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.
236
datasets available to search
ShareScore release 0.7.1
Dataset results
236 results for “Modeling Methods”
Data from: De novo transcriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set
High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without a high-quality reference genome. For every stage of analysis – from assembly to annotation to variant discovery – researchers have to distinguish technical artefacts from the biological realities of their data before they can make inference. In this work, I explore these challenges by generating a large de novo comparative transcriptomic data set data for a clade of lizards and constructing a pipeline to analyse these data. Then, using a combination of novel metrics and an externally validated variant data set, I test the efficacy of my approach, identify areas of improvement, and propose ways to minimize these errors. I find that with careful data curation, HTS can be a powerful tool for generating genomic data for non-model organisms.
Data from: Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods
The increasing ability to extract and sequence DNA from non-contemporaneous tissue offers biologists the opportunity to analyze ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. Here we provide a critical assessment of Bayesian MCMC analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates due to model misspecification when the data comes from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However when model misspecification is only mild, then the 95% HPD intervals provide adequate frequentist coverage of the true rates.
Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms
Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized equipment, is highly flexible, and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.
3D photogrammetry as a low cost and noninvasive method for acoustic modeling of animal hearing
Open the record for dataset details and reuse information.
Dataset [ref. paper "Predictive modeling of drivers' brake reaction time through machine learning methods"]
Open the record for dataset details and reuse information.
method of homogeneous microzones in seismic perspective (MOPS) with geological-technical sections of reference for the subsoil model.
<p>Method of homogeneous microzones in seismic perspective (MOPS) with geological-technical sections of reference for the subsoil model.</p>
Dynamic Uncertainty Lot Sizing Model: Formulation, Solution Methods, and Potential over the Static-Dynamic Uncertainty Model
<p>Test data used in Section 6</p>
Simulation data for "Modeling radiation belt dynamics using a positivity-preserving finite volume method on general meshes"
Open the record for dataset details and reuse information.
WRF model output used in an ideal model experiment demonstrating the applicability of a channel-synthesizing method for reducing uncertainties in satellite radiance transfer modeling
<p>This repository stores the WRF model output used in the paper "A novel channel-synthesizing method for reducing uncertainties in satellite radiance transfer modeling" submitted to Geophysical Research Letters.</p>
Figure 5 from: Tzankova D, Peikova L, Vladimirova S, Georgieva M (2019) Development and validation of RP-HPLC method for stability evaluation of model hydrazone, containing a pyrrole ring. Pharmacia 66(3): 127-134. https://doi.org/10.3897/pharmacia.66.e47035
Figure 5 Chromatogram of the separated mixture of the analyzed hydrazone D-5d (tR = 6.800) and its possible degradation products – the hydrazide D-5 (tR = 4.387) and the corresponding aldehyde d (tR = 1.387).
Figure 7 from: Tzankova D, Peikova L, Vladimirova S, Georgieva M (2019) Development and validation of RP-HPLC method for stability evaluation of model hydrazone, containing a pyrrole ring. Pharmacia 66(3): 127-134. https://doi.org/10.3897/pharmacia.66.e47035
Figure 7 Chromatograms indicating the behavior of D_5d in the presence of buffer with pH 2.0 and at 37°C at 0th min (A) and at 30th min (B).
Figure 4 from: Tzankova D, Peikova L, Vladimirova S, Georgieva M (2019) Development and validation of RP-HPLC method for stability evaluation of model hydrazone, containing a pyrrole ring. Pharmacia 66(3): 127-134. https://doi.org/10.3897/pharmacia.66.e47035
Figure 4 Chromatogram of standard solution of the aldehyde d (tR = 1.283) as possible degradation product.
Figure 3 from: Tzankova D, Peikova L, Vladimirova S, Georgieva M (2019) Development and validation of RP-HPLC method for stability evaluation of model hydrazone, containing a pyrrole ring. Pharmacia 66(3): 127-134. https://doi.org/10.3897/pharmacia.66.e47035
Figure 3 Chromatogram of standard solution of the hydrazide D-5 (tR = 4.380) as possible degradation product.
Figure 8 from: Tzankova D, Peikova L, Vladimirova S, Georgieva M (2019) Development and validation of RP-HPLC method for stability evaluation of model hydrazone, containing a pyrrole ring. Pharmacia 66(3): 127-134. https://doi.org/10.3897/pharmacia.66.e47035
Figure 8 Chromatograms indicating the behavior of D_5d in the presence of buffer with pH 9.0 and at 37°C at 0th min (A) and at 210th min (B).
Figure 9 from: Tzankova D, Peikova L, Vladimirova S, Georgieva M (2019) Development and validation of RP-HPLC method for stability evaluation of model hydrazone, containing a pyrrole ring. Pharmacia 66(3): 127-134. https://doi.org/10.3897/pharmacia.66.e47035
Figure 9 Chromatograms indicating the behavior of D_5d in the presence of buffer with pH 13.0 and at 37°C at 0th min (A) and at 30th min (B).
Simulation data and code for "Modeling radiation belt dynamics using a positivity-preserving finite volume method on general meshes"
Open the record for dataset details and reuse information.
Models, scripts, simulated data, and results from the article "Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework."
Open the record for dataset details and reuse information.
Modelling pasta drying and deformation with a moving-lattice Boltzmann method
<p>Modelling pasta drying and deformation with a moving-lattice Boltzmann method</p>
Advanced methods for uncertainty assessment and global sensitivity analysis of a Eulerian atmospheric chemistry transport model
<p>Atmospheric chemistry transport models (ACTMs) are extensively used to provide scientific support for the development of policies to mitigate against the detrimental effects of air pollution on human health and ecosystems. Therefore, it is essential to quantitatively assess the level of model uncertainty and to identify the model input parameters that contribute the most to the uncertainty. For complex process-based models, such as ACTMs, uncertainty and global sensitivity analyses are still challenging and are often limited by computational constraints due to the requirement of a large number of model runs. In this work, we demonstrate an emulator-based approach to uncertainty quantification and variance-based sensitivity analysis for the EMEP4UK model (regional application of the European Monitoring and Evaluation Programme Meteorological Synthesizing Centre-West). A separate Gaussian process emulator was used to estimate model predictions at unsampled points in the space of the uncertain model inputs for every modelled grid cell. The training points for the emulator were chosen using an optimised Latin hypercube sampling design. The uncertainties in surface concentrations of O<sub>3</sub>, NO<sub>2</sub>, and PM<sub>2.5</sub> were propagated from the uncertainties in the anthropogenic emissions of NO<sub>x</sub>, SO<sub>2</sub>, NH<sub>3</sub>, VOC, and primary PM<sub>2.5</sub> reported by the UK National Atmospheric Emissions Inventory. The results of the EMEP4UK uncertainty analysis for the annually averaged model predictions indicate that modelled surface concentrations of O<sub>3</sub>, NO<sub>2</sub>, and PM<sub>2.5</sub> have the highest level of uncertainty in the grid cells comprising urban areas (up to ± 7%, ± 9%, and ± 9% respectively). The uncertainty in the surface concentrations of O<sub>3 </sub>and NO<sub>2</sub> were dominated by uncertainties in NO<sub>x</sub> emissions combined from non-dominant sectors (i.e. all sectors excluding energy production and road transport) and shipping emissions. Additionally, uncertainty in O<sub>3</sub> was driven by uncertainty VOC emissions combined from sectors excluding solvent use. Uncertainties in the modelled PM<sub>2.5</sub> concentrations were mainly driven by uncertainties in primary PM<sub>2.5</sub> emissions and NH<sub>3</sub> emissions from the agricultural sector. Uncertainty and sensitivity analyses were also performed for five selected grid sells for monthly averaged model predictions to illustrate the seasonal change in the magnitude of uncertainty and change in the contribution of different model inputs to the overall uncertainty. Our study demonstrates the viability of a Gaussian process emulator-based approach for uncertainty and global sensitivity analyses, which can be applied to other ACTMs. Conducting these analyses helps to increase the confidence in model predictions. Additionally, the emulators created for these analyses can be used to predict the ACTM response for any other combination of perturbed input emissions within the ranges set for the original Latin hypercube sampling design without the need to re-run the ACTM, thus allowing fast exploratory assessments at significantly reduced computational costs.</p> <p>The upload contains the uncertainty and sensitivity data together with the analysis scripts.</p>
Utilizing Qualitative and Quantitative Methods to Understand a New Model of Type 1 and 2 Systemic Lupus Erythematosus (SLE)
ClinicalTrials.gov study NCT05426902. IPD Sharing: NO. Countries: 1. Publications: 0.
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.