Find research datasets worth reusing

Magnetotelluric data in Subei area, northern Tibet and the 3D isotropic/anisotropic models

This dataset contains four folders. They are ‘aniinv’, ‘isoinv’, ‘sensitivity_test’, ‘syn_mod_test’, respectively. In the ‘aniinv’ folder, there are three sub-folders include ‘azimu_ani_inv’, ‘gener_ani_inv’, ‘verti_ani_inv’, indicating the inversion results for azimuthal, general, and vertical anisotropic inversions, respectively. The ‘isoinv’ folder contains results for isotropic inversion. The ‘sensitivity_test’ folders contains modeified models and their responses for sensitivity tests of anomalies. The ‘syn_mod_test’ folder contains a synthetic model constructed according the final model, the responses of this model, and the recovering for this model. In each folder, there is a ‘readme.txt’ file describing the details of individual files.

Supplemental 3D Model Data - Hapalosiphonacean cyanobacteria (Nostocales) thrived amid emerging embryophytes in a 407-million-year-old landscape

Three-dimensional reconstruction models of cyanobacteria from a 407 million year old fossil from the Lower Devonian Rhynie chert, UK. Thin sections SU.PB. 2023.0.1.2.8 from the Palaeobotany Collection in the Pôle Collections scientifiques et patrimoniales. Bibliothèque de Sorbonne Université, Paris (France). Imaris files (.IMS) can be viewed using the Imaris Viewer software, freely available in both Windows and Mac versions from https://imaris.oxinst.com/imaris-viewer.

Structures and data for minimalistic models of cage-like molecules in "Systematic exploration of accessible topologies of cage molecules via minimalistic models"

Archives of .csv files containing data of lowest energy conformers for all cage configurations tested and associated .mol files.  For paper: Systematic exploration of accessible topologies of cage molecules via minimalistic models with DOI: <a href="https://doi.org/10.1039/D3SC03991A">10.1039/D3SC03991A</a>

opencc-by-4.0May 2023View details →

Data for: Contributions of deep learning to automated numerical modelling of the interaction of electric fields and cartilage tissue based on 3D images

Replication data for: Contributions of deep learning to automated numerical modelling of the interaction of electric fields and cartilage tissue based on 3D images

Data -- Experiment Series Three -- Game Model Recognition

Dataset generated from Experiment Series Three: Game Model Recognition from in-progress doctoral thesis Cooperative Intent: An Exploration of Computational Learning in a Discrete Preference Space. Code -- Experiment Series Three -- Game Model Recognition  v0.1-alpha <a href="https://doi.org/10.5281/zenodo.8188155">10.5281/zenodo.8188155</a>

openmit-licenseJul 2023View details →

Data -- Experiment Series One -- Multi-Model Tournament

Dataset generated from Experiment Series One: Multi-Model Tournament from in-progress doctoral thesis Cooperative Intent: An Exploration of Computational Learning in a Discrete Preference Space. Code -- Experiment Series One -- Multi-Model Tournament v0.1-alpha <a href="https://doi.org/10.5281/zenodo.8188104">10.5281/zenodo.8188104</a>.

Supporting data for manuscript: "Global-scale evaluation of coastal ocean alkalinity enhancement in a fully-coupled Earth system model"

Supporting data for manuscript: "Global-scale evaluation of coastal ocean alkalinity enhancement in a fully-coupled Earth system model" Authors: Julien Palmieri and Andrew Yool Institute: National Oceanography Centre, European Way, Southampton SO14 3ZH, UK This repository consists of four main sets of files: 1. Matlab scripts used for analysis, figure plotting and table    preparation    Filenames of the format: Figure_??.m 2. Raw netCDF output files from UKESM1 for six model experiments    Filenames of the format: medusa_c*.nc 3. BGCVal processed timeseries shelve files    Filenames of the format: u-c*.shelve.txt 4. CMM2 processed timeseries netCDF files    Filenames of the format: c*_global.nc File sets 2-4 are read and processed by script files in file set 1

data shown in manuscript "WRF-Comfort: Simulating micro-scale variability of outdoor heat stress at the city scale with a mesoscale model"

<blockquote> data shown in manuscript "WRF-Comfort: Simulating micro-scale variability of outdoor heat stress at the city scale with a mesoscale model" </blockquote>

Assessing the improvement of Tropical Cyclone representation in the IPSL model with increasing resolution -- Data

This folder contains the following data, used in the artcle "Assessing the improvement of Tropical Cyclone representation in the IPSL model with increasing resolution": * TC tracks in all the simulations, before and after the STJ filtering * Composite NetCDFs * Large scale variables used in the GPI, and the GPI itself, in ICO-VHR and ERA5

Anonymized data for paper "Automatic Bug Fixing in the Era of Large Language Models: Interactive Simulation of Programmer Behavior" submitted to ICSE 2024

The project includes the BFP benchmark used in the submitted ICSE 2024 paper titled "Automatic Bug Fixing in the Era of Large Language Models: Interactive Simulation of Programmer Behavior"

opencc-zeroJul 2023View details →

dryad32/100

Data from: Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution

Flaveria (Asteraceae) is the prime model for the study of C4 photosynthesis evolution and seems to support a stepwise acquisition of the pathway through C3-C4 intermediate phenotypes, still existing in Flaveria today. Molecular phylogenies of Flaveria based on concatenated data matrices are currently used to reconstruct the complex sequence of trait shifts during C4 evolution. To assess the possible role of hybridization in C4 evolution in Flaveria, we re-analyzed transcriptome data of 17 Flaveria species to infer the extent of gene tree discordance and possible reticulation events. We found massive gene tree discordance as well as reticulation along the backbone and within clades containing C3-C4 intermediate and C4-like species. An early hybridization event between two C3 species might have triggered C4 evolution in the genus. The clade containing all C4 species plus the C4-like species F. vaginata and F. palmeri is highly supported in our phylogenetic analyses, but it might be of hybrid origin involving F. angustifolia and F. sonorensis (both C3-C4 intermediate) as parental lineages. Hybridization seems to be a driver of C4 evolution in Flaveria and likely promoted the fast acquisition of C4 traits. This new insight can be used in further exploring C4 evolution and can inform C4 bioengineering efforts.

openagpl-3.0-or-laterJul 2023View details →

Data from "Connecting large-scale meteorological patterns to extratropical cyclones in CMIP6 climate models using self-organizing maps"

The following files were used as data and analysis in the article "Connecting large-scale meteorological patterns to extratropical cyclones in CMIP6 climate models using self-organizing maps" (<a href="https://doi.org/10.1029/2022EF003211">https://doi.org/10.1029/2022EF003211</a>). In the study, we applied self-organizing maps (SOMs) as an automated machine-learning approach to characterize the large-scale meteorological patterns (LSMP) and associated frequency and intensity of discrete extratropical cyclone (ETC) events over the northeastern U.S. The dominant patterns of geopotential height variability are identified through SOM analysis of five reanalysis products during 1980 - 2019. ETC events are tracked using TempestExtremes and are integrated with SOMs to classify the accumulated cyclone activity associated with each pattern. We then evaluate the skill of CMIP6 historical experiments in simulating the LSMP and ETC events identified in the SOM. Please see the published paper for more details. Here we have archived:  - data pre-processing scripts - code to run the self-organizing map analysis - code to calculate the SOM and ETC statistics - composites of 500-hPa geopotential height for each dataset as organized by the SOM - ETC tracking script and tracking output for each dataset - SOM output for each dataset

Modified Fuchs et al. model Synthetic Data Sets

Synthetic data sets used for machine learning of laser acceleration of protons

Data release: Comparing gravitational waveform models for binary black hole mergers - a hypermodels approach

We include two main directories, one with the power spectral densities (PSDs) estimated for the events, and one with the posteriors of our analysis for each event.   PSDs For most of the events, the sampling rate required for our analysis was higher than the one employed in LVK catalog paper studies. We upload here the PSDs computed for our analysis, divided into two main directories: 2048 for the PSDs computed with sampling rate = 2048 Hz, and 4096 for the ones computed with sampling rate = 4096 Hz. Each directory contains specific directories corresponding to each event, with the PSD for each detector as a *.dat file.   Posteriors The 'posteriors.tar.gz' directory contains the *.json files, one for each event, with the results of our analysis.

Jet feature data from PAMIP model simulations

Author: Yvonne Anderson Contact: ee22ya@leeds.ac.uk Dataset created: 21/08/2023 Paper title: Minimal influence of future Arctic sea ice loss on North Atlantic jet stream morphology   Dataset information CSV files contain arrays of daily jet feature data for all ensemble member winters for a given model. Dimensions of the arrays are (number of ensemble members, 90 winter days). Filename structure Filenames of CSV files can be interpreted as: timeperiod_jetfeature_model.csv Example filename structure <table> <thead> <tr> <th scope="col">Time period</th> <th scope="col">Jet feature</th> <th scope="col">Model</th> <th scope="col">Example filename</th> </tr> </thead> <tbody> <tr> <td>Present-day</td> <td>Latitude</td> <td>AWI-CM-1-1-MR</td> <td>present-day_jet_latitude_AWI-CM-1-1-MR.csv</td> </tr> <tr> <td>Future</td> <td>Speed</td> <td>HadGEM3-GC31-MM</td> <td>future_jet_speed_HadGEM3-GC31-MM.csv</td> </tr> </tbody> </table> Jet feature description Jet feature data are for the largest mass jet region found on each day of winter, where jet mass is the area weighted jet speed. The jet features and corresponding units contained in the csv files are as follows: <table> <thead> <tr> <th scope="col">Jet feature</th> <th scope="col">Units</th> </tr> </thead> <tbody> <tr> <td>Latitude</td> <td>°</td> </tr> <tr> <td>Speed</td> <td>ms-1</td> </tr> <tr> <td>Mass</td> <td>ms-1</td> </tr> <tr> <td>Tilt</td> <td>°</td> </tr> <tr> <td>Area</td> <td>m2</td> </tr> </tbody> </table> Time periods Time periods are present-day and future, which refer to simulations forced by present-day and future sea ice concentrations, from which the jet features have been extracted. Models Models are AWI-CM-1-1-MR, CanESM5, FGOALS-f3-L, HadGEM3-GC31-MM, IPSL-CM6A-LR and MIROC6 from the Polar Amplification Model Intercomparison Project (PAMIP; https://doi.org/10.5194/gmd-12-1139-2019) Spatial and temporal information Arrays contain daily jet feature data that has been constrained to the North Atlantic region (0-60 &deg; W, 15-75 &deg; N) and to the winter period (December, January and February) Prior processing <ul> <li>Original dataset: netcdf files of daily zonal wind data from Polar Amplification Model Intercomparison Project simulations forced by present-day and future sea ice concentrations</li> <li>850 hPa wind speed data was extracted and regridded to 2.81 ° x 2.81 ° resolution</li> <li>Constrained to North Atlantic region and winter period</li> <li>Wind speed data was filtered using a 10-day Lanczos filter with a 61 day window</li> <li>Jet feature data was extracted for each day in ensemble member winters and saved to numpy arrays</li> </ul> Example code for loading jet variables from csv file To generate a numpy array of jet variable arrays contained in the csv file: <pre><code class="language-python">loaded_jet_variable_arrays = np.genfromtxt((path_to_file/filename.csv'), delimiter=',')</code></pre> To combine arrays for all ensemble member winters, which allows plotting of daily jet feature distributions: <pre><code class="language-python">jet_variable_array_all_winters = np.concatenate(loaded_jet_variable_arrays)</code></pre>

opencc-by-4.0May 2023View details →

Data set supporting publication "Hydrological Coupling and Decoupling of Hydric Hemi-boreal Forest Sites Inferred from Soil Water Models and Tree-Ring Chronology" by Kalvāns A. and Dauškane I. accepted for publication in the scientific journal Forests

These files are supporting information for the article: Kalvāns, Dauk&scaron;kane (accepted). Hydrological Coupling and  Decoupling of Hydric Hemi-boreal  Forest Sites Inferred from Soil Water Models and Tree-Ring Chronology. Forests The data set comprises following elements: <ol> <li>Hydrus-1D soil water model setup files and calculation results ([1_Hydrus_1D_hydric_forest_soil_water_model_instances.zip]) for two study plots and 12 model instances, with following naming convention: [{Site Identifier}__{proportion of active leaf area index}_kLAI__{forced groundwater exfiltration rate cm/day}_SeepIn_const]. That is model instance named [P1__0.4_kLAI__0.05_SeepIn_const.h1d], considers the study site Plot_1, the active leafe area proportion is 0.4 and it has applied constant rate of groundwater exfiltration at the base of the soil column of 0.05 cm/day. The models are forced by E-OBS v26.0e data set for the period from 1980-01-01 to 2022-06-30.</li> <li>Black alder Alnus glutinosa tree ring chronologies for the two study plots ([2_tree_ring_data.zip])</li> <li>Soil and ground-water observation time series for the two study plots ([3_soil_ground_water_observations.zip])</li> </ol>

opencc-by-4.0Jun 2021View details →

Data set used in article: Model Predictive Control for Wake Redirection in Wind Farms: a Koopman Dynamic Mode Decomposition Approach

Step-wise yaw deflection in 2 wind turbines in SOWFA. More information in the article.

Data for "A thermal-hydro-mechanical model for evaluating the stability of mountain glaciers"

This dataset details the data produced in our study "A thermal-hydro-mechanical model for evaluating the stability of mountain glaciers".

opencc-zeroAug 2023View details →

dryad32/100

Data for: Modelling the surprising recolonisation of an understudied aquatic mammal in a highly urbanised area: Fortune favored the Smooth-coated otter in Singapore

Ever-growing human activities present an active and continuing threat to many species throughout the world. Nevertheless, concerted conservation efforts in some regions have balanced these threats and allowed endangered species to recolonise former parts of their original ranges and reverse their decline. This is notably the case of the smooth-coated otter (Lutrogale perspicillata). In 1998, individuals returned to Singapore after more than a 20-year absence. In 2017, 79 otters were counted throughout the heavily urbanized city. Despite this comeback, the future of the species in Singapore is unclear. By collating information on the species' life history traits, we implemented a spatially explicit individual-based model. The model demonstrated that successful establishment of Singapore's population from the initial immigrants was highly uncertain. In 43% of cases, stochastic extinction occurred. From the 9% of model replicates that closely reproduced the observed colonisation history, projections showed that the population would reach close to 200 individuals in 50 years. This study successfully demonstrates the use of individual-based modelling to simulate the inherently stochastic recolonisation dynamics of an endangered species and predict its longer-term future. We discuss emerging issues that may arise from increasing negative interactions between otters and humans and the general challenges associated with rewilding highly urbanized environments. We stress the importance of long-term monitoring surveys and education campaigns to mitigate human-wildlife conflicts. With species and natural habitats increasingly threatened by our ever-growing human expansion, understanding the factors that allow human-dominated landscapes to be compatible with biodiversity is of the utmost importance.