Find research datasets worth reusing

opencc-by-4.0Apr 2020View details →

Data supplement for "Gradient dynamics model for drops spreading on polymer brushes"

This dataset contains the data and source files for the diagrams of the following publication: Thiele, U. & Hartmann, S. Gradient dynamics model for drops spreading on polymer brushes arXiv preprint arXiv:1910.10582, 2019 We provide the data and sources necessary to generate the figures 3 & 4 of the manuscript. For more information, please see the included README.md

Model data(Figures 4 and S1)

2.5-layer model data used to generate Figures 4 and S1.

openmit-licenseNov 2019View details →

Efficient ensemble data assimilation for coupled models with the Parallel Data Assimilation Framework: Example of AWI-CM - output files and plot scripts

This archive outputs_plotting.zip contains the raw output files (STDOUT) from the scaling runs performed for the paper "Efficient ensemble data assimilation for coupled models with the Parallel Data Assimilation Framework: Example of AWI-CM" submitted to GMD (gmd-2019-167). Further the scripts to extract timing information from the raw output files and plot scripts are included. The archive SST-DA_plotting.zip contains the scripts to compute RMS errors for the free ensemble run (output file in gmd_N46_free.zip) and the SST assimilation run (gmd_N46_sst.zip) and to plot these. The two output files contain each a Netcdf file with the ensemble mean state information and the stdout file from the model run.

opencc-by-4.0Oct 2019View details →

Data Files for PyGDSM: Python interface to the Global Diffuse Sky Model

HDF5 data files for PyGDSM: Python interface to Global Diffuse Sky Models PyGDSM is a Python interface for the Global Diffuse Sky Models (GDSM ascl:1011.010). GDSM are models of diffuse galactic radio emission, constructed from a variety of all-sky surveys spanning the radio band (e.g. Haslam and WMAP). PyGDSM uses the Global Sky Model (GSM2008) of <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2008.13376.x/abstract">Oliveira-Costa et. al., (2008)</a>,  <a href="http://arxiv.org/abs/1605.04920">Zheng et. al., (2016)</a> model GSM2016, and <a href="https://lda10g.alliance.unm.edu/LWA1LowFrequencySkySurvey/">LWA1 Low Frequency Sky Model</a> (LFSM). The PyGDSM module provides visualization utilities, file output in FITS format, and the ability to generate observed skies for a given location and date. PyGDSM requires <a href="https://healpy.readthedocs.org/en/latest/">Healpy</a>, PyEphem (ascl:1112.014), and AstroPy (ascl:1304.002).

Flow of Agricultural Nitrogen, version 2 (FANv2): Model input and output data

This upload includes data associated with the manuscript "An improved mechanistic model for ammonia volatilization in Earth system models: Flow of Agricultural Nitrogen, version 2 (FANv2)" submitted to Geoscientific Model Development. The dataset includes an input file for use with the Community Land Model, and an output file with the simulated ammonia emissions for the agricultural sector. The emissions are monthly averages from the simulation for 2010-2015. Additional information is given in the readme file.

openapache2.0May 2020View details →

Data Sets for Measuring and Modeling the Performance Configurations of Distributed DBMS

These data sets contain the performance measurements and additional metadata  as accompanying material for the research paper Baloo: Measuring and Modeling the Performance Configurations of Distributed DBMS that is published in the Symposium on Modelling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS) 2020. The attached readme describes the data set structure.

Data-driven Household Load Flexibility Modelling: Shiftable Atomic Load

This is flexibility model for shiftable atomic loads (i.e. washing machine, dryers and dish washers). The model is based on real 1-minute level measurements from real households over period of time. The details of the model are described in [R]. The model is implemented in Excel for cloth washing machines weekday consumption and flexibility scenario and all the required data is included for modelling the other equipment. [R] Degefa, M.Z., Sæle, H., Petersen, I. and Ahcin, P., 2018, October. Data-driven Household Load Flexibility Modelling: Shiftable Atomic Load. In 2018 IEEE PES Innovative Smart Grid Technologies Conference Europe (ISGT-Europe) (pp. 1-6). IEEE. <a href="https://ieeexplore.ieee.org/document/8571836">https://ieeexplore.ieee.org/document/8571836</a>

opencc-zeroMay 2020View details →

Data from: A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface

The dynamics and organization of the actin cytoskeleton are crucial to many cellular events such as motility, polarization, cell shaping, and cell division. The intracellular and extracellular signaling associated with this cytoskeletal network is communicated through cell membranes. Hence the organization of membrane macromolecules and actin filament assembly are highly interdependent. Although the actin-membrane linkage is known to happen through many routes, the major class of interactions is through the direct interaction of actin-binding proteins with the lipid class containing poly-phosphatidylinositols (PPIs). Among the PPIs, phosphatidylinositol bisphosphate (PI(4,5)P2) acts as a significant factor controlling actin polymerization in the proximity of the membrane by binding to actin-associated proteins. The molecular interactions between these actin-binding proteins and the membrane lipids remain elusive. Here, using molecular modeling, analytical theory, and experimental methods, we investigate the binding of three different actin-binding proteins, mDia2, NWASP, and gelsolin, to membranes containing PI(4,5)P2 lipids. We perform molecular dynamics simulations on the protein-bilayer system and analyze the membrane binding in the form of hydrogen bonds and salt bridges at various PI(4,5)P2 and cholesterol concentrations. Our experimental study with PI(4,5)P2-containing large unilamellar vesicles mimics the computational experiments. Using the multivalencies of the proteins obtained in molecular simulations and the cooperative binding mechanisms of the proteins, we also propose a multivalent binding model that predicts the actin filament distributions at various PI(4,5)P2 and protein concentrations.

Model data repository of "How sediment thickness influences subduction dynamics and seismicity"

This repository provides the code and data to run the Seismo-Thermo-Mechanical model with a sediment thickness Tsed of 4 km on a cluster using executables.

opencc-by-4.0Jan 2018View details →

Spherical harmonic model of the Moon's magnetic field derived from gridded data in Tsunakawa et al. (2015)

T2015_449 is a 449 degree and order spherical harmonic model of the magnetic potential of the Moon. This model was used in Wieczorek (2018) and is a spherical harmonic expansion of the global magnetic field model of Tsunakawa et al. (2015). The original gridded data are from the file "globalSVM20150511/LunarSVM_000_02_v01.dat" and the spherical harmonic coefficients use the standard Schmidt semi-normalization, excluding the Condon-Shortley phase factor of (-1)m. The coefficients are in units of Teslas.

opencc-zeroJun 2020View details →

Data from: Modeling the mito-nuclear compatibility and its role in species identification

Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation -- as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA's. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (T. californicus). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.

The observed data used in paper titled "An analytic method for calculating parameters of the van Genuchten model for soil water retention curve"

In the file, the 46 soil samples from UNSODA were used to test the proposed method of estimating the parameters of VG model, including the physical and hydraulic properties data, PSD, SWRC, saturated hydraulic conductivity, porosity and saturated water content. Also, this data file includes some process data and results data, Di, psd, predicted Ks , the data relate to a and n and sensitivity analysis.

Interstate Transport of CO and BC and other relevant model evaluation data

This zip file contains four sub-folders and 4 other files which are used in Bhardwaj et al., 2020 submitted in JGR:Atmospheres 1. bc_data : contains 15 files <ul> <li>12 netcdf files (2014*_bc.nc) for each month having co-located WRF and observation data</li> <li>2 files (BC_seasonal_*.txt) which contains all BC surface observations over India from Kumar et al., (2015)</li> </ul> 2. comp_MOPITT : contains 8 files <ul> <li>4 netcdf files (wrf_mop_tc_co_*.nc; for four seasons defined in the paper) with WRF and MOPITT total CO column data</li> <li>4 netcdf files (wrf_mop_co_*.nc; for four seasons defined in the paper) with WRF and MOPITT CO profile data.</li> </ul> 3. comp_TRMM contains 12 monthly netCDF files (comp_wrf_trmm_prec_2014*.nc) with WRF and TRMM data used in this study 4. NOAA_NCDC_ISD contains six netcdf files (wrf_obs_*.nc) for six regions (defined in this study) with co-located temperature and wind speed observations over India. The file also has WRF data for the same sites <ul> <li>Two “wrfchemi_*z_d01” input emission files which are used for making emission flux (the above files) and mixing ratio plots (below files)</li> <li>Two files “state_contri_2014.nc” and “region_contri_2014.nc” have all information on interstate CO, BC for every six hours during 2014 from 30 states or six regions. These files are used for most plots in Bhardwaj et al., 2020.</li> </ul>

numerical modeling data

The first release of our numerical modeling data on the eastern Tibet.

opencc-zeroJul 2020View details →

Spectral data and R modeling code from: Polarized light sensitivity in Pieris rapae is dependent on both color and intensity

This dataset provides supplementary spectral data and the R code underlying the spectral sensitivy moding of female Pieris rapae photoreceptors used in the manuscript "Polarized light sensitivity in Pieris rapae is dependent on both color and intensity".

opencc-zeroApr 2020View details →

Data from: Modeling phylogenetic biome shifts on a planet with a past

The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage's biome affinity and location relative to the spatiotemporal distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 Viburnum species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure. Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of Viburnum, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond Viburnum, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.

opencc-zeroJul 2020View details →

Data from: Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling

Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport, and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the "ecology of eDNA" is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.

Data for: Historical earthquake scenarios for the middle strand of the North Anatolian Fault deduced from archeo-damage inventory and building deformation modeling

This dataset is associated to the article "Historical earthquake scenarios for the middle strand of the North Anatolian Fault deduced from archeo-damage inventory and building deformation modeling " published in Seismological Research Letters (<a href="https://pubs.geoscienceworld.org/ssa/srl/article-abstract/doi/10.1785/0220200278/592607/Historical-Earthquake-Scenarios-for-the-Middle?">link</a>). It includes the following: <ul> <li>The annotated photographs of the EAE (Earthquake Archeological Effects) inventoried in Iznik ("EAE_xxx.pdf").</li> <li>The 3D displacement signals used as input for obelisk modeling ("Displacement_xxx").</li> <li>The output obelisk displacement curves and final block shift values relative to base ("Obelisk_block_motion.pdf").</li> </ul>

opencc-by-4.0Aug 2020View details →

Model simulation data used in "Modelling mineral dust emissions and atmospheric dispersion with MADE3 in EMAC v2.54" (Beer et al., Geosci. Model Dev., 2020)

This dataset contains the output and the namelist setups of the EMAC-MADE3 global model simulations analysed and discussed in Beer et al. (Geosci. Model Dev., 2020).