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236 results for “Modeling Methods”
Antibody-Antigen Models for McCoy 2024 Paper: "A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases"
<p>Up to the top 20 models generated for each method tested in the 2024 Paper: "A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases"</p>
A computationally efficient method for parameter sensitivity analysis of microbially-explicit biogeochemical models accounting for long-term behavior
<p>The dataset is for the manuscript entitled "A computationally efficient method for parameter sensitivity analysis of microbially-explicit biogeochemical models accounting for long-term behavior".</p>
Evaluating Feature Attribution Methods in the Image Domain: Benchmark results and model parameters
<p>This dataset contains the experimental results, adversarial patches and model parameters used in the paper Evaluating Feature Attribution Methods in the Image Domain.</p>
Optical modeling of nonspherical pine and mugwort pollen aerosols using the invariant imbedding T-matrix and improved geometric optics methods
<p><strong>Data for </strong></p> <p><strong><em>Optical modeling of nonspherical pine and mugwort pollen aerosols using the invariant imbedding T-matrix and improved geometric optics methods</em>.</strong></p> <p> </p> <p>Mail:</p> <p><a href="mailto:bilei@zju.edu.cn">bilei@zju.edu.cn</a></p>
Quantitative and qualitative methods complementing: Bridging modelling and policy-making efforts to realise the European bioeconomy
<p>The European Bioeconomy Strategy aims to facilitate the transition from a take-make-dispose fossil economy into one fostering circular bio-based value chains linking sustainable land use with cutting-edge products. Optimised designs, implementation and monitoring rely on continuous interactions between policymakers and modellers who run multiple scenarios for environmentally, economically and socially desirable futures. "Bridging modelling and policy-making efforts to realise the European bioeconomy" leverages a multi-layered framework that cross-references 39 policies and 32 models to assess how they address the five principle objectives of the Bioeconomy Strategy in terms of accompanying sectors, value-chains, and multi-dimensional indicators. The framework identifies gaps in bioeconomy knowledge both in policy and modelling. The analysis stemming from this framework matching policies and models based on their scope and aim, and reviewing how each addresses bioeconomy objectives, sectors, value chain stages and indicators, was built using mixed methods. The files complement the Supplementary Files of "Bridging modelling and policy-making efforts to realise the European bioeconomy" to produce a comprehensive compendium of the key findings extracted from the main publication. </p>
Selected data analysed in the JGR Atmosphere manuscript " An application of the maximum entropy production method in the WRF Noah land surface model"
<p>The control experiment (hereafter WRF-CTL) and the MEP experiment (hereafter WRF-MEP) simulations results interpolated to the observation stations. The simulation period was 1 June to 31 August 2015 with 30 hours from 12:00 UTC (20:00 Beijing time (BJT)) each day, and the latest 24-hour outputs are provided.</p>
A conservative immersed boundary method for the multi-physics urban large-eddy simulation model uDALES v2.0
<p>This dataset accompanies the GMD article 'A conservative immersed boundary method for the multi-physics urban large-eddy simulation model uDALES v2.0' (https://doi.org/10.5194/egusphere-2024-96).</p> <ul> <li>The input files to run the presented cases using uDALES are contained in 'inputs'.</li> <li>The model outputs are contained in separate folders: 'XCC', 'indoor-outdoor', 'XCB', and 'SEB'. When downloaded, move into a folder called 'outputs' so that the paths defined in the scripts work as intended (see below).</li> <li>The Matlab scripts to plot the figures are contained in 'scripts'.</li> <li>The figures shown in the article are contained in 'figures'.</li> </ul>
Representation of model error in convective-scale data assimilation: additive noise, relaxation methods and combinations
<p>ModelError_1_dpsdt.tar.xz for Fig. 11<br> <br> ModelError_1_innovstat.tar.xz for Fig. 4, 10 and 13<br> <br> ModelError_1_KESpectrum.tar.xz for Fig. 1<br> <br> ModelError_1_pre_veri.tar.xz for Fig. 8 and 9<br> <br> ModelError_1_precipobs_tau.tar.xz for Fig. 2<br> <br> ModelError_1_refl_veri.tar.xz for Fig. 6, 12 and 14</p> <p>For plotting, MATLAB (R2017b) and python are used</p> <p> </p>
Dataset: Methods for computing the maximum performance of computational models of fMRI responses.
<p>Accompanying data for the revised version of the manuscript: Methods for computing the maximum performance of computational models of fMRI responses. written by Agustin Lage-Castellanos, Giancarlo Valente, Elia Formisano, Federico De Martino, submitted for publication in Plos Computational Biology, November 2018.</p> <p>The dataset (01.rar) contains the fMRI time series for one subject in Nifti format acquired on an actively shielded MAGNETOM 7T whole body system driven by a Siemens console at Scannexus (<a href="http://www.scannexus.nl)">www.scannexus.nl)</a>. Every folder (24 runs, one folder per run) contains 150 Nifti files, one Nifti file for each fMRI volume. Preprocessing consisted of slice scan-time correction (with sinc interpolation), 3-dimensional motion correction, and temporal high pass filtering (removing drifts of 4 cycles or less per run).</p> <p>The matlab file dmS01_24runs.mat contains a 24-length cell array of fMRI design matrices, one for every run. Every fMRI design matrix is size 150 volumes x 51 covariates. The first 42 columns correspond to the stimuli presented (42 sounds per run). Columns 43, and 44, correspond to the run mean and the linear trend covariates. The rest of the columns correspond to the covariates obtained with GLMdenoise. The matlab variable <em>stimulus</em> of size 24 x 42 contains the index of the sounds presented at every run. A total of 168 sounds were presented, each sound was presented 6 times across the 24 fMRI runs.</p> <p>The file SPMgls0.rar contains the Beta images in Nifti format for every column of the fMRI design matrix, including noise covariates, for every fMRI run. This model was estimated assuming i.i.d fMRI noise (OLS). The codes for computing the noise ceiling are available in the file nccodes.rar, together with a two of examples of their use. SPM is required.</p>
Figures for "New method for computing post-seismic deformations in a realistic gravitational viscoelastic Earth model"
<p>Here are all the figures used in the paper "New method for computing post-seismic deformations in a realistic gravitational viscoelastic Earth model". </p>
Supplemental material to 'Evaluation of force-based and displacement-based out-of-plane seismic assessment methods for unreinforced masonry walls through refined model simulations'
<p>This repository contains the results of discrete element simulations used to study the response of vertically-spanning unreinforced masonry walls under different wall configurations. The simulations are run using the software package UDEC 6.0 (<a href="https://www.itascacg.com/">Itasca</a>). The dataset has served as basis for the study conducted in the following paper:</p> <blockquote> <p>Godio M, Beyer K. Evaluation of force-based and displacement-based out-of-plane seismic assessmentmethods for unreinforced masonrywalls through refined model simulations. Earthquake Engng Struct Dyn. 2019;48:454-475. <a href="http://doi.org/10.1002/eqe.3144">DOI:10.1002/eqe.3144</a></p> </blockquote> <p>Version history:<br> V1: datasets '01_UDEC_VALIDATION' and '02_UDEC_RESULTS are added<br> V2: minor modifications to the datasets: deletion of unwanted temporary files from the datasets<br> V3: '00_CONTENT' PDF-file is added </p>
All figures for "Application of a new method to simulate post-seismic deformations in a realistic Earth model"
<p>It is a zip file for the figures used in paper "Application of a new method to simulate post-seismic deformations in a realistic Earth model".</p>
D3.10 - Users document for methods and models of the long-term coastline evolution.
<p>The D3.10, related to Task 3.5 and entitled "User Document for Methods and Models of the Long-term Coastline Evolution," is a WP3 deliverable, specifically a report describing the methods and models used to study long-term morpho-dynamic processes in a climate-change scenario. </p>
Evaluating the method reproducibility of deep learning models in the biodiversity research
Open the record for dataset details and reuse information.
Dataset supporting the manuscript "Establishment of a Newborn Lamb Gut-Loop Model to Evaluate New Methods of Enteric Disease Control and Reduce Experimental Animal Use" (Baillou, Kasal-Hoc et al, Veterinary Sciences, 2021)
<p>These are the data supporting reported results in the publication "Establishment of a Newborn Lamb Gut-Loop Model to Evaluate New Methods of Enteric Disease Control and Reduce Experimental Animal Use" (Baillou, A, Kasal-Hoc N. et al, Veterinary Sciences, 2021). DOI not yet available.</p>
Data and analysis for "A process-conditioned and spatially consistent method for reducing systematic biases in modeled streamflow"
<p>This contains all of the necessary data and code to reproduce the results of the manuscript submitted to the Journal of</p> <p>Hydrometeorology entitled "A process-conditioned and spatially consistent method for reducing systematic biases in modeled streamflow"</p>
Simulations scripts for: Strain localization patterns and thrust propagation in 3-D discrete element method (DEM) models of accretionary wedges
<p>High-resolution three-dimensional discrete element method (DEM) simulations of sandbox-scale models of accretionary wedges performed in this study suggest thrusts follow a variety of propagation processes and orientations in the wedges depending on a number of factors including the stage of development of the wedge (precritical vs. critical), basal friction, and type of thrust (forward vs. backward-vergent). In terms of propagation processes, two clear mechanisms are identified. The first involves propagation from the decollement to the wedge top, similar to the standard model of thrust propagation seen in many kinematic models, and in the second, thrusts grow downward from an initial nucleation point just below the top surface of the wedge as well as upward from the decollement joining in the middle. In terms of orientation, forward-vergent thrusts initially form at Roscoe or Arthur orientations, and over shortening, form at Coulomb orientations. To arrive at these results, a wide array of continuum parameters and fields were extracted from the granular assembly of the DEM simulations, including stress, strain, strain rate, kinetic energy, Mohr-Coulomb parameters, and proximity to yielding using the Drucker-Prager criterion to visualize thrust nucleation and propagation. Lastly, the advantages and disadvantages of these continuum proxies for discerning failure in the granular assembly are considered, and the spatial and temporal relationship between proximity to yielding and strain localization (both pre-peak and persistent shear banding) in the granular model of an accretionary wedge is explored.</p>
Results and assumptions for: Modeling the Circular Economy in Environmentally Extended Input-Output Tables: methods, software and case study
<p>This dataset presents supplementary information for <em>"Modeling the Circular Economy in Environmentally Extended Input-Output Tables: methods, software and case study" </em><a href="https://doi.org/10.1016/j.resconrec.2019.104508">https://doi.org/10.1016/j.resconrec.2019.104508</a></p> <p>The data was processed and results were obtained through https://cmlplatform.github.io/pycirk/</p> <p> </p> <p><br> Annex I: Scenario assumptions and modeling choices and complete results (file Annex_I.xlsx) <br> Annex II: Contains analysis of other software, database modifications, and list of affected categories (file Annex_II.docx) <br> Results: settings, assumptions, results and their analysis from the case study presented in the paper (file Donati_CE_EEIO_Mo_SI.tar.gz)</p>
Bayesian models' outputs for: A new method to explicitly estimate the shift of optimum along gradients in multispecies studies
<p>This repository contains data to reproduce analysis presented in the paper:</p> <p>B. Mourguiart, B. Liquet, K. Mengersen, T. Couturier, J. Mansons, Y. Braud, A. Besnard . A new method to explicitly estimate the shift of optimum along gradients in multispecies studies. <em>Journal of Biogeography</em>, (in press).</p> <p>The paper introduces a new formulation of a Bayesian hierarchical linear model that explicitly estimates optimum shifts for multiple species having symmetrical response curves. This new formulation, called Explicit Hierarchical Model of Optimum Shifts (EHMOS), is compared to a mean comparison method and a Bayesian generalized linear mixed model (GLMM) using simulated and real datasets. Fitting the models to the simulated data took several days. Here we provide the models' outputs needed to reproduce the results presented in the paper without re-running the models. </p>
Last glacial cycle simulations forced by PMIP3 climate with a matrix and index method using a 3D thermodynamical ice-sheet model IMAU-ICE
<p>IMAU-ICE 2.0 model output of the ice evolution during the last glacial cycle at a 10 ka temporal resolution, as described in Scherrenberg at al., 2023.</p>
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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.