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1,028 results for “simulation model”
Data from: Using hidden Markov models to improve quantifying physical activity in accelerometer data – a simulation study
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Sacramento River RAFT water temperature model simulations based on hypothetical reservoir perturbations in the historical record
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Integrated Biosphere Simulator Model (IBIS), Version 2.5
The Integrated Biosphere Simulator (or IBIS) is designed to be a comprehensive model of the terrestrial biosphere; the model represents a wide range of processes, including land surface physics, canopy physiology, plant phenology, vegetation dynamics and competition, and carbon and nutrient cycling. The model generates global simulations of the surface water balance (e.g., runoff), the terrestrial carbon balance (e.g., net primary production, net ecosystem exchange, soil carbon, aboveground and belowground litter, and soil CO2 fluxes), and vegetation structure (e.g., biomass, leaf area index, and vegetation composition). IBIS was developed by Center for Sustainability and the Global Environment (SAGE) researchers as a first step toward gaining an improved understanding of global biospheric processes and studying their potential response to human activity [Foley et al., 1996]. IBIS was constructed to explicitly link land surface and hydrological processes, terrestrial biogeochemical cycles, and vegetation dynamics within a single, physically consistent framework. Furthermore, IBIS was one of a new generation of global biosphere models, termed Dynamic Global Vegetation Models (or DGVMs), that consider transient changes in vegetation composition and structure in response to environmental change. Previous global ecosystem models have typically focused on the equilibrium state of vegetation and could not allow vegetation patterns to change over time.Version 2.5 of IBIS includes several major improvements and additions [Kucharik et al. 2000]. SAGE continues to test the performance of the model, assembling a wide range of continental- and global-scale data, including measurements of river discharge, net primary production, vegetation structure, root biomass, soil carbon, litter carbon, and soil CO2 flux. Using these field data and model results for the contemporary biosphere (1965-1994), their evaluation shows that simulated patterns of runoff, NPP, biomass, leaf area index, soil carbon, and total soil CO2 flux agreed reasonably well with measurements that have been compiled from numerous ecosystems. These results also compare favorably to other global model results [Kucharik et al. 2000].
ATom: Simulated Data Stream for Modeling ATom-like Measurements
This dataset provides a simulated data stream representative of an Atmospheric Tomography mission (ATom) data collection flight and also modeled reactivities for ozone (O3) production and loss and methane (CH4) loss from six global atmospheric chemistry models: CAM, GEOS-Chem, GFDL, GISS-E2.1, GMI, and UCI. The simulated data include concentrations of selected atmospheric trace gases for 14,880 air parcels along a simulated north-south ATom flight path along 180-degrees longitude over the Pacific basin. Each of the six models produced ozone production and loss and methane loss reactivities initialized using the simulated data beginning with five different days in August (8-01, 8-06, 8-11, 8-16, 8-21). Modeled years for each individual model varied from 1997 to 2016.
BOREAS RSS-08 BIOME-BGC Model Simulations at Tower Flux Sites in 1994
BIOME-BGC is a general ecosystem process model designed to simulate biogeochemical and hydrologic processes across multiple scales (Running and Hunt, 1993). In this investigation, BIOME-BGC was used to estimate daily water and carbon budgets for the BOREAS tower flux sites for 1994. Carbon variables estimated by the model include gross primary production (i.e., net photosynthesis), maintenance and heterotrophic respiration, net primary production, and net ecosystem carbon exchange. Hydrologic variables estimated by the model include snowcover, evaporation, transpiration, evapotranspiration, soil moisture, and outflow. The information provided by the investigation includes input initialization and model output files for various sites in tabular ASCII format.
LBA-ECO LC-04 IBIS Model Simulations for the Amazon and Tocantins Basins: 1921-1998
The provided data were generated by the Integrated BIosphere Simulator (IBIS) terrestrial ecosystem model (Foley et al. 1996, Kucharik et al. 2000) using data from the CRU05 climate record for the years 1921-1998 (New et al. 2000). Data are included for the annual net ecosystem exchange of the surface, microbial respiration, root respiration, total soil respiration, soil moisture, leaf area index, drainage, and surface and subsurface runoff, for the entire Amazon and Tocantins basins. The data files are provided in netCDF format and standard ESRI ARCGIS ARC/INFO ASCIIGRID format. The netCDF files consist of either annual or monthly means from 1921 to 1998. The ASCII files are available only for the annual mean files.
Improved Simulations of Biomass Burning Aerosol Optical Properties and Lifetimes during the ORACLES-I Campaign: Results from the NASA GEOS Model
This dataset contains model results and satellite-based research retrievals associated with the manuscript submitted in Atmospheric Chemistry and Physics Journal, titled, " Improved Simulations of Biomass Burning Aerosol Optical Properties and Lifetimes in the NASA GEOS Model during the ORACLES-I Campaign". There were multiple NASA GEOS global model simulations performed for this study. Following are the name of the simulation and their description corresponding to the file names within this dataset: 1. Baseline: Default version of the GEOS model 2. Smoke Age: Default version of the GEOS model run with biomass burning OA tagged by day of the week it was emitted. 3. Smoke Composition: Default version of the GEOS model run with biomass burning OA tagged by type of vegetation burned. 4. OA-loss: Hydrophilic OA from biomass burning is assigned a 6-day e-folding loss time; OA from biomass burning sources is enhanced 60%, BC from biomass burning sources is enhanced 15%. 5. OA-loss+updated optics: As in OA-loss but with updated aerosol optical properties.
CMS: Simulated Physical-Biogeochemical Data, SABGOM Model, Gulf of America, 2005-2010
This dataset contains monthly mean ocean surface physical and biogeochemical data for the Gulf of America simulated by the South Atlantic Bight and Gulf of America (SABGOM) model on a 5-km grid from 2005 to 2010. The simulated data include ocean surface salinity, temperature, dissolved inorganic nitrogen (DIN), dissolved inorganic carbon (DIC), partial pressure of CO2 (pCO2), air-sea CO2 flux, surface currents, and primary production. The SABGOM model is a coupled physical-biogeochemical model for studying circulation and biochemical cycling for the entire Gulf of America to achieve an improved understanding of marine ecosystem variations and their relations with three-dimensional ocean circulation in a gulf-wide context.
LBA-ECO LC-04 THMB Model Simulations for the Amazon and Tocantins Basins: 1939-1998
The model output data provided were generated by the THMB 1.2 (Terrestrial Hydrology Model with Biogeochemistry) model which simulates the flow of water through groundwater systems, rivers, lakes and wetlands. The model operates at a 5-minute latitude-by-longitude grid with a 1-hour time step and requires as boundary conditions: topography, evaporation from water surfaces, surface runoff, base flow, and precipitation. Data are included for the mean monthly simulated water height above flood stage, mean monthly simulated river discharge, and mean monthly inundated area for the period 1939-1998 for the entire Amazon and Tocantins River basins. There are three netCDF files (.nc) with this data set.
Optimization of a Mouse Model of Pancreatic Cancer to More Closely Simulate the Human Phenotypes of Metastasis and Cachexia
GEO Series GSE251864. Mus musculus. 22 samples. Type: Expression profiling by high throughput sequencing.
Brain transcriptome profiles in mouse model simulating features of post-traumatic stress disorder
GEO Series GSE45035. Mus musculus. 230 samples. Type: Expression profiling by array.
Spaceflight and simulated microgravity conditions increase virulence of Serratia marcescens in the Drosophila melanogaster infection model
GEO Series GSE138116. Drosophila melanogaster. 12 samples. Type: Expression profiling by high throughput sequencing.
Mechanical Unloading of Engineered Human Meniscus Models Under Simulated Microgravity
GEO Series GSE192983. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Improving genome-scale metabolic model simulations by measuring exchange fluxes during exponential growth phase
GEO Series GSE293588. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Molecular indicators of stress-induced neuroinflammation in a mouse model simulating features of post-traumatic stress disorder
GEO Series GSE85495. Mus musculus. 40 samples. Type: Methylation profiling by genome tiling array.
Numerical simulations of the geospace response to a perfect interplanetary coronal mass ejection: Model Data
<p>This is the model output data discussed in the article, "Numerical simulations of the geospace response to a perfect interplanetary coronal mass ejection." See README.txt for information on dataset contents, formats, and suggested software libraries.</p> <p> </p>
Simulation of POPC:POPE 1:1 membrane, model by Maciejewski and Rog
<p>A POPC:POPE 1:1 bilayer with 64 lipids per leaflet is simulated for 300 ns using the model by Maciejewski and Rog [1,2] and Gromacs simulation engine version 2019.4. The trajectory (.xtc) is saved every 100ps. The simulation parameters (.mdp), the energy file (.edr), the continue point to extend the simulation (.cpt), the run input parameters (.tpr), and the final structure (.gro) are also given. The lipid topologies (.itp) are attached, and they are obtained from the authors. Note that unlike in the original paper [2], buffered Verlet lists are used for efficiency.</p> <p>[1] DOI: 10.1016/j.dib.2016.03.067</p> <p>[2] DOI: 10.1021/jp5016627</p>
Output of CAM simulations performed for study "Impact of cloud physics on the Greenland Ice Sheet near-surface climate: a study with the Community Atmosphere Model"
<p>Output of CAM simulations performed for study "Impact of cloud physics on the Greenland Ice Sheet near-surface climate: a study with the Community Atmosphere Model" in JGR-Atmospheres (2020). </p> <p>Output are NetCDF files containing annual means (named 'yearmean', 2007-2013), or multi-annual monthly means ('ymonmean', 2007-2012) of various variables that are of interest and/or used for analysis in this study. The file name starts with the variable name. Fields are global, at a resolution of 0.9 x 1.25 degrees latitude/longitude.</p> <p>The test simulations are named (as discussed in the paper):</p> <p>cam4_clm5<br> cam5_clm5<br> cam6_noicenucl_clm5<br> cam6_noclubb_clm5<br> cam6_mg1_clm5<br> cam6</p>
Application of a Modified Spheromak Model to Simulations of Coronal Mass Ejection in the Inner Heliosphere
<p>Data for the Space Weather paper titled "Application of a Modified Spheromak Model to Simulations of Coronal Mass Ejection in the Inner Heliosphere"</p>
Simulations of the air-water interface at the presence of salt, ECC ions + OPC water model
<p>Simulations of a water–air interface. There are ~20000 water molecules with various concentrations of NaCl or CaCl_2 in a simulation box of 12*12*22 nm^3. The 4-point OPC water and the ions with scaled charges based on the electronic continuum correction (ECC) are used. The numbering in file names corresponds to the different concentrations. GROMACS-compatible inputs are provided: simulation parameters (md.mdp), topologies (top), and index (ndx) files. Initial structure can be extracted from the tpr file using gmx editconf. The run input (tpr) is provided, as are the outputs: energy file (edr), trajectory (xtc), and final structure (gro). Surface tensions can be extracted by gmx energy.</p> <p>These values are reported in DOI: [ADD].</p> <p>Data for these ECC ions with SPCE water is provided at DOI: 10.5281/zenodo.3888383 and for the full charge ions by Dang et al. in SPCE water at DOI: 10.5281/zenodo.3888436 .</p>
ScienceDex guides
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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.