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575
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Dataset results
575 results for “Modeling Codes”
Data archive and code for "Predicting September Arctic Sea Ice: A Multi-Model Seasonal Skill Comparison"
<p>This upload contains data and code related to the paper "Predicting September Arctic Sea Ice: A Multi-Model Seasonal Skill Comparison" by M. Bushuk, S. Ali, D. Bailey, Q. Bao, L. Batte, U. S. Bhatt, E. Blanchard-Wrigglesworth, E. Blockley, G. Cawley, J. Chi, F. Counillon, P. Goulet Coulombe, R. Cullather, F. X. Diebold, A. Dirkson, E. Exarchou, M. Gobel, W. Gregory, V. Guemas, L. Hamilton, B. He, S. Horvath, M. Ionita, J. E. Kay, E. Kim, N. Kimura, D. Kondrashov, Z. M. Labe, W. Lee, Y. J. Lee, C. Li, X. Li, Y. Lin, Y. Liu, W. Maslowski, F. Massonnet, W. N. Meier, W. J. Merryfield, H. Myint, J. C. Acosta Navarro, A. Petty, F. Qiao, D. Schroder, A. Schweiger, Q. Shu, M. Sigmond, M. Steele, J. Stroeve, N. Sun, S. Tietsche, M. Tsamados, K. Wang, J. Wang, W. Wang, Y. Wang, Y. Wang, J. Williams, Q. Yang, X. Yuan, J. Zhang, and Y. Zhang, published in the Bulletin of the American Meteorological Society, DOI: https://doi.org/10.1175/BAMS-D-23-0163.1.</p> <p>See README.txt for a description of the datasets and code.</p>
Data and code for "Strong plasmon-molecule coupling at the nanoscale revealed by first-principles modeling"
<p>The data includes atomic structures, time-dependent dipole moments, and photoabsorption spectra of the systems modeled and analyzed in the article "Strong plasmon-molecule coupling at the nanoscale revealed by first-principles modeling" by Tuomas P. Rossi, Timur Shegai, Paul Erhart, and Tomasz J. Antosiewicz.</p> <p>The input scripts for reproducing the data are also included. The time-dependent density-functional theory calculations use the LCAOTDDFT module of <a href="https://wiki.fysik.dtu.dk/gpaw/">the GPAW code</a>, and the atomic structures are created with <a href="https://wiki.fysik.dtu.dk/ase/">the ASE code</a>.</p> <p>See <em>README.md</em> in the archive for a detailed description.</p>
DeepPredSpeech: computational models of predictive speech coding based on deep learning
<p>This dataset contains all data, source code, pre-trained computational predictive models and experimental results related to: </p> <p>Hueber T., Tatulli E., Girin L., Schwatz, J-L "How predictive can be predictions in the neurocognitive processing of auditory and audiovisual speech? A deep learning study." (<a href="https://doi.org/10.1101/471581">biorXiv preprint https://doi.org/10.1101/471581</a>). </p> <ul> <li>Raw data are extracted from the publicly available database NTCD-TIMIT (10.5281/zenodo.260228). <ul> <li>Audio recordings are available in the audio_clean/ directory</li> <li>Post-processed lip image sequences are available in the lips_roi/ directory (67x67 pixels, 8bits, obtained by lossless inverse DCT-2D transform from the DCT feature available in the original repository of NTCD-TIMIT)</li> <li>Phonetic segmentation (extracted from NTCD-TIMIT original zenodo repository) is available in the HTK MLF file volunteer_labelfiles.mlf</li> </ul> </li> <li>Audio features (MFCC-spectrogram and log-spectrogram) are available in the mfcc_16k/ and fft_16k/ directories. </li> <li>Models (audio-only, video-only and audiovisual, based on deep feed-forward neural networks and/or convolutional neural network, in .h5 format, trained with Keras 2.0 toolkit) and data normalization parameters (in .dat scikit-learn format) are available in models_mfcc/ and models_logspectro/ directories</li> <li>Predicted and target (ground truth) MFCC-spectro (resp. log-spectro) for the test databases (1909 sentences), and for the different values of <span class="math-tex">\(\tau_p\)</span> or <span class="math-tex">\(\tau_f\)</span> are available in pred_testdb_mfccspectro/ (resp. pred_testdb_logspectro/) directory</li> </ul> <p>Source code for extracting audio features, training and evaluating the models is available on GitHub https://github.com/thueber/DeepPredSpeech/</p> <p>All directories have been zipped before upload.</p> <p>Feel free to contact me for more details.</p> <p>Thomas Hueber, Ph. D., CNRS research fellow, GIPSA-lab, Grenoble, France, thomas.hueber@gipsa-lab.fr </p>
Data and Code for: 'Stellar Models are Reliable at Low Metallicity: An Asteroseismic Age for the Ancient Very Metal-Poor Star KIC 8144907', Huber et al. 2024.
<p>Data and code to reproduce plots for the paper '<em>Stellar Models are Reliable at Low Metallicity: An Asteroseismic Age for the Ancient Very Metal-Poor Star KIC 8144907'</em>, Huber et al. 2024.</p> <p>Descriptions of the enclosed data files are as follows:</p> <div> <ul> <li>Freqs_best_fit.dat: Best-fitting GARSTEC model frequencies (Figure 3, right)</li> <li>KIC10006158_spec.txt: Reduced and normalized HDS spectrum of KIC10006158 (Figure 1)</li> <li>KIC8144907_ps.txt: Power spectrum of the Kepler light curve of KIC8144907 (Figure 3, left)</li> <li>KIC8144907_spec.txt: Reduced and normalized HDS spectrum of KIC8144907 (Figure 1)</li> <li>apokasc2.tsv: APOKASC sample from Pinsonneault+ 2014 (Figure 2)</li> <li>dwarfs.csv: Asteroseismic sample from Serenelli+ 2017 (Figure 2) </li> <li>freqs.csv: Data in Table 1</li> <li>hosts.tsv: Asteroseismic ages from Silva Aguirre+ 2015 (Figure 4) </li> <li>legacy-t1.tsv: Asteroseismic ages from Silva Aguirre+ 2017 (Figure 4) </li> <li>legacy-t2.tsv: Asteroseismic ages from Silva Aguirre+ 2017 (Figure 4) </li> <li>li-2020.csv: Asteroseismic ages from Li+ 2020 (Figure 4) </li> <li>matsuno.txt: Asteroseismic sample from Matsuno+ 2021 (Figure 2) </li> </ul> </div>
Personalized in silico model for radiation-induced pulmonary fibrosis | (source code, simulation input+output data)
<p>This repository concerns the supplementary material data of the research article entitled "<em>Personalised in silico model for radiation-induced pulmonary fibrosis</em>" that is published in the Royal Society Interface journal (rsif.royalsocietypublishing.org). More specifically, the repository contains the source code of the radiation-induced pulmonary fibrosis simulator, the results produced from the medical image analysis of this study (CT scans and RT dosage maps) for each patient case, the input files necessary to run the simulator and the corresponding output produced respectively. Each patient ID corresponds to each case documented in the research article.</p>
Model data and code for "Freeze-thaw effects on daily sediment transport in an Alpine river"
<p>Supporting information for the research article "Freeze-thaw effects on daily sediment transport in an Alpine river" by Skålevåg et al., submitted to Water Resources Research.</p> <p>This data repository contains the processed data, model code, and results presented in the research article. Please refer to the article and its supplementary information for details on primary data.</p> <p> </p> <p><strong>Contents:</strong></p> <ul> <li>processed data: <ul> <li>Standardised target and predictor variables, in addition to non-standardised data used for freeze-thaw state classification <a href="https://zenodo.org/api/records/13928999/draft/files/model_variables.csv/content" target="_blank" rel="noopener noreferrer">model_variables.csv</a></li> <li>Means and standard deviations of standardised variables <a href="https://zenodo.org/api/records/13928999/draft/files/regression_variables_mean_std.csv/content" target="_blank" rel="noopener noreferrer">regression_variables_mean_std.csv</a></li> </ul> </li> <li>model code: <ul> <li>final model presented in research article: <a href="https://zenodo.org/api/records/13928999/draft/files/model.py/content" target="_blank" rel="noopener noreferrer">model.py</a></li> <li>model comparison performed as part of model development: <a href="https://zenodo.org/api/records/13928999/draft/files/model_comparison_predictors_and_segmentation.html/content" target="_blank" rel="noopener noreferrer">model_comparison_predictors_and_segmentation.html</a></li> </ul> </li> <li>results: <ul> <li>final model: <ul> <li>Inference trace from the pymc model <a href="https://zenodo.org/api/records/13928999/draft/files/inference.nc/content" target="_blank" rel="noopener noreferrer">inference.nc</a></li> <li>Summary table of the inference trace <a href="https://zenodo.org/api/records/13928999/draft/files/inference_summary.csv/content" target="_blank" rel="noopener noreferrer">inference_summary.csv</a></li> <li>Visualisation of the inference trace <a href="https://zenodo.org/api/records/13928999/draft/files/inference_trace.png/content" target="_blank" rel="noopener noreferrer">inference_trace.png</a></li> </ul> </li> <li>other models: <ul> <li>non-segmented sediment rating curve: <a href="https://zenodo.org/api/records/13928999/draft/files/inference_SRC.nc/content" target="_blank" rel="noopener noreferrer">inference_SRC.nc</a> and <a href="https://zenodo.org/api/records/13928999/draft/files/inference_summary_SRC.csv/content" target="_blank" rel="noopener noreferrer">inference_summary_SRC.csv</a></li> <li>non-segmented "pooled" model with all predictors: <a href="https://zenodo.org/api/records/13928999/draft/files/inference_summary_full_nonsegmented.csv/content" target="_blank" rel="noopener noreferrer">inference_summary_full_nonsegmented.csv</a></li> <li>freeze-thaw-state-segmented sediment rating curve: <a href="https://zenodo.org/api/records/13928999/draft/files/inference_summary_segm_SRC.csv/content" target="_blank" rel="noopener noreferrer">inference_summary_segm_SRC.csv</a></li> <li>freeze-thaw-state-segmented "unpooled" model with all predictors: <a href="https://zenodo.org/api/records/13928999/draft/files/inference_summary_full_unpooled.csv/content" target="_blank" rel="noopener noreferrer">inference_summary_full_unpooled.csv</a></li> </ul> </li> <li>model comparison: <ul> <li><a href="https://zenodo.org/api/records/13928999/draft/files/model_comparison_waic.csv/content" target="_blank" rel="noopener noreferrer">model_comparison_waic.csv</a></li> <li> <div><a href="https://zenodo.org/api/records/13928999/draft/files/model_comparison_loo.csv/content" target="_blank" rel="noopener noreferrer">model_comparison_loo.csv</a></div> </li> </ul> </li> </ul> </li> </ul>
Data, Analytical Code, and Model Outputs From: "Green is the New Black: Outcomes of Post-Fire Tree Planting Across the Interior West, USA"
<p>This archive includes data (locations of tree plantings, one-year survival records, remotely sensed canopy cover change), statistical code, and model outputs from Rodman et al. (2024). For more information on specific information, processing methods, and data formats, see "README.md" or "README.html" files associated with this archive</p>
Code and data for "KGML-ag: A Modeling Framework of Knowledge-Guided Machine Learning to Simulate Agroecosystems: A Case Study of Estimating N2O Emission using Data from Mesocosm Experiments "
<p>This is code and data for manuscript: <br> "KGML-ag: A Modeling Framework of Knowledge-Guided Machine Learning to Simulate Agroecosystems: <br> A Case Study of Estimating N<sub>2</sub>O Emission using Data from Mesocosm Experiments"<br> Licheng Liu, Shaoming Xu, Zhenong Jin*, Jinyun Tang, Kaiyu Guan, Timothy J. Griffis, <br> Matt D. Erickson, Alexander L. Frie, Xiaowei Jia, Taegon Kim, Lee T. Miller, Bin Peng, Shaowei Wu, Yufeng Yang, Wang Zhou, Vipin Kumar</p> <p>All the files belong to Prof. Zhenong Jin, University of Minnesota, UA. jinzn@umn.edu<br> "code" foler includes code for data processing, model training, and results plotting.<br> "trained_model_saved" includes all trained model so you can use to reproduce the results showed in the study;<br> "data" includes all data presented in the study. Finetuning data is refering to Miller, L.T. , Griffis, T. J., Erickson, M. D., Turner, P. A., Deventer, M. J., Chen, Z., Yu, Z., Venterea, R.T., Baker, J. M., and Frie, A. L. (2021). Response of nitrous oxide emissions to future changes in precipitation and individual rain events. Journal of Environmental Quality, In review</p>
R code and data for "Flake selection and scraper retouch probability: an alternative model for explaining Middle Paleolithic assemblage retouch variability"
<p>R code and data used for "Flake selection and scraper retouch probability: an alternative model for explaining Middle Paleolithic assemblage retouch variability" (Archaeological and Anthropological Sciences, Volume 10, Issue 7, pp 1791–1806)</p>
ConFiRMa dataset_04: simulation of tests on CRM strengthened masonry buildings with the OOFEM code (intermediate, multi-layer level modelling)
<p>The Dataset collects the input files developed for the simulation of tests on one, two and three stroeys masonry buildings strengthened through Composite Reinforced Mortar with the free open-source code OOFEM (intermediate, multi-layer level modelling).</p> <p>OOFEM Version 2.5 (https://doi.org/10.5281/zenodo.4339630) was used for running the analyzes.</p> <p>ReadMe file provides a description of the different input files.</p>
Small-scale farming in drylands: New models for resilient practices of millet and sorghum cultivation - Dataset and code
<p>This repository contains the primary research data and R code used for data analysis for the article "<em>Small-scale farming in drylands: New models for resilient practices of millet and sorghum cultivation"</em> Published in the journal PLOS ONE (<a href="https://doi.org/10.1371/journal.pone.0268120">https://doi.org/10.1371/journal.pone.0268120</a>)</p> <p>N.B. To run the code unzip the folder 9-RData.zip and save it in the same working directory as the datasets</p> <p>V 2.0 changes:</p> <p>A. Datasets 1-2-3 - small formatting corrections</p> <p>B. Dataset 7 - fixing some errors in the calculations</p> <p>C. Code - minor fixes and seimplicifaction</p> <p> </p>
Data, code and software to reproduce the article entitled "Modeling soil-plant functioning of intercrops using comprehensive and generic formalisms implemented in the STICS model"
<p>This is the data, code and software to reproduce the article entitled " Modeling soil-plant functioning of intercrops using comprehensive and generic formalisms implemented in the STICS model". Here is a summary of the paper:</p> <p>The growing demand for sustainable agriculture is raising interest in intercropping for its multiple potential benefits to avoid or limit the use of chemical inputs or increase the production per surface unit. Predicting the existence and magnitude of those benefits remains a challenge given the numerous interactions between interspecific plant-plant relationships, their environment and the agricultural practices. Soil-crop models are critical in understanding these interactions in dynamics during the whole growing season, but few models are capable of accurately simulating intercropping systems.</p> <p>In this study, we propose a set of simple and generic formalisms for simulating key interactions in intercropping systems that can be readily included into existing dynamic crop models. This requires simulating important processes such as development, light interception, plant growth, N and water balance, and yield formation in response to management practices, soil conditions, and climate. These formalisms were integrated into the STICS soil-crop model and evaluated using observed data of intercropping systems of cereal and legumes mixtures, including Faba bean-Wheat, Pea-Barley, Sunflower-Soybean, and Wheat-Pea mixtures. We demonstrate that the proposed formalisms provide a comprehensive simulation of soil-plant interactions in various types of bispecific intercrops. The model was found consistent and generic under a range of spring and winter intercrops (nRMSE = 25% for maximum leaf area index, 23% for shoot biomass at harvest, and 18% for yield).</p> <p>This is the first time a complete set of formalisms has been developed and published for simulating intercropping systems and integrated into a soil-crop model. With its emphasis on being generic, sufficiently accurate, simple, and easy to parameterize, STICS is well-suited to help researchers designing <em>in silico</em> the agroecological transition by virtually pre-screening sustainable, manageable intercrop systems adapted to local conditions.</p> <p> </p> <p> </p> <p> </p>
Open-population models for estimating roadkill rates - Data and R Code
<p>Roadkill carcass capture-recapture data, capture histories for four and eight-occasion designs, and R code (with JAGS code) for roadkill rates estimation.</p>
Data and code for gmd-2023-113 "Parameter estimation for ocean background vertical diffusivity coefficients in the Community Earth System Model (v1.2.1) and its impact on ENSO forecast"
<p>Data and code for the paper "Parameter estimation for ocean background vertical diffusivity coefficients in the Community Earth System Model (v1.2.1) and its impact on ENSO forecast"</p> <p>includes: </p> <p>The model is Community Earth System Model (v1.2.1) (provided by www.cesm.ucar.edu)</p> <p>Data assimilation code is initially provided by Data Assimilation Research Testbed (DART) (https://dart.ucar.edu/), some modifications are made to enable parameter estimation function of ocean background vertical diffusivity coefficients. And the programs and scripts for deal with OISST and EN4 profiles are also developed.</p> <p>The parameter sensitivity experiment results are saved as <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/sensitive2008-2012.nc">sensitive2008-2012.nc</a> and <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/sensitive2008-2012salt.nc">sensitive2008-2012salt.nc</a> for temperature and salinity, respectively. And the python script to draw the results is </p> <p>The state estimation results are provided as <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/Temp_05-17.nc">Temp_05-17.nc</a> and <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/Temp_05-17.nc">Salt_05-17.nc</a> for temperature and salinity, respectively.</p> <p>The parameter estimation results are provided as <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/PE_Temp_05-17.nc">PE_Temp_05-17.nc</a> and <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/PE_Temp_05-17.nc">PE_Salt_05-17.nc</a> for temperature and salinity, respectively.</p> <p>the estimated paremeter ensemble is saved in <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/parameters.nc">parameters.nc</a></p> <p>the python script for comparing the SE and PE results is <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/plot_analysis.py">plot_analysis.py</a></p> <p>the nino3.4 indices computed by the forecast experiment is saved in <a href="https://zenodo.org/api/files/6e5b4bfa-61cf-44bc-8e15-e62fab467ea6/fcst_correlation.nc">fcst_correlation.nc</a></p> <p> </p>
Codes and data set for Cryoconite hole model (CryHo)
<p><strong>Codes and data set for cryoconite hole model (CryHo)</strong> (Onuma et al., 2023, <em>The Cryosphere</em>). The content is as below.</p> <p><strong>- cryho_disclose_v1</strong>: readme, the model codes, parameter files for the model, model outputs and shell scripts for sensitivity tests <br> <strong>- data</strong>: model input data (meteorological conditions), model data of extinction coefficient for ice* and observational data of cryoconite hole depths<br> <strong>- python</strong>: Python scripts for the visualization<br> <strong>- figure</strong>: png files created by the Python scripts<br> <br> *If you have any questions about extinction coefficients for ice, please contact Dr. Teruo Aoki, a co-author in this dataset.</p>
Interaction of waves with idealized high-relief bottom roughness, model parameters and code
Interactions between waves and large bottom roughness were investigated using Large Eddy Simulations of oscillatory flow over infinite hemisphere arrays. Simulations were made using the open source computational fluid dynamics code OpenFOAM. Wave amplitude, period, and hemisphere spacing were varied to investigate the dependence of kinematics and dynamics on dimensionless parameters, including the Keulegan-Carpenter number (KC), the ratio of wave orbital excursion to roughness element size. This archive includes the input files and user written routines to reproduce the simulations in the paper. Yu, X., J. H. Rosman, and J. L. Hench, 2018. Interaction of waves with idealized high-relief bottom roughness, Journal of Geophysical Research (Oceans), doi:10.1002/2017JC013515.
Data and code related to the article "Characterization of the Log-normal Model for Received Signal Strength Measurements in Real Wireless Sensor Networks"
<p>This upload contains the data and code related to the article "Characterization of the Log-normal Model for Received Signal Strength Measurements in Real Wireless Sensor Networks", (D.O.I: <a href="https://doi.org/10.3390/jsan9010012">10.3390/jsan9010012</a>) published in the the special issue on "Localization in Wireless Sensor Networks" of the <a href="https://www.mdpi.com/journal/jsan"><em>Journal of Sensor and Actuator Networks</em></a> (ISSN 2224-2708).</p> <p>The data and code included allows to replicate the results of the article.</p>
R code and data to reproduce figures from the "Multivariate autoregressive modelling and conditional simulation for temporal uncertainty analysis of an urban water system in Luxembourg" paper
<p>This repository contains the R code and data to reproduce figures from the "Multivariate autoregressive modelling and conditional simulation for temporal uncertainty analysis of an urban water system in Luxembourg" paper.</p>
Database and model code for "Material efficiency and climate change mitigation of passenger vehicles"
<p>This record provides all data points and model code necessary to compute the results presented in P. Wolfram, Q. Tu, N. Heeren, S. Pauliuk, E. Hertwich (2020) "Material efficiency and climate change mitigation of passenger vehicles", published in Journal of Industrial Ecology. All data is described in section 2 of the manuscript. The code can be run in MATLAB. </p>
Data and code for the manuscript: "Varying richness need not imply non-random species co-occurrence: implications for specifying null models"
<p>Data and R code for the manuscript "Varying richness need not imply non-random species co-occurrence: implications for specifying null models".</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.