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Dataset results
2,152 results for “outputs”
Raw data for TrackMate tracking output and R script for data analysis
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WF_test_mitoflash_output_files
<p>Mitoflash outputfiles for workflow test on Mitoflash events detection in Galaxy.</p>
Simulation output for "The influence of experimental imperfections on photonic GHZ state generation"
<p>The simulation output data that was used in the paper "The influence of experimental imperfections on photonic GHZ state generation" (<a href="https://doi.org/10.1088/1367-2630/ad916f">https://doi.org/10.1088/1367-2630/ad916f</a>) is saved in Data.zip. Note, that the raw output data the tool in <a href="https://doi.org/10.5281/zenodo.11518712">https://doi.org/10.5281/zenodo.11518712</a> provides is here already split into two-photon events (*_p2.txt), loss events (*_pl.txt) and fidelity/success probability data (*_f.txt). Further, the data is sorted so that one number (i_*.txt) indicates the data for one overlap value. </p> <p>A small C++ program (example.cpp) allows one to compute the fidelity and success probability from the data. Once compiled one calls the program with five arguments: overlap, two-photon probability, loss probability for preparation, loss probability for components, and loss probability for detection. If the compiled binary is named <em>example</em> such a call could be <code>./example 0.97 0.01 0.1 0.01 0.1</code></p> <p>To compile example.cpp one can use/adapt the Makefile. This should work immediately if clang++ is installed.</p>
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics (output data)
<p>This contains the output results of CalicoST (inferred CNAs and cancer clones), results of comparison methods, and CNAs inferred from WES data of 13 samples across four cancer types.</p> <p>In this updated version, we also included the simulated data and the results from CalicoST and other methods in CalicoST_simulation_deposit.zip. README contains the details of deposited files.</p>
Numerical Electrostatic Simulations Output
<p>A .zip file containing the following:</p> <p>Simulation outputs saved as Matlab .mat files.</p> <p>Matlab .m scripts to make figures from each of the .mat files.</p>
Simulated wind field outputs from WRF and significant wave height results from SWAN simulations.
<p>Supplementary materials for the article titled <em>“Super Typhoons Simulation: A Comparison of WRF and Empirical Parameterized Models for High Wind Speeds.”</em> The data include simulated wind field outputs and significant wave height results from SWAN simulations.</p>
Multi-LES code output of Flower-type organized convection on 02 February, 2020 - 0-1D Files
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BAMBI outputs of bedform morphologies from the Mekong River, accommpanying analysis presented in Hackney et al. (2025)
<p>Morphometric data output from BAMBI (see Cisneros et al., 2020) of bedform morphologies in the Mekong river. This dataset accompanies the manuscript "Increased Hydraulic Roughness in Alluvial Rivers Created by Sand-Mining Sculpted Bed Features" published in the Journal of Geophysical Research - Earth Surface available at <a href="https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2024JF008189#">https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2024JF008189#.</a> The dataset contains morphological data of natural sand dunes, and sand mining impacted sand dunes. </p>
Simulation outputs associated with Maffre et al. "GEOCLIM7, an Earth System Model for multi-million years evolution of the geochemical cycles and climate." (submitted to GMD)
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Model code and output for "Transformation Processes in the Oder Lagoon as seen from a Model Perspective"
<p>This dataset contains the numerical model output files that were used in the analysis, the numerical model input files that were used to produce the model simulation, and the specific source code for the model components presented in "Transformation Processes in the Oder Lagoon as seen from a Model Perspective", submitted to Biogeoscience.</p> <p>data1.tar is the direct diagnostic model output. data2.tar are condensed data which are used for the analysis.</p> <p>forcing.tar contains data to run the model. Most files should be placed inside a directory named INPUT/ that resides in the working directory where the model is being run. The following files should be at the top level in the working directory: data_table, diag_table, field_table, input.nml.</p> <p>For large files, a subset in time (1995) is provided for the first year of the simulation. This dataset does not include the coastdat atmospheric data, which can be downloaded directly from https://www.wdc-climate.de/ui/entry?acronym=coastDat-2_COSMO-CLM.</p> <p>src.tar contains the model source code.</p>
The HEC method processing code and output for constrained precipitation extremes reveal unequal future socioeconomic exposure
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Model output (ROMS_HH2) of simulating OAE in Halifax Harbour
<p><span>This repository provides model output (HRM2) for analysis in the following article:</span></p> <p><span>Wang B., Laurent A., Pei Q., Sheng J., Atamanchuk D., Fennel K. Maximizing the detectability of Ocean Alkalinity Enhancement (OAE) while minimizing its exposure risks: Insights from a numerical study. preprint</span></p>
Model output (ROMS_HH3) of simulating OAE in Halifax Harbour
<p>This repository provides model output (HRM3) for analysis in the following article:</p> <p>Wang B., Laurent A., Pei Q., Sheng J., Atamanchuk D., Fennel K. Maximizing the detectability of Ocean Alkalinity Enhancement (OAE) while minimizing its exposure risks: Insights from a numerical study. preprint</p>
Input data and outputs for the OCALM project
<p>This repository contain a zip file with input and output data for an experiment with OCALM (<a href="https://github.com/fanavarro/ocalm">https://github.com/fanavarro/ocalm</a>):</p> <ul> <li>input <ul> <li>ontologies: ontologies used as input (FoodOn, LKIF, GeneOntology), together with their normalized form.</li> <li>text <ul> <li>food_text: natural language text corpus about food, including the original and the processed text.</li> <li>gene_text: natural language text corpus about genetics, including the original and the processed text.</li> <li>legal_text: natural language text corpus about legal topics, including the original and the processed text.</li> </ul> </li> </ul> </li> <li>results: the results derived from comparing each ontology with each natural language text corpus by using OCALM.</li> <li>NCBO_Recommender_results: the results of the NCBO Recommender with the same experiment performed by OCALM.</li> <li>analysis.R: R script to get figures summarizing the results.</li> </ul> <p>The SNOMED ontology and the medical text corpus used for input were not included due to licensing issues; however, the results are included in this repository.</p>
Outputs of ENERWAT-GLOB - Water Treatment
<p>Output data of the 5 arcmin modelling framework calculating the global energy consumption of water treatment technologies (conventional drinking water treatment, desalination, wastewater treatment). Contains both model output data and visualization (figures at 300 dpi). Energy consumption of desalination was calculated for 1945-2019, while energy consumption of wastewater treatment and conventional drinking water treatment was calculated for 2015. All technologies were then compared to the year 2015. Energy consumption of desalination and wastewater treatment was calculated at the plant scale, while for conventional drinking water treatment it was calculated at the catchment scale. These outputs were then aggregated to the country level.</p> <p>Model outputs include the following. 1) For desalination: calculated cumulative capacities and energy consumption ranges for technologies, subregions and feedwaters, in addition to plant-level and country-level energy consumption ranges and ratios, and feedwater-level energy efficiency of reverse osmosis (1962-2021). Licensed information from DesalData was removed. 2) For conventional drinking water treatment (folder "dwt"): the calculated 5 arcmin water access (safe, basic and untreated water use), the pixel-scale allocated water withdrawal sources (desalination, groundwater, surface water) and the country-level energy consumption ranges and ratios. Licensed information from DesalData for the allocation of desalinated drinking water was removed. 3) For wastewater treatment (folder "wwt"): the 5 arcmin modelled wastewater flows (from treated wastewater pixel to wastewater treatment plant pixels) and modelled offline plants, in addition to the plant-level and country-level energy consumption ranges. </p>
Small model output dataset for teaching use
<p>Small model output dataset from CAM6-Nor for teaching use.</p>
Raw cutadapt miseq output - minibarcode 18S-V7 of macroalgae
<p>Macroalgae are key primary producers in North Atlantic and Arctic coastal ecosystems, and tracing their fate and distribution is vital to improve our understanding of their ecological role and provision of ecosystem services. Recent advances from environmental DNA (eDNA) have added a new capacity to fingerprint and trace macroalgae. However, further development of resources for amplifying and identifying macroalgal eDNA are much needed. Here, we examined the performance in terms of resolution and specificity of two 18S primers (18S-V7 & 18S-V9) recently applied in identifying macroalgae from eDNA. We also built a local barcode database for primer 18S-V7 with 31 widespread Arctic and North Atlantic macroalgal species to complement the existing DNA databases. Furthermore, we applied metabarcoding of eDNA to identify macroalgae in Arctic marine sediments (Disko Bay, W. Greenland) and evaluated the contributions from our local barcode database. We identified macroalgal DNA from 19 families across 11 orders in surface (0-1 cm, with both primers) and sub-surface (5-10 cm, with 18S-V7 primer) sediments. The barcode database developed here with the 18S-V7 primer improved the identification of unique families, from 16 to 19 families, thereby strengthening the taxonomic assignment possible relative to pre-existing barcode reference sequences. Overall, this study demonstrates the feasibility of eDNA to resolve contributions of macroalgae in Arctic marine sediments, and enhances the fingerprinting resolution. We thereby document a novel pathway to answer key questions on the ecological role and fate of macroalgae in the Arctic.</p>
Fleshy red algae mats act as temporary reservoirs for sessile invertebrate biodiversity - Raw data for biodiversity analysis, species list and detailed output data from iNEXT procedure
<p>Raw data for biodiversity analysis, species list and detailed output data from iNEXT procedure for manuscript entitled "Fleshy red algae mats act as temporary reservoirs for sessile invertebrate biodiversity".</p>
E3SM/EAM Simulation Data Outputs
<p>Simulation data provided from the Energy Exascale Earth System Model (E3SM) simulation code in association to a paper to be published, <em>Fast Gaussian Process Estimation for Large-Scale In Situ Inference using Convolutional Neural Networks.</em></p> <p>E3SM is a fully coupled Earth model system that combines independent components for atmosphere, ocean, land surface, sea ice and land ice. It includes a driver and flux coupler to exchange data across components, resulting in an integrated modeling system. Through the simulations are fully coupled, we focus our analyses on the atmospheric component, the E3SM Atmosphere Model (EAM) to generate the data. EAM data is discretized using a variable resolution spectral element method, allowing for a regionally refined mesh that can be tessellated at higher resolutions in particular regions of interest. EAM consists of the High-Order Methods Modeling Environment Spectral Element dynamical core and the EAM physics and chemistry parameterizations.</p>
Model output for "Groundwater affects the geomorphic and hydrologic properties of coevolved landscapes"
<p>Model output supporting "Groundwater affects the geomorphic and hydrologic properties of coevolved landscapes" in JGR Earth Surface, DOI:10.1029/2021JF006239. The Python package DupuitLEM v1.0-beta (DOI:10.5281/zenodo.5522828) contains the models and scripts used to generate and post-process output.</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.