Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
700
datasets available to search
ShareScore release 0.9.0
Dataset results
700 results for “Dynamical model”
Data from: Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon
<ul> <li><span>Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. </span></li> <li><span>Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272 Mb genome of the Mediterranean grass <i>Brachypodium distachyon. </i></span></li> <li><span>We find that much of the recent transpositional activity in the <i>B. distachyon </i>genome is due to centromeric <i>Gypsy </i>families and <i>Copia </i>elements belonging to the Angela lineage. With a half-life as low as 66 ky, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich <i>Gypsy </i>elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains more than 20 percent of the genome-wide variation in GC content and is associated with higher methylation levels. </span></li> <li><span>Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size. </span></li> </ul>
Dataset - Dynamic persistence of intracellular bacterial communities of uropathogenic Escherichia coli in a human bladder-chip model of urinary tract infections
<p>Dataset for manuscript posted at biorxiv: https://doi.org/10.1101/2021.01.03.42483 and in revision for eLife. Data corresponding to each main figure and its associated figure supplements are in seperate .zip folders.</p>
Lumped Element Rigid Panel Dynamics Model
<p>This code is a lumped element rigid panel dynamics model calculating natural frequencies and mode shapes for radiator panels connected by thin kinked tubes. The panels are connected by torsional spring elements, and this work is compared against a continuous equivalent stiffness beam model. Data is included for the example being calculated, however, it can be easily modified for any number of panels.</p> <p>This work is part of Kyle Marquis' 2021 Master's Thesis at the University of Colorado Boulder, titled "A Novel Deployable Radiator Architecture for High-Power Spacecraft Missions by Connecting Tapered and Layered Panels with Thin Kinked Tubes".</p>
Model output data for compressible EULAG dynamical core in COSMO: convective-scale Alpine weather forecasts
<p>The archive contains model output data for article "Compressible EULAG dynamical core in COSMO: convective-scale Alpine weather forecasts" to be published in Monthly Weather Review.</p> <p>The article presents the semi-implicit compressible EULAGas a newdynamical core for convective-scale<br> numerical weather prediction. The core is implemented within the infrastructure of the<br> operational model of the Consortium for Small Scale Modeling (COSMO), forming the NWP<br> COSMO-EULAG model (CE). This regional high-resolution implementation of the dynamical<br> core complements its global implementation in the Finite-Volume Module of ECMWF’s Integrated<br> Forecasting System. The paper documents the first operational-like application of the dynamical<br> core for realistic weather forecasts. After discussing the formulation of the core and its coupling<br> with the host model, the paper considers several high-resolution prognostic experiments over<br> complex Alpine orography. Standard verification experiments examine the sensitivity of the CE<br> forecast to the choice of the advection routine and assess the forecast skills against those of the<br> default COSMO Runge-Kutta dynamical core at the 2.2 km grid showing a general improvement.<br> The skills are also compared using satellite observations for a weak-flow convective Alpine weather<br> case-study, showing favorable results. Additional validation of the new CE framework for partly<br> convection-resolving forecasts using 1.1 km, 0.55 km, 0.22 km, and 0.1 km grids, designed to<br> challenge its numerics and test the dynamics-physics coupling, demonstrates its high robustness in<br> simulating multi-phase flows over complex mountain terrain, with slopes reaching 85 degrees, and<br> the flow’s realistic representation.</p>
An Assessment of Nonhydrostatic and Hydrostatic Dynamical Cores at Seasonal Time Scales in the Energy Exascale Earth System Model (E3SMv1)
<p>This is the companion data for the manuscript of the same title, submitted to Journal of Advances in Modeling Earth Systems on 09/03/2021. </p> <p><strong>summer: </strong>this folder contains part of the model outputs I ran on NERSC Cori in 2020-2021 corresponding to the summer simulations in the manuscript.</p> <p><strong>winter: </strong>this folder contains part of the outputs I ran on NERSC Cori in 2020-2021 corresponding to the winter simulations in the manuscript.</p> <p><strong>ne256: </strong>this folder contains part of the outputs I ran on NERSC Cori in 2021 corresponding to the ne256 simulations in the manuscript.</p> <p><strong>bubble</strong>: this folder includes the namelists used in the rising bubble experiments.</p> <p><strong>script: </strong>this folder includes an example of a script to generate the realistic SCREAM simulation </p> <p> </p> <p>Unfortunately, model outputs are too large (~ 30 TB). Therefore, I only provide mean data, used directly to generate figures, in this repository. All model output are archived on tape at NERSC. </p> <p>For more details, refer to the manuscript, or contact me (wrliu@ucdavis.edu). </p>
Multispecies modelling reveals potential for habitat restoration to re-establish boreal vertebrate community dynamics
<p>1. The restoration of habitats degraded by industrial disturbance is essential for achieving conservation objectives in disturbed landscapes. In boreal ecosystems, disturbances from seismic exploration lines and other linear features have adversely affected biodiversity, most notably leading to declines in threatened woodland caribou. Large-scale restoration of disturbed habitats is needed, yet empirical assessments of restoration effectiveness on wildlife communities remain rare.</p> <p>2. We used 73 camera trap deployments from 2015-2019 and joint species distribution models to investigate how habitat use by the larger vertebrate community (>0.2 kg) responded to variation in key seismic line characteristics (line-of-sight, width, density and mounding) following restoration treatments in a landscape disturbed by oil and gas development in northeastern Alberta.</p> <p>3. The proportion of variation explained by line characteristics was low in comparison to habitat type and season, suggesting short-term responses to restoration treatments were relatively weak. However, we predicted that lines with characteristics consistent with restored conditions would support altered community composition, with reduced use by wolf and coyote, thereby indicating that line restoration will result in reduced contact rates between caribou and these key predators.</p> <p>4. Our analysis provides a framework to assess and predict wildlife community responses to emerging restoration efforts. With the growing importance of habitat restoration for caribou and other vertebrate species, we recommend longer-term monitoring combined with landscape-scale comparisons of different restoration approaches to more fully understand and direct these critical conservation investments. Only by combining rigorous multispecies monitoring with large-scale restoration will we effectively conserve biodiversity within rapidly changing environments.</p>
Modeling cyanobacteria life cycle dynamics and historical nitrogen fixation in the Baltic Proper - Datasets
<p>Observational and model datasets used in: Modeling cyanobacteria life cycle dynamics and historical nitrogen fixation in the Baltic Proper.</p>
Model data repository of "The role of sediment accretion and buoyancy on subduction dynamics and geometry"
<p>This dataset contains the code and data used in Brizzi et al. (2021): The role of sediment accretion and buoyancy on subduction dynamics and geometry</p>
Scripts to perform dynamic optimization of a model of invasive aspergillosis
<p>Matlab scripts to perform optimization and analyses of a dynamic optimization model of invasive aspergillosis:<br> "Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis"<br> Jan Ewald, Flora Rivieccio, Lukáš Radosa, Stefan Schuster, Axel A. Brakhage, Christoph Kaleta<br> https://doi.org/10.1101/2021.05.12.443764</p> <p>File structure:</p> <p>--- Core optimization files ---<br> -- simulation.cpp --<br> Description of ODE model in 'C', used by solver to calculate the time course given the parameters, initial states and control variables</p> <p>-- simulation.mexa64 --<br> Compiled mex-File from simulation.cpp used as interface by MATLAB to 'C' files.</p> <p>-- optFun.m --<br> Definition of the objective function. Uses a control vector 'u' to calculate the, objective function value F, the time course of state variables 'x' and gradients used by the solver to determine the optimal control of 'u'.</p> <p>-- single_opt.m --<br> Function which performs an optimization run for a given parameter set and a randomized initial solution u0. Optimization can be conducted by SNOPT or in conjunction with IPOPT. Both solver are not provided here (proprietary).</p> <p><br> --- Additional files ---<br> -- solve_with_ipopt.m --<br> Configuration file and interface to call the solver IPOPT.</p> <p>-- lognorm_mu.m --<br> Function to provide log-normal distributed samples given the standard deviation, reference value (mode of distribution) and number of samples which should be calculated.</p> <p>-- mice_param_alv.m --<br> Reference parameter set of the model for mice as host organism and cell numbers normalized per alveolus.</p> <p>-- parameter_model.m --<br> Definition of parameter container to handle interface to optFun-call by solvers which do not allow parameter in function call.</p> <p>--- Optimization Runs ---<br> -- rand_params.m --<br> Performs optimization runs for multiple randomized parameter sets and several scenarios to determine parameter sensitivity.</p> <p>-- doseresponse.m --<br> Performs optimization runs for a sequnce of initial conidial dosages to determine the dose response of the system.</p> <p>--- Scripts for post-analysis ---<br> -- rand_analysis.m --<br> Loads the data created by the optimization runs (rand_params.m) and performs parameter sensitivity analysis as well as produces plots for analysis related to parameter influence.</p> <p>-- doseanalysis.m --<br> Loads the data created by the optimization runs (doseresponse.m ) and produces dose response curves as well as additional plots and analyses.</p> <p>--- Optimization output files ---<br> -- rand_param_out/ --<br> Folder contains optimization results as MATLAB session-file for randomized parameters used for parameter sensitivity analysis.</p> <p>-- dose_out/ --<br> Folder contains optimization results as MATLAB session-file for dose response curve calculation.</p>
Supplementary material to "A dynamic flight model for Slocum gliders and implications for turbulence microstructure measurements" by Merckelbach et al.
<p>Supplementary information to the publication "A dynamic flight model for Slocum gliders and implications for turbulence microstructure measurements" by Lucas Merckelbach, Anja Berger, Gerd Krahmann, Marcus Dengler and Jeffrey R. Carpenter, Journal of Atmospheric and Oceanic Technology, 2019, 36(2), DOI: 10.1175/JTECH-D-18-0168.1. The supplementary information consists of the set of glider data and DVL data as used in the manuscript.</p> <p> </p>
CESM 1.2 climate model simulation output for: The Essential Role of Westerly Wind Bursts in ENSO Dynamics and Extreme Events Quantified in Model 'Wind Stress Shaving' Experiments
<p>Westerly wind bursts (WWBs)—brief but strong westerly wind anomalies in the equatorial Pacific—are believed to play an important role in El Niño Southern Oscillation (ENSO) dynamics, but quantifying their effects is challenging. Here, we investigate the cumulative effects of WWBs on ENSO characteristics, including the occurrence of extreme El Niño events, via modified coupled model experiments within Community Earth System Model (CESM1) in which we progressively reduce the impacts of wind stress anomalies associated with model-generated WWBs. In these "wind stress shaving" experiments we limit momentum transfer from the atmosphere to the ocean above a preset threshold, thus "shaving off" wind bursts. To reduce the tropical Pacific mean state drift, both westerly and easterly wind bursts are removed, although the changes are dominated by WWB reduction. As we impose progressively stronger thresholds, both ENSO amplitude and the frequency of extreme El Niño decrease, and ENSO becomes less asymmetric. The warming center of El Niño shifts westward, indicating less frequent and weaker Eastern Pacific (EP) El Niño events. Removing most of wind bursts-related wind stress anomalies reduces ENSO amplitude by 22%. The essential role of WWBs in the development of extreme El Niño events is revealed in the suppressed eastward migration of the western Pacific warm pool and hence a weaker Bjerknes feedback under wind shaving. Overall, our results reaffirm the importance of WWBs in shaping the characteristics of ENSO and its extreme events and imply that WWB changes with global warming could influence future ENSO.</p>
Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas: An assessment of population connectivity and ocean dynamics
<p>Biophysical models are a powerful tool for assessing population connectivity of marine organisms that broadcast spawn. <em>Albula</em> <em>vulpes</em> is a species of bonefish that is an economically and culturally important sportfish found throughout the Caribbean and that exhibits genetic connectivity among geographically distant populations. We created ontogenetically relevant biophysical models for bonefish larval dispersal based upon multiple observed spawning events in Abaco, The Bahamas in 2013, 2018, and 2019. Biological parameterizations were informed through active acoustic telemetry, CTD casts, captive larval rearing, and field collections of related albulids and anguillids. Ocean conditions were derived from the Regional Navy Coastal Ocean Model American Seas dataset. Each spawning event was simulated 100 times using the program Ichthyop. Ten thousand particles were released at observed and putative spawning locations and were allowed to disperse for the full 71-day pelagic larval duration for <em>A</em>. <em>vulpes</em>. Settlement densities in defined settlement zones were assessed along with interactions with oceanographic features. The prevailing Northern dispersal paradigm exhibited strong connectivity with Grand Bahama, the Berry Islands, Andros, and self-recruitment to lower and upper Abaco. Ephemeral gyres and flow direction within Northwest and Northeast Providence Channels were shown to have important roles in larval retention to the Bahamian Archipelago. Larval development environments for larvae settling upon different islands showed few differences and dispersal was closely associated with the thermocline. Settlement patterns informed the suggestion for expansion of conservation parks in Grand Bahama, Abaco, and Andros, and the creation of a park in Eleuthera and the Berry Islands to protect fisheries. Further observation of spawning events and the creation of biophysical models will help to maximize protection for bonefish spawning locations and nursery habitat, and may help to predict year-class strength for bonefish stocks throughout the Greater Caribbean.</p>
Dynamic Rupture Modeling of the 2019 Ridgecrest Earthquakes
<p>This repository contains files needed to reproduce the 2019 Ridgecrest earthquake sequence dynamic rupture models using SeisSol (<a href="https://github.com/SeisSol/SeisSol">https://github.com/SeisSol/SeisSol</a>).</p>
Coupled stochastic modelling of hierarchical channel network dynamics and metapopulation persistency - Dataset
<p>Dynamic changes in the active portion of stream networks represent a phenomenon common to diverse climates and geologic settings. However, the ecological implications of river network expansions/retractions remain poorly understood owing to operational difficulties in mechanistically describing these processes at the relevant spatio-temporal scales. Here we present a novel Bayesian framework for the simulation of event-based channel network dynamics capitalizing on the concept of "hierarchical structuring of temporary streams" - a general principle to identify the activation/deactivation order of network nodes. The framework incorporates a dynamic version of a stochastic occupancy metapopulation model, and is used to analyze the impact of pulsing river networks on species persistence in different scenarios. Climate strongly controls temporal variations of the active length, influencing the preferential configuration of the active channels and the speed of network retraction during drying. We also identify a climate-dependent detrimental effect of network dynamics on species spread and persistence. This effect is enhanced by dry climates, where flashy expansions and retractions of the flowing channels induce metapopulation extinction. Survival probabilities are particularly reduced in settings where the spatial heterogeneity of network connectivity is pronounced. The proposed framework provides novel insight on the multi-faced ecological legacies of channel network dynamics.</p>
Predictive Search Model of Flocking for Quadcopter Swarm in the Presence of Static and Dynamic Obstacles
<p>The folder includes experimental data for the paper titled "Predictive Search Model of Flocking for Quadcopter Swarm in the Presence of Static and Dynamic Obstacles".</p> <p>In the paper, we present a Predictive Search Model (PSM) for flocking with Heading and Speed Shared (HSS) and Heading and Speed Unshared (HSU) prediction methods. We compare the performance of PSM with Potential Field Model (PFM) in the presence of static and dynamic obstacles in simulation. Also, we validate the performance of PSM with a quadcopter swarm indoors.</p> <p>The 'simulation experiments' folder includes simulation experiment data and MATLAB scripts that can simulate the experiments and provide plots for analysis.</p> <p>The 'quadcopter experiments' folder includes quadcopter experiment data and MATLAB scripts that can simulate the experiments and provide plots for analysis.</p>
Supplementary data to: Soil Moisture to Runoff (SM2R) A data-driven model for runoff estimation across poorly gauged Asian water towers based on soil moisture dynamics
<p>This data archive includes simulated monthly runoff anomaly using the Soil Moisture to Runoff model during 1981‒2020 over the representative drainage basin in each water tower. Please see Readme for more data information. For calculation details please see the publication.</p>
Figures from the paper "The diversity of canonical and ubiquitous progress in computer vision: A dynamic topic modeling approach"(v2))
<p>Figures from the paper "The diversity of canonical and ubiquitous progress in computer vision: A dynamic topic modeling approach".</p> <p><strong>The second version:</strong> Corrections to Figure 1. (fig1-> fig_v2).</p>
Revealing the drivers of parasite community assembly: using avian haemosporidians to model global dynamics of parasite species turnover
<p>Why do some regions share more or fewer species than others? Community assembly relies on the ability of individuals to disperse, colonize, and thrive in new regions. Therefore, many distinct factors, such as geographic distance and environmental features, can determine the odds of a species colonizing a new environment. For parasites, host community composition (i.e., resources) also plays a key role in their ability to colonize a new environment as they rely on their hosts to complete their life cycle. Thus, variation in host community composition and environmental conditions should determine parasite turnover among regions. Here, we explored the global drivers of parasite turnover using avian malaria and malaria-like (haemosporidian) parasites. We compiled global databases on avian haemosporidian lineages distributions, environmental conditions, avian species distributions and functional traits and ran generalized dissimilarity models to uncover the main drivers of parasite turnover. We demonstrated that haemosporidian parasite turnover is mainly driven by geographic distance followed by host functional traits, environmental conditions, and host distributions. The main host functional traits associated with high parasite turnover were the predominance of resident (i.e., non-migratory) species and strong territoriality while the most important climatic drivers of haemosporidian turnover were mean temperature and temperature seasonality. Overall, we establish the importance of geographic distance as a key predictor of ecological dissimilarity and show that host resources influence parasite turnover more strongly than environmental conditions. We also evidenced that parasite turnover is most pronounced among tropical and less interconnected regions (i.e., regions with mostly territorial and non-migratory hosts). Our findings provide a robust foundation for the prediction of avian pathogen spread and the emergence of infectious diseases.</p>
Modeled wintertime sea ice drift, sea ice thickness, dynamic sea surface height and sea ice drift budget terms in the Arctic
<p>Modeled wintertime sea ice drift, sea ice thickness, dynamic sea surface height and sea ice drift budget terms in the Arctic between 1981 and 2020.</p>
Dynamic Vegetation Model Dynamic Organic Soil Terrestrial Ecosystem Model (DVM-DOS-TEM) simulations focused on Eight Mile Lake, Alaska and Imnavait Creek, Alaska [2000-2015]
<p>This set of files store model simulations using the biosphere model Dynamic Vegetation Model Dynamic Organic Soil Terrestrial Ecosystem Model (DVM-DOS-TEM), developed to simulate biophysical and biogeochemical interactions between the soil, vegetation and atmosphere. To improve predictions of net carbon releases from thawing permafrost, we tested the sensitivity of a suite of model parameters. We analyzed the responses of ecosystem carbon balances to permafrost thaw by running site-level simulations at two long-term tundra ecological monitoring sites in Alaska: Eight Mile Lake (EML) and Imnavait Creek watershed (IMN). These sites are characterized by similar tussock tundra vegetation but differing soil drainage conditions and climate, IMN consists of well-drained soils, and EML has historically well-drained soils, however permafrost thaw has altered drainage conditions to wetter soils. Simulations were conducted at a 1km resolution, over a 1,000 km2 area (10x10 km square) centered on two long term ecological research sites in Alaska: Eight Mile Lake located in Interior Alaska (63.8900° N, 149.2535° W), and Imnavait creek watershed located on the northern foothills of the Brooks range (68°37′ N, 149°18′ W).</p> <p>Historical simulations are spanning the 2000 to 2015, and forced using climate simulations from the Climate Research Unit, time series 4.0. We ran 1,000 site level simulations for each model variable. The variables that are produced are gross primary productivity (GPP, in gC.m-2.m-1), net ecosystem exchange (NEE, gC.m-2.m-1), ecosystem respiration (RECO, gC/m2/m-1), active layer thickness (ALT, m), soil temperature (TLAYER,°C) at 5, 10, 40 cm depths, soil moisture (LWCLAYER, m-3/m-3) at 5, 10 cm depths, and snow depth (SNOWDEPTH, m), evapotransipiration(EET, mm/m2/time), potential evapotransipiration (PET, mm/m2/time), leaf area index (LAI, m2/m2), organic layer thickness (OLT, m). The data are stored as compiled csv files, with time as the index, and each model sample output stored in the columns. In addition, there is a postprocessing python script to demonstrate the step and workflow used to generate the individual csv files post processed from the raw model outputs stored as netcdfs.</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.