rejoin them through RNA splicing. We fused de-novo designed external guide sequences (EGSs) to the intron halves, to improve the efficiency, programmability, predictability with machine-learning, and orthogonality of conventional split intron design. This repository deposits:</p> <ol> <li>The source data file for the paper "Programmable Trans-splicing Riboregulators for Complex Cellular Logic Computation"</li> <li>The NUPACK scripts to design the EGS library, orthogonal EGS library and other EGS structures for mRNA sensing and ribocomputing</li> <li>The sequences, performance data, and codes for machine-learning</li> </ol>
Processed model of a Computed Tomography scan of Roman window glass from Ephesos
<h1>Origin</h1> <p>The model is based on a tomography scan on an antique window glass fragment from Ephesos (today Efes, Turkey). The sample was contributed by the <em>Austrian Archaeological Institute</em>, Vienna, and has the inventory ID EVH12/1017/1322.</p> <p>The original scan data is published as</p> <p>Grobe and Schuetz (2021). Computed tomography scan of Roman window glass from Ephesos. <a href="https://doi.org/10.5281/zenodo.5651890">doi:10.5281/zenodo.5651890</a></p> <p>and is described in:</p> <p>Grobe, Noback, and Schuetz (2021). A model chain to simulate daylight in historic built environments. Presented at: <em>Widening Horizons - 27 Annual Meeting of the European Association of Archaeologists</em>, Kiel, Germany. <a href="https://doi.org/10.5281/zenodo.5495764">doi:10.5281/zenodo.5495764</a></p> <h1>Processing</h1> <p>The scan was processed to prepare its conversion into a simulation model, i.e.</p> <ul> <li>small isolated mesh components were deleted,</li> <li>disconnected and duplicate vertices and faces were removed,</li> <li>the outer surfaces were re-constructed by meshlab's implementation of the _Screened Poisson_ algorithm, and</li> <li>the resulting mesh was intersected with an exctruded rectangle.</li> </ul>
Computed data for the paper "Deciphering Faujasite Zeolite Dealumination at the Atomic Scale" by Z. Wang, T. Jarrin, [...], G. Pirngruber, C. Chizallet, A. Lesage, https://doi.org/10.1021/acscatal.4c03036
<p>The presented data correspond to NMR calculations done with the VASP code, for models of zeolite faujasite (bulk and external surfaces, possibly with defects), silica, and amorphous silica-alumina surfaces. For details on the format of the files, see https://www.vasp.at/wiki/index.php/The_VASP_Manual. </p> <p>The date correspond to the following paper: <span><em>ACS Catal.</em></span> <span>2024</span><span>, 14</span><span>, 24</span><span>, 18442–18456,</span> https://doi.org/10.1021/acscatal.4c03036 </p>
Data for "Direct observation of the neural computations underlying a single decision"
<p>This repository contains the data required to reproduce all figures and results of the paper "Direct observation of the neural computations underlying a single decision" by Natalie A Steinemann*, Gabriel M Stine*, Eric M Trautmann, Ariel Zylberberg, Daniel M Wolpert & Michael N Shadlen (https://doi.org/10.7554/eLife.90859.1). The associated code is deposited on Github (https://github.com/Nat-Stein/LIP_single_trial_decision_variable). </p>
Data for: A computational pipeline to observe the flexibility and dynamics of (plant) cytochrome P450 binding sites
<p>Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate substrates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on human CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. Firstly, we use molecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyse a number of binding site properties - size, flexibility, shape, hydrophobicity, and accessibility - using the fpocket and mdpocket packages on MD-generated trajectories. This led to a first categorization of 15 chosen plant CYPs based on their binding site's (dis)similarities. The workflow was tested and verified on human CYPs 1A2, 2A6, and 3A4 as their binding site characteristics are well known. In addition to confirming known binding site properties, we identified and named previously unseen binding site channels for CYPs 1A2 and 2A6. This study gives initial insights into the largely uncharted fields plant CYP substrate specificity and facilitates a more precise understanding of their largely unknown specific biological functions. It offers new insights into the structural and functional dynamics of plant CYPs, which may facilitate a more accurate understanding of the fate of agrochemicals or the biotechnological design and exploitation of enzymes with specific functions. Additionally, it serves as a reference for future structural-functional analyses of CYP enzymes across various biological kingdoms.</p>
High-throughput robotic determination of hydrogen peroxide using computer vision
<p>A fully automated process of high-throughput determination of hydrogen peroxide integrating a liquid handling robot (Opentrons, OT-2) with a webcam based on chemical titration.</p>
Dataset for article: Gait Speed Assessment in the 10-meter Walk Test for Older Adults Using a Computer Vision-based System: A Cross-sectional Study on Validity, Reliability, and Usability
<p>This dataset provides the Validity, Reliability, and Usability for an assessment of gait speed detection system in the 10-meter Walk Test for Older Adults.</p> <p>The dataset is formatted for easy import into microsoft excel software consist of:<br>Supplementary1.xlsx - Validity <br>Supplementary2.xlsx - Reliability<br>Supplementary3.xlsx - Usability test</p>
Dataset associated with A. Hallou, R. He, et al. A computational pipeline for spatial mechano-transcriptomics. bioRxiv 2023.08.03.551894
<p>Dataset associated with:</p> <p>Adrien Hallou, Ruiyang He, Benjamin David Simons and Bianca Dumitrascu. A computational pipeline for spatial mechano-transcriptomics. bioRxiv 2023.08.03.551894; doi: <a href="https://doi.org/10.1101/2023.08.03.551894">https://doi.org/10.1101/2023.08.03.551894</a></p> <p>Licence</p> <p>This dataset is licensed under the <a href="https://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International License</a>.</p>
Reduced atomic models for large-scale computations: Fe XIII near-infrared lines
<p>The tar file contains two directories. One contains the CHIANTI v.8-11 format main files<br>produced relative to a 33 merged states Fe XIII model.</p> <p>The other contains CHIANTI and P-CORONA format files for a 55-states Fe XIII model.</p> <p>In both cases the models were built to obtain accurate emissivities of the Fe XIII near-infrared lines withtin the ground configuration. </p> <p><br>The models are described in Del Zanna and Hebbur Dayananda, 2024, submitted to MNRAS.</p> <p>Information on the CHIANTI programs can be found in chianti-vip.com</p> <p>Information on P-CORONA can be found on https://research.iac.es/proyecto/polmag/pages/codes/p-corona.php</p>
CLDF dataset underlying the study "First steps towards the detection of contact layers in Bangime: a multi-disciplinary, computer-assisted approach" from 2022
<p>Cite the source of the dataset as:</p> <blockquote> <p>Hantgan, Abbie and Babiker, Hiba and List, Johann-Mattis (2022): First steps towards the detection of contact layers in Bangime: a multi-disciplinary, computer-assisted approach [version 2; peer review: 2 approved]. Open Research Europe 2022, 2:10.</p> </blockquote>
Prevalence of endoepicardial asynchrony and breakthrough patterns in a bilayer computational model of heterogeneous endoepicardial dissociation in the left atrium
Open the record for dataset details and reuse information.
Supplementary material for the paper: Linking megaliths: A computational approach to the study of movement and mobility in the megalithic complex of Galicia (North-west of the Iberian Peninsula)
<p>Supplementary material for the paper: Carrero-Pazos, M., White, D., Linking megaliths: A computational approach to the study of movement and mobility in the megalithic complex of Galicia (North-west of the Iberian Peninsula). To be appeared in: G. M. Higginbottom, C. Scarre, A. C. González-García, F. Criado-Boado, <em>Megalithic Societies: Old Questions, New Narratives. </em>Oxford: BAR International Series</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.