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Data to support "Marks et al 2016. Assessment of control methods for the invasive seaweed Sargassum horneri in California, USA"
Determining the feasibility of controlling marine invasive algae through removal is critical to developing a strategy to manage their spread and impact. To inform control strategies, we investigated the efficacy and efficiency of removing an invasive seaweed, Sargassum horneri, from rocky reefs on Santa Catalina Island, southern California, USA. We tested the efficacy of removal as a means of reducing colonization and survivorship by clearing S. horneri from 60 m2 circular plots. We also examined whether S. horneri is able to regenerate from remnant holdfasts with severed stipes to determine whether efforts to control S. horneri require the complete removal of entire individuals. In addition, we developed efficiency metrics for manual removal with and without the aid of an underwater suction device. These data have been presented in: Marks, L.M., D.C. Reed and A.K. Obaza. 2016. Assessment of control methods for the invasive seaweed Sargassum horneri in California, USA. Management of Biological Invasions, DOI: 10.3391/mbi.2017.8.2.08, <ulink url="https://doi.org/10.3391/mbi.2017.8.2.08">https://doi.org/10.3391/mbi.2017.8.2.08</ulink>
Evaluation and Calibration of a Low-cost Particle Sensor in Ambient Conditions Using Machine Learning Methods
<p>Particle sensing technology has shown great potential for monitoring particulate matter (PM) with very few temporal and spatial restrictions because of its low-cost, compact size, and easy operation. However, the performance of low-cost sensors for PM monitoring in ambient conditions has not been thoroughly evaluated. Monitoring results by low-cost sensors are often questionable. In this study, a low-cost fine particle monitor (Plantower PMS 5003) was co-located with a reference instrument, named Synchronized Hybrid Ambient Real-time Particulate (SHARP) monitor, in Calgary Varsity air monitoring station from December 2018 to April 2019. The study evaluated the performance of this low-cost PM sensor in ambient conditions and calibrated its readings using simple linear regression (SLR), multiple linear regression (MLR), and two more powerful machine learning algorithms using random search techniques for the best model architectures. The two machine learning algorithms are XGBoost and feedforward neural network (NN). Field evaluation showed that the Pearson r between the low-cost sensor and the SHARP instrument was 0.78. Fligner and Killeen (F-K) test indicated a statistically significant difference between the variances of the PM<sub>2.5 </sub>values by the low-cost sensor and by the SHARP instrument. Large overestimations by the low-cost sensor before calibration were observed in the field and were believed to be caused by the variation of ambient relative humidity. The root mean square error (RMSE) was 9.93 when comparing the low-cost sensor with the SHARP instrument. The calibration by the feedforward NN had the smallest RMSE of 3.91 in the test dataset, compared to the calibrations by SLR (4.91), MLR (4.65), and XGBoost (4.19). After calibrations, the F-K test using the test dataset showed that the variances of the PM<sub>2.5</sub> values by the NN and the XGBoost and by the reference method were not statistically significantly different. From this study, we conclude that feedforward NN is a promising method to address the poor performance of the low-cost sensors for PM<sub>2.5</sub> monitoring. In addition, the random search method for hyperparameters was demonstrated to be an efficient approach for selecting the best model structure.</p>
Quantification of 3D spatial correlations between state variables and distances to the grain boundary network in full-field crystal plasticity spectral method simulations
<p>This repository provides supplementary material to our paper: <a href="https://doi.org/10.1088/1361-651X/ab7f8c">https://doi.org/10.1088/1361-651X/ab7f8c</a></p> <p><strong>DAMASKPhenoPowerLaw75x75x75TestCase.zip</strong><br> An exemplary DAMASK simulation and corresponding output, generated from DAMASK v2.0.3. We used this to debug more productively the implementation of the post-processing tools. Furthermore we employed this simulation in the paper to identify why the graph clustering grain reconstruction method in many cases fuses neighboring grains in similar orientation.</p> <p><strong>DAMASKPhenoPowerLaw256x256x256ProductionRun.zip</strong><br> All input to run the DAMASK simulation that we discussed in the paper.</p> <p><strong>DAMASKPDTSettings256x256x256ProductionRun.zip</strong><br> All damaskpdt settings files to execute the individual post-processing studies of the paper.</p> <p><strong>DAMASKPDTSlurmSubmissionScripts256x256x256ProductionRun.zip</strong><br> All SLURM scripts we used to execute the compilation of damaskpdt and post-processing on TALOS.</p> <p><strong>DAMASKPDTSlurmLogs256x256x256ProductionRun.zip</strong><br> All logs from the SLURM job management system from the individual post-processing runs.</p> <p><strong>DAMASKPDTSourceCode_USedForAnalyticalDistanceToVoronoiCellFacets.zip</strong><br> The source code to the tool we developed during the revision process of our paper to verify the methods<br> via computing analytically exact distances to the facets of the Poisson-Voronoi tessellation from the<br> DAMASK microstructure instantiation.<br> <br> <strong>DAMASKPDTSourceCode_Production.zip</strong><br> The source code we used to post-process all results from the DAMASK simulations.</p> <p><strong>GitHub repository:</strong><br> https://github.com/mkuehbach/damaskpdt</p>
A Data Set of 255,000 Randomly Selected and Manually Classified Extracted Ion Chromatograms for Evaluation of Peak Detection Methods
<p>Non-targeted mass spectrometry (MS) has become an important method over the last years in the fields of metabolomics and environmental research. While more and more algorithms and workflows become available to process a large number of data sets nontargeted, there still exist few manually evaluated universal test data sets for refining and evaluating these methods. The first step of non-targeted screening, peak detection (and refinement of it) is arguably the most important step for non-targeted screening. However, the absence of a model data set makes it harder for researchers to evaluate peak detection methods. In this Data Descriptor, we provide a manually checked data set consisting of 255,000 EICs (5000 peaks randomly sampled from across 51 samples) for the evaluation on peak detection and gap filling algorithms. The data set was created from a previous real-world study, of which a subset was used to extract and manually classify ion chromatograms by three mass spectrometry experts. The data set consists of:</p> <ul> <li>51 converted mass spectral files in mzML format</li> <li>An .RData-file containing the extracted ion chromtograms (EICs)</li> <li>The randomly selected subset and the original output table of MZmine in .csv-format</li> <li>Example .xlsx files for the classification</li> <li>2 central classification tables</li> <li>Several tables with additional information about the sampling, chemical analysis and expert jugdement on EICs</li> </ul> <p>For a full description of the experiment and the data set, please read the related Data Descriptor with the title "A data set of 255000 randomly selected and manually classified extracted ion chromatograms for evaluation of peak detection methods" in Metabolites (https://www.mdpi.com/journal/metabolites; DOI: https://doi.org/10.3390/metabo10040162).</p>
Dynamic meta-analysis: a method of using global evidence for local decision making (supplementary materials)
<p>Dynamic meta-analysis: a method of using global evidence for local decision making (supplementary materials)</p>
UM experiments for "Continuous Structural Parameterization: A proposed method for representing different model parameterizations within one structure demonstrated for atmospheric convection"
<p>NetCDF4 files containing UM vn 11.1 data used in Lambert et al., 2020, Continuous Structural Parameterization: A proposed method for representing different model parameterizations within one structure demonstrated for atmospheric convection, submitted to Journal of Advances in Modeling Earth Systems.</p> <p>Key:</p> <p>"summaryday.nc" contain eleven months of data in each year, excluding either February or March.</p> <p>"summarydat2.nc" contain one month of data in each year, either February or March.</p> <p>"last5" indicates that for this simulation only the last five years of data are available.</p> <p>"llcs" are simulations with Lambert-Lewis.</p> <p>"gr" are simulations with Gregory-Rowntree.</p> <p>"llcsemu" are simulations with the Lambert-Lewis emulator.</p> <p>"gremu" are simulations with the Gregory-Rowntree emulator.</p> <p>"llcsemu_llcs" is the test simulation wherein the LLCS emulator is run equatorward of 30 degrees and the original LLCS convection scheme is run poleward of 30 degrees.</p> <p>"4xco2" have 4 x pre-industrial atmospheric carbon dioxide concentration. (Others have 1 x pre-industrial atmospheric carbon dioxide concentration.)</p> <p>"rh0.7" and "rh0.9" have LLCS RHCRIT set to 70% and 90% respectively.</p> <p>"30day" are one month simulations for July for which daily output are available. Other data are monthly mean only.</p> <p> </p>
Occurrence data used to create species distribution models and apply an evaluation method
<p>These two files containing a table with three columns: species names, longitude, latitude. Each row of the tables represents a georeferenced presence record for the corresponding species. The original presence data were downloaded from the GBIF database and after going through a cleaning process, we ended with these records that passed all the tests.</p> <p>These datasets were used to create species distribution models (SDMs) that were then used to apply a new method to evaluate the performance of different SDMs. Jiménez & Soberón (2020)</p>
Dataset of BattLeDIM: Battle of the Leakage Detection and Isolation Methods
<p>Drinking Water Distribution Networks (DWDN) are susceptible to infrastructure failures, which may lead to water losses. Typically, these water losses are due to background leakages and pipe bursts which may occur anywhere within the distribution network. Background leakages are normally difficult to detect due to their small size, whereas pipe bursts are easier to locate as they are of larger size and may appear on the surface. The early detection and localization of some leakage event is extremely important, as this would reduce the time required for accommodating the event and therefore reducing the risk of further infrastructure degradation, contamination events and consumer complaints.</p> <p>In previous years, a number of methodologies have been proposed to detect and isolate the location of leakage events using various types of sensor measurements. These methods were commonly evaluated on private commercial datasets, and as a result, it is not possible to objectively compare these methods in their ability to detect and isolate leaks. In the past year, a leakage detection dataset has been proposed, LeakDB, based on benchmark networks and created using the WNTR tool, using pressure-driven demands and realistic leakage modelling. Inspired by the “BATtle of the Attack Detection ALgorithms” (BATADAL), which focused on the detection of cyber-physical attacks, our team decided to organize a similar “battle” focusing on leakage events.</p> <p>The Battle of the Leakage Detection and Isolation Methods (BattLeDIM), aims at objectively comparing the performance of methods for the detection and localization of leakage events, relying on SCADA measurements of flow and pressure sensors installed within water distribution networks. Participants may use different types of tools and methods, including (but not limited to) engineering judgement, machine learning, statistical methods, signal processing, and model-based fault diagnosis approaches.</p>
A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog - Supporting Data
<p><strong>Description </strong></p> <p>The following files are available : </p> <ul> <li>Simulated non-redundant Gene Catalog (SGC) composed of 128267 genes;</li> <li>Gene abundance profiles across 40 samples: raw read counts, gene length normalized base counts, depth file computed by the jgi_summarize_bam_contig_depth script provided by MetaBAT;</li> <li>Gold Standard (GS) and Gold Standard Single Assignment (GS_SA) binning results;</li> <li>Binning results obtained on the SGC with nine binning methods: MSPminer, MGS-canopy, DAS Tool, MaxBin2, MetaBAT2, SolidBin, CONCOCT, COCACOLA and MyCC.</li> </ul> <p><strong>License</strong></p> <p>These files are licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p>
Data for: Physics-based Reconstruction Methods for Magnetic Resonance Imaging
<p>Magnetic Resonance Imaging measurement data used in our paper about 'Physics-based Reconstruction Methods for Magnetic Resonance Imaging' (DOI: 10.1098/rsta.2020.0196). (In version 2 the IR-FLASH data set was replaced with one which is from the same volunteer and slice as the ME-SE data set.) </p> <p>The data is acquired from healthy volunteers and stored in the format of the BART toolbox (DOI: <a href="http://doi.org/10.5281/zenodo.592960">10.5281/zenodo.592960</a>).</p> <p>The acquisition parameters are shown in the following table:</p> <p>flip angle[◦] TR/TE/ Delta TE[ms] bandwidth [Hz/px] matrix spokes TA[s] FOV[mm] slice[mm]</p> <p>IR-FLASH 6 4.10/2.58 630 256 × 256 1020 4 192 5<br> ME-SE 90/180 2500/9.9/9.9 390 256 × 256 25 × 16 80 192 3<br> ME-FLASH 5 10.60/1.37/1.34 960 200× 200 33 × 7 0.35a 320 5<br> PC-FLASH 10 4.46/2.96 1250 210 × 210 2 × 7 15 320 5<br> fmSSFPb 15 4.5/2.25 840 192× 192 4 × 101 × 40 137 192 1</p>
Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods
<p>Data collected in the Print-aid interlaboratory study (ring trial) to evaluate the repeatability and reproducibility of three microtiter plate based methods: crystal violet, resazurin and plate counts. The files contain all the raw data collected for each laboratory as well as the tranformed data. Analysis and protocol details can be found in the following publication https://www.nature.com/articles/s41598-021-93115-w </p>
Data set from Pouzat and Chaffiol (2009) Journal of Neuroscience Methods 181:119.
<p><span>1</span></p> <p>1</p> <p>1This is the data set of Cockroach first olfactory relay recordings used in Pouzat and Chaffiol (2009) Automatic Spike Train Analysis and Report Generation. An Implementation with R, R2HTML and STAR <em>Journal of Neuroscience Methods</em> <strong>181</strong>: 119-1443. These data are also included in the R package STAR. The data are in HDF5 format.</p>
Contour method dataset for as-deposited and rolled wire+arc additive manufacturing Ti–6Al–4V components
<p>This is an archive of the raw metrology of the EDM cut surface data files used for the contour method analysis of Wire+Arc Additive Manufacture (WAAM) Ti6Al4V components appearing in: "Residual stress of as-deposited and rolled wire+arc additive manufacturing Ti–6Al–4V components" by F. Martina, M. J. Roy, B. A. Szost, S. Terzi, P. A. Colegrove, S. W. Williams, P. J. Withers, J. Meyer and M. Hofmann.</p> <p>The files are described by their filenames and side of each EDM cut. For example, 'Control_1.dat' refers to one side of the cut performed on the as-deposited specimen, while '50kN_1.dat' refers to one side of a specimen rolled at 50 kN load, etc.</p> <p>Data is in the form of a point cloud with one point per line, whitespace delimited in microns. Data was captured with a Nanofocus CF-4 laser profilometer sensor with point spacing 30 µm apart. Data with z coordinates below or above 500 µm are considered outside of the surface detection limits.</p>
Contour method and neutron diffraction dataset to determine the weld fusion zone shape on residual stress in submerged arc welding
<p>This is a dataset which formed the basis for "The effect of the weld fusion zone shape on residual stress in submerged arc welding" by A. Ishigami, M. J. Roy, J. N. Walsh and P. J. Withers appearing in the Journal of Advanced Manufacturing Technology.</p> <p>Two X-grade steel specimens with different high speed, submerged arc welds with very slight differences in fusion zone shape were compared with a novel contour method application as well as with neutron diffraction. Neutron diffraction was carried out with the SALSA instrument at the Institut Laue-Langevin in Grenoble, France with the assistance of T. Pirling. Data files with 441 in the descriptor refer to 'conventional' parameters (see publication), while 241 refers to 'new'.</p> <p>Provided in this dataset are four *.dat files, which contains data is in the form of a point cloud with one point per line, whitespace delimited in microns. Data was captured with a Nanofocus CF-4 laser profilometer sensor with point spacing 30 µm apart. Data with z coordinates below or above 500 µm are considered outside of the surface detection limits.</p> <p>Also included is an Excel worksheet, which contains the calculated residual stresses as found with LAMP (https://www.ill.eu/instruments-support/computing-for-science/cs-software/all-software/lamp/). Raw data is available here:</p> <p>P. J. Withers, A. Ishigami, T. Pirling, M. Roy, J. Walsh (2014). The effect of weld bead shape on residual stress in novel low heat input welding of steel [Data set]. ILL. http://doi.ill.fr/10.5291/ILL-DATA.1-02-145</p> <p>The authors would like to thank JFE Steel Corporation for both direct and in-direct support of this research. The authors would also like to thank the Institut Max von Laue-Paul Langevin for the allocation of beamtime at SALSA and gratefully acknowledge the help of Thilo Pirling for his assistance in performing the neutron diffraction experiments. A. Ishigami would like to thank Kenji Oi for his support of this research. M. J. Roy would like to thank Ian Winstanley for his assistance in performing the contour cuts. M. J. Roy acknowledges financial support from the EPSRC (EP/L01680X/1) through the Materials for Demanding Environments Centre for Doctoral Training.</p>
Accelerating Performance Inference over Closed Systems by Asymptotic Methods
<p>This archive includes the research data associated to the paper:</p> <p>Giuliano Casale. Accelerating Performance Inference over Closed Systems by Asymptotic Methods. Proc. ACM Meas. Anal. Comput. Syst., 1(1), 2017. The paper is accepted for presentation at ACM SIGMETRICS 2017.</p> <p>The research data requires MATLAB 2015a or later. Four datasets are included, each corresponding to a section of the paper:<br> - sec5.3.1: Small and medium models without infinite server nodes (Section 5.3.1)<br> - sec5.3.2: Large models without infinite server nodes (Section 5.3.2)<br> - sec5.3.3: Models with infinite server nodes (Section 5.3.3)<br> - sec5.4: Optimization programs (Section 5.4)</p> <p>A description of each dataset is included in the README.TXT file inside each folder.</p>
Developing Digital Image Processing methods to quantify internal and interfacial convection in the Hele-Shaw cell, with applications to the laboratory ice-ocean boundary layer
<p>This dataset provides the video and image files obtained from Schlieren optical experiment 3 performed in the <span>Laboratoire de Glaciologie (GLACIOL)</span> at the Universite de libre Bruxelles. A document detailing the visual data and supporting figures is presented (DataOverview.pdf). </p>
Dynobench - extended Strogatz benchmark for system identification methods
<p>The dynobench repository contains a benchmark for system identification methods. Currently includes models of 10 dynamical systems: Bacterial respiration, Bar magnets, Glider, Lotka-Volterra, Predator-Prey, Shearflow and Van der Pol from the Strogatz dataset, as well as Lorenz, Coupled phase oscillators and Stuart-Landau models for dynamical systems that often appear in the research community. They also add variety to the benchmark as the Lorenz oscillator model introduces a larger set of state variables (three compared to two), and the coupled phase oscillators model is non-autonomous, which is reflected in the explicit incorporation of time in its equations.</p><p>The repository contains the 'data' folder, where the simulations of ten dynamical systems are stored, simulated under 6 different configurations of data quality. The first dimention modifies the data length and coarseness, where a 'small' dataset includes simulations of 10 seconds with a 0.1 sampling step, and a 'large' dataset includes simulations of 20 seconds with a 0.01 sampling step. The second dimention of data quality modifies the amount of noise in the data, where there are three levels of noise (no noise, moderate levels with 30 dB signal-to-noise ratio and high levels of noise with 13 dB signal-to-noise ratio). The data can be used by itself, without the need to look at the python code.</p><p>The repository also contains the main.py script by which the data can be generated. The 'src' folder contains additional python scripts that are needed to generate the data. The data were created by first randomly setting the initial values for one category, in particular a configuration of 'small', 'noise-free' and 'train' data (using inits_type = "random"). Then, all the other configurations were generated by using the same initial values. Inside the script main.py there is more information about the settings and how to run the script. </p><p>The benchmark was created as a part of the research described in the paper titled <i>Probabilistic grammars for modeling dynamical systems from coarse, noisy, and partial data, </i>written by Omejc et al.<i> </i>(in submission).</p>
A machine learning-based high-precision density functional method for drug-like molecules
<h2><strong>Models</strong></h2><p>The repo contains the models and test datasets for our aticles. The energy unit is in <strong>Hartree,</strong> The coordinate unit is in<strong> Bohr.</strong></p><p><strong>## DeePHF</strong></p><p>you need first prepare the `dm_eig.npy` in data_test and do predict `l_e_delta.npy`, you can use</p><p>```</p><p>deepks test -m model.pth -o test/test -d data_test/* -D dm_eig -G</p><p>```</p><p><strong>## DeePKS</strong></p><p>first you should prepare the `atom.npy`, and `energy.npy` in data_test. you can test the datasets by command. </p><p>```</p><p>deepks scf scf_input.yaml -m model.pth -s data_test -d test_out</p><p>```</p><p><strong># Datasets</strong></p><p>All datasets only have `atom.npy` and `energy.npy`. The coordinate unit is `bohr`, and energy unit is `Hartree`.</p><p><strong>## small molecules torsion</strong></p><p>Contains 62 small molecules with 36 conformation for each under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] B. D. Sellers, N. C. James, A. Gobbi, A comparison of quantum and molecular mechanical methods to estimate strain energy in druglike fragments, Journal of chemical information and modeling 57 (6) (2017) 1265–127</p><p><br> </p><p><strong>## MPCONF91</strong></p><p>Contains 6 molecules with 91 conformations under LNO-CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] J. Rezac, D. Bím, O. Gutten, L. Rulisek, Toward accurate conformational energies of smaller peptides and medium-sized macrocycles: Mpconf196 benchmark energy data set, Journal of chemical theory and computation 14 (3) (2018) 1254–1</p><p><br> </p><p><strong>## torsionNet206</strong></p><p>Contains 206 molecules with 4494 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] B. K. Rai, V. Sresht, Q. Yang, R. Unwalla, M. Tu, A. M. Mathiowetz,G. A. Bakken, Torsionnet: A deep neural network to rapidly predict small-molecule torsional energy profiles with the accuracy of quantum mechanics, Journal of Chemical Information and Modeling 62 (4) (2022) 785–80</p><p><br> </p><p><strong>## Out-of-plane bending</strong></p><p>Contains 242 molecules with 3315 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] X. Yang, C. Liu, P. Ren, High order ab initio valence force field with chemical pattern based parameter assignment., Journal of Computational Biophysics and Chemistry 21 (4) (2021) 43</p><p><br><br> </p><p><strong>## DrugBank-T</strong></p><p>Contains 165 molecules with 1155 conformations under CCSD(T)/def2-TZVP.</p><p><br> </p><p>[1] V. Law, C. Knox, Y. Djoumbou, T. Jewison, A. C. Guo, Y. Liu, A. Maciejewski, D. Arndt, M. Wilson, V. Neveu, et al., Drugbank</p><p>4.0: shedding new light on drug metabolism, Nucleic acids research 42 (D1) (2014) D1091–D1097 </p><p>[2] Z. Qiao, M. Welborn, A. Anandkumar, F. R. Manby, T. F. Miller III, Orbnet: Deep learning for quantum chemistry using symmetry adapted atomic-orbital features, The Journal of chemical physics 153 (12) (2020) 124111</p><p><strong>## Notice</strong></p><p>if you use above datasets, please cite the original articals too</p>
BSEC Method for Unveiling Clusters and 83 New Clusters
<p>Data of star clusters that are used in the paper entitled "BSEC method for unveiling open clusters and its application to Gaia DR3: 83 new clusters".</p>
Supporting Data: ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology-informed phylogenetic methods
<p>This dataset contains all scripts and data for reproducing the analyses of the paper. The README files contain additional information.</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.