Find research datasets worth reusing

opencc-by-4.0Apr 2022View details →

Molecular dynamics trajectories of C3 H8 O molecule and its structural isomers

Forces and Energies for 200 ps MD trajectory of OCH2C2H6 molecule by xTB/GFN-2, NVE ensemble -------------------------------------------------- MD params: temp = 300.0  K / 500.0 K time = 200.0  ps dump time = 10.0   fs step =  0.4  fs ------------------------------------------------ Energies and forces are in eV and eV/Angstrom Filenames are intended to be self-explanatory Dataset is intended to be used for machine learning algorithms tests.

opencc-by-4.0Jun 2020View details →

Combining dynamic and static analysis for automated grading SQL statements

Introduction Our experiment was conducted in an undergraduate Relational Database course at the Australian National University. The experiment was conducted on August 10th 2018 when students enrolled in the Relational Database course started to learn relational data model and SQL. The experiment was carried out fully online for three weeks and a total of 393 students were enrolled. The students were asked to login in an online assessment platform and complete 15 exercises. This platform provided an SQLite environment in students browsers by compiling the SQLite C code with Emscripten. Students were allowed to submit and execute their answers in the form of SQL statements. If the execution result of the statement submitted by the student is the same as that of the reference statement, the online assessment platforms will return a feedback message indicating that the execution result is correct. During the interaction with the assessment platform, statements submitted by students were recorded and archived. Overall, our experiment had collected 12,899 statements submitted by students. To create a benchmark dataset that can be used to evaluate different grading approaches, we randomly selected 45 SQL statements submitted by students for each exercise, and asked three teaching assistants to grade them manually. Finally, we average the scores provided by the three assistants and take it as the final score of each statement. The dataset collected in this experiment is ready for public release. All experimental data are stored in Submission.sqlite, which is an SQLite database file. It is recommended to use software such as DB browser or SQLite expert to explore the database.   Datatable description   exercises_result This datatable stores the statements submitted by students. Based on the execution result of statement, statements were divided into three categories. <ul> <li>noninterpretable: the statement is non-executable.</li> <li>partially correct: the execution result of statement is different from the expected result.</li> <li>correct: the execution result of the SQL statement is the same as the expected result.</li> </ul> After analyzing the correct statements, we found that the correct set contains some statements carefully constructed by students to deceive the examination system. Take exercise 1 as an example, the task is to answer the following questions using SQL statements. Question: Assume persons who were born in the same year are the same age and there is only one youngest person (with no ties/draws) in this database, who is/are the second youngest person(s) in the database? List the id(s) of the person(s). The reference statement to this exercise is: <pre><code class="language-sql">SELECT p.id FROM person p WHERE p.year_born = (SELECT MAX(year_born) FROM person WHERE year_born < (SELECT MAX(year_born) FROM person)); </code></pre> By exploring the database or trying to execute different statements, some students found that the ID of the person who met the conditions was '00000842', so the following statement was submitted. <pre><code class="language-sql">select id from person where id ='00000842'; </code></pre> The execution result of the above code was correct, but it was obviously not what the tutor expected. Therefore, we identified such statements as 'cheating'. Table 1 Description of exercises_result table. <table> <thead> <tr> <th> field </th> <th> desc </th> <th> datatype </th> </tr> </thead> <tbody> <tr> <td> submission_id </td> <td> Submission ID </td> <td> INT </td> </tr> <tr> <td> submitted_answer </td> <td> statement submitted by student </td> <td> TEXT </td> </tr> <tr> <td> submission_time </td> <td> Submission time </td> <td> NUM </td> </tr> <tr> <td> exercise_id </td> <td> Exercise ID </td> <td> INT </td> </tr> <tr> <td> is_correct </td> <td> Mark whether the statement is correct </td> <td> INT </td> </tr> <tr> <td> student_id </td> <td> Student ID </td> <td> INT </td> </tr> <tr> <td> category </td> <td> categories of statement </td> <td> TEXT </td> </tr> </tbody> </table>   exercises_benchmark This datatable stores the scores provided by different assistants. We randomly selected 45 SQL statements submitted by students for each exercise, and asked three teaching assistants to grade them manually. Finally, we averaged the scores provided by the three assistants as the final score of each statement. Table 2 Description of exercises_benchmark table. <table> <thead> <tr> <th> Field </th> <th> comment </th> <th> datatype </th> </tr> </thead> <tbody> <tr> <td> Submission_id </td> <td> Submission ID </td> <td> INT </td> </tr> <tr> <td> grade </td> <td> grade provided by tutor </td> <td> REAL </td> </tr> <tr> <td> tutor </td> <td> tutor </td> <td> TEXT </td> </tr> </tbody> </table>   exercises_exercise This datatable stores the exercises provided by tutor. Table 3 Description of exercises_exercise table. <table> <thead> <tr> <th> Field </th> <th> comment </th> <th> datatype </th> </tr> </thead> <tbody> <tr> <td> id </td> <td> Exercise ID </td> <td> INT </td> </tr> <tr> <td> title </td> <td> Title of exercise </td> <td> TEXT </td> </tr> <tr> <td> preamble </td> <td> Description of exercise </td> <td> TEXT </td> </tr> <tr> <td> difficulty </td> <td> Coefficient of difficulty </td> <td> integer </td> </tr> <tr> <td> ref </td> <td> Reference statement </td> <td> integer </td> </tr> </tbody> </table>   database schema Please refer to db_schema.pdf for the database schema used in the experiment.   BibTex if you want to cite our paper:   <blockquote> <pre>@article{wang2020combining, title={Combining dynamic and static analysis for automated grading SQL statements}, author={Wang, Jinshui and Zhao, Yunpeng and Tang, Zhengyi and Xing, Zhenchang}, journal={J Netw Intell}, volume={5}, number={4}, pages={179--190}, year={2020} }</pre> </blockquote>

opencc-by-4.0Jun 2015View details →

KEasyLogger: Keystroke Dynamics Dataset

KEasyLogger is a keystroke dynamics dataset containing labeled data of users typing free text on a desktop computer. The main characteristics of the dataset are: <ul> <li>17 unique different users.</li> <li>379 sessions. Each session last one day.</li> <li>2,726,203 total digraphs.</li> <li>2,553,494 total trigraphs.</li> <li>Type of keystroke is free text.</li> <li>Scenario is desktop personal computer.</li> <li>Uncontrolled environment.</li> </ul> The dataset is in MySQL format and consists of two tables, one for digraphs and one for trigraphs. Each row of the digraphs and trigraph table has the following attributes: <ul> <li>Id: unique row identifiation number.</li> <li>KeyFrom: the first key of thediagraph.</li> <li>KeyTo: the second key of the digraph.</li> <li>Time: microseconds between keys</li> <li>idUser: unique user identifiation number</li> <li>idlogfile: unique session identification number. </li> </ul>

FORECASTING MOLECULAR DYNAMICS SIMULATIONS OF POLYMER-LIPIDS IN SOLUTION WITH RNNs

Files and scripts pertaining to our work:  <ul> <li>GROMACS files for the topology (DSPE+PEG.top) and the initial structure of the aggregate (DSPE+PEG_EA_NPT.gro)</li> <li>GROMACS topology file for the ethyl acetate molecule: EA_SI.top</li> <li>Scripts to submit the GROMACS utilities for calculation of the interaction energies are described in README.txt (Subset_energy.sh , Interaction_energies.sh)</li> <li>Scripts pertaining to PyTorch use and access of methods are described in README.txt (Multiple-run.sh. Job.sh, Pytorch_train-model.py)</li> <li>Scripts pertaining to scikit learn access for the Expectation Maximization clustering are described in the README.txt (Job_EM.sh, EM_Clustering.py)</li> <li>Files with the time series of the potential energy (PE) and interaction energy (IE) of the DSPE-PEG aggregate with the ethyl acetate solvent. Series contain 500,000 snapshots taken every 10 fs along the NVT Molecular Dynamics trajectory at 300 K and 906.3 kg/m3 density. The molecular solution is in a cubic box of edge length 13.76 nm, containing 16,000 ethyl acetate molecules and one aggregate of 4 DSPE-PEG-amide macromolecules (224,000 atoms): Data_Andrews_etal_DSPE-PEG_2022.zip</li> <li>ArXiv preprint: https://doi.org/10.48550/arXiv.2203.00151 (JAndrews_etal_arXiv-doi.pdf)</li> </ul>

Dataset for Dynamic Analysis of Quantum Annealing Programs

Quantum software engineering is emerging as a relevant field as it deals with the challenges of producing the new quantum software, whose adoption is increasing progressively. One of those challenges is how quantum software is migrated, how it operates in combination with classical software, or how it should be maintained. In this context this research focuses on reverse engineering of quantum annealing software to facilitates its integration in hybrid software systems. Quantum annealing software has gained a certain market penetration, demonstrating a good performance for optimization problems. While there are some preliminary reverse engineering techniques for gate-based quantum software, there is no reverse engineering techniques to discover the underlying optimization problem definitions (Hamiltonians functions to be minimized). Problem definitions are, in turn, dynamically defined through classical software, and can evolve over time, which make it difficult its accurate comprehension and abstract representation. Thereby, this paper presents a dynamic analysis technique for D-Wave (python) programs for reversing Hamiltonians expressions, that are additionally represented according to the Knowledge Discovery Metamodel. Due to the usage of this standard, the reversed Hamiltonians can be represented in combination with other parts of classical-quantum software systems. In order to facilitates its adoption, the proposed technique has been empirically validated through a case study with 27 D-Wave programs that demonstrates the effectiveness and efficiency. This dataset includes measures derived from that case study.

opencc-zeroMay 2022View details →

Online electronic material for: Macroevolutionary dynamics of climatic niche space

How and why lineages evolve along niche space as they diversify and adapt to different environments is fundamental to evolution. Progress has been hampered by the difficulties of linking a robust empirical characterization of species niches with flexible evolutionary models that describe their evolution. Consequently, the relative influence of abiotic and biotic factors remains poorly understood. Here we characterize species' two-dimensional temperature and precipitation niche space occupied (i.e., species niche envelope) as complex geometries and assess their evolution across all Aves using a model that captures heterogeneous evolutionary rates on time-calibrated phylogenies. We find that extant birds coevolved from warm, mesic climatic niches into colder and drier environments and responded to the K-Pg boundary with a dramatic increase in disparity. Contrary to expectations of subsiding rates of niche evolution, our results show that overall rates have increased steadily, with some lineages experiencing exceptionally high evolutionary rates, associated with colonization of novel niche spaces, and others showing niche stasis. Both competition- and environmental change-driven niche evolution transpire and result in highly heterogeneous rates near the present. Our findings highlight the growing ecological and conservation insights arising from model-based integration of comprehensive environmental and phylogenetic information.

Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter

Data and code for mixed-model analysis for the article:  Mukhacheva S.V. (2022) Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter" // Russian Journal of Ecology. Vol. 5.  Data provided by S.V. Mukhacheva Code provided by A.N. Sozontov

Data for "Engineering Higgs dynamics by spectral singularities"

These files contain the data for the article "Engineering Higgs dynamics by spectral singularities" (<a href="https://doi.org/10.48550/arXiv.2205.06826">https://doi.org/10.48550/arXiv.2205.06826</a>). In each .zip file, it is possible to find not only the relevant data, but also a script (.sh file extension) to generate each one of the 5 figures shown in the paper and Supplemental Information Material. The file "Phasediagram.zip" contains the data corresponding to the dynamical phase diagrams (Fig. 1 of the manuscript) for the model of flat and graphene-like density of states (DOS). The data for the representative dynamical phases and Fourier Transforms for the constant DOS and graphene-like DOS model can be found in the files "Dynamics_flatDOS.zip" and "Dynamics_grapheneDOS.zip" respectively.  The Fourier Transforms of the x-component of pseudospins texture are stored in the files "FFT_x-componentofpseudospintexture_flatDOS.zip" and "FFT_x-componentofpseudospintexture_grapheneDOS.zip" for the flat DOS  and graphene DOS case respectively. For all the .txt files inside the .zip files, we have added at the top of each column a brief description of the data recorded below. Some notations have been used and read as follows:  "Delta" indicates the superconducting order parameter, and "\xi_k" means the quasiparticle energy.

Isomorph Invariant Dynamic Mechanical Analysis: A Molecular Dynamics Study

This data set contains the data required to reproduce most of the figures in our paper, [arXiv:2204.06962] which will soon be submitted to a journal. Abstract of the paper: We simulate dynamic mechanical analysis experiments for the Kob-Andersen binary Lennard-Jones system. For this, the SLLOD algorithm with time-dependent strain rates is applied to give a sinusoidally varying strain at different densities and temperatures. The starting point is a temperature scan at a fixed reference density. Isomorph theory predicts that for other densities corresponding temperatures can be identified at which the mechanical properties are unchanged when scaled appropriately. We determine the isomorphically equivalent temperatures by analysing how particle forces change upon scaling configurations to the new density. Loss moduli expressed in suitable reduced units are compared for isomorphic state points. When plotted against the unscaled temperatures, these reduced loss curves are observed to collapse indicating the validity of isomorph theory for dynamic mechanical analysis experiments. Two different methods to determine isomorphic temperatures are considered. While one of them breaks down for the largest density rescalings considered in this study, the other one is still applicable in this region. The decorrelation of force vectors upon rescaling is investigated as a possible origin of this effect. Our results demonstrate that the simplification of the phase diagram entailed by isomorph theory for a wide class of system is relevant also for the mechanical properties of glasses.

Screening routine for integrative dynamic structural biology using SAXS and intramolecular FRET and DEER-EPR on hGBP1 (human guanalyte binding protein 1)

Initial and selected ensemble for major and minor species of the human guanalyte binding protein 1 with scripts for the reading routine to combine and analyse jointly SAXS, EPR and FRET data.

Data from journal article "Amplifying effects of recurrent drought on the dynamics of tree growth and water use in a subalpine forest"

This dataset contains all data used in the above mentioned publication (DOI: tba). The data was obtained in a field drought experiment in a subalpine forest in the Austrian Central Alps, where adult trees were exposed to either ambient conditions or recurrent summer drought. The experiment was conducted from 2016-2018. All data were measured on individual tree level. All dataset contains the following, pre-processed data (processed as described in the corresponding journal article): - Micrometeorological data - Dendrometer data - Tree ring data - Sapflow data - Stem electrical resistivity data - Non-structural carbohydrate (NSC) and soluble sugar carbon isotopic composition (d13C) data The metadata.xlsx file contains all metadata, including units and descriptions of the variables.

opencc-zeroDec 2021View details →

Quantifying phenology and migratory behaviours of hummingbirds using single-site dynamics and mark-detection analyses

Nuanced understanding of seasonal movements of partially migratory birds is paramount to species and habitat conservation. Using nascent statistical methods, we identified migratory strategies of birds outfitted with radio-frequency identification (RFID) tags detected at RFID feeders in two sites in California, USA. We quantified proportions of migrants and residents and the seasonal phenology for each movement strategy in Allen's and Anna's hummingbirds; we also validated our methodology by fitting our model to obligate migratory black-chinned hummingbirds. Allen's and Anna's hummingbirds exhibited characteristics of facultative migratory behaviour. We also quantified apparent annual survival for each migratory strategy and found that residents had significantly higher probabilities of apparent survival. Low survival estimates for migrants suggest that a high proportion of birds in the migrant group permanently emigrated from our study sites. Considered together, our analyses suggest that hummingbirds in both northern and southern California sites partake in diverse and highly plastic migratory behaviours. Our assessment elucidates the dynamics underlying idiosyncratic migratory behaviours of two species of hummingbirds, in addition to describing a framework for similar assessments of migratory behaviours using the multi-state open robust design with state uncertainty (MSORD-SU) model and single-site dynamics.

opencc-zeroMay 2022View details →

Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory

The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. In this study we investigated the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) present throughout the Lamiaceae (mint) family. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions, such as chemical defense. Based on core genes found in the BGCs of all species examined across the Lamiaceae, we predict a simplified version of this cluster evolved in an early Lamiaceae ancestor. The current composition of the extant BGCs highlights the dynamic nature of its evolution. We elucidate the terpene backbones made by the Callicarpa americana BGC enzymes, including miltiradiene and the novel terpene (+)-kaurene, and show oxidization activities of BGC cytochrome P450s. Our work reveals the fluid nature of BGC assembly and the importance of genome structure in contributing to the origin of novel metabolites.

opencc-zeroMay 2022View details →

Molecular dynamics simulations of intrinsically disordered proteins p53TAD and Pup

Intrinsically disordered proteins (IDPs) are highly dynamic systems that play an important role in cell signaling processes and their misfunction often causes human disease. Proper understanding of IDP function not only requires the realistic characterization of their three-dimensional conformational ensembles at atomic-level resolution but also of the time scales of interconversion between their conformational substates. Large sets of experimental data are often used in combination with molecular modeling to restrain or bias models to improve agreement with experiment. It is shown here for the N-terminal transactivation domain of p53 (p53TAD) and Pup how the latest advancements in molecular dynamics (MD) simulations methodology produces native conformational ensembles by combining replica exchange with series of microsecond MD simulations. They closely reproduce experimental data at the global conformational ensemble level, in terms of the distribution properties of the radius of gyration tensor, and at the local level, in terms of NMR properties including 15N spin relaxation, without the need for reweighting. The IDP ensembles were analyzed by graph theory to identify dominant inter-residue contact clusters and characteristic amino-acid contact propensities. These findings indicate that modern MD force fields with residue-specific backbone potentials can produce highly realistic IDP ensembles sampling a hierarchy of nano- and picosecond time scales providing new insights into their biological function.

SupportingDataset Identification and Quantification of Within-Burst Dynamics in Singly-Labeled Single-Molecule Fluorescence Lifetime Experiments

The Jupyter notebooks and resulting files used to demonstrate divisor-based mpH2MM. The analysis is demonstrated with both simulations and analyses of alpha-synuclein. <ol> <li> Notebooks.zip:* Zip file containing the Jupyter notebooks for producing, analyzing and visualizing the simulated photon trajectories. Note: this folder contains all code needed to reproduce simulations. All other files related to the simulations are produced by one of the notebooks in this trajectory. However, as simulations can take a long time, the various results files are included in this repository so that notebooks can be run from intermediate steps. <ol> <li> 1-PIFE-pybromo-sims.ipynb : The code for producing simulated diffusion trajectories and photon-HDF5 files of two-state systems undergoing transition dynamics (the results of this notebook are stored in the sub-folder PyBroMo_photonHDF5) </li> <li> 2-PIFE-mpH2MM-sim-[lifetime components].ipynb : Notebooks performing divisor-based mpH2MM on simulated datasets for a given combination of lifetime states. (these notebooks store files that are contained in the sub-folder H2MMresults) </li> <li> 3-PIFE-mpH2MM-compiled-plots.ipynb : Jupyter notebook for producing figures comparing all results globally </li> <li> 532nm_IRF_19-10-2021.csb: the file containing the experimental IRF used in the simulations </li> </ol> </li> <li> PyBroMo_photonHDF5.zip:* Zip file containing the simulated results of 1-PIFE-pybromo-sims notebook as photon-HDF5 files (1 file per transition rate/lifetime combination) </li> <li> PIFE-sim-dynamicmix_[lifetime components]_result.hdf5: special HDF5 files containing the results of each notebook in Notebooks, which are used by 3-PIFE-mpH2MM-compiled-plots </li> <li> PIFE-mpH2MM-alpha-syn-vFinal.ipynb: divisor-based mpH2MM analysis of alpha-synuclein smPIFE data </li> <li> H2MM-Lifetime_example.ipynb: A demonstration of divisor-based mpH2MM using nsALEX-smFRET data. This method could potentially demonstrate states differentiated in lifetimes independently of potential changes in E & S. </li> <li> Template_ltH2MM.ipynb: An easy-to-follow implementation of divisor-based mpH2MM demonstrated on a single alpha-synuclein experimental data acquisition file. This can be used for learning how to implement and analyze single dye fluorescence lifetime data with mpH2MM </li> </ol>   * For running these notebooks, generally, all files in PyBroMo_photonHDF5.zip should be placed into a single directory (i.e., the files in Notebooks.zip should be placed into the same directory as the files in PyBroMo_photonHDF5.zip) as the notebooks are set to read in files from their current directory.

Molecular dynamics simulations of an Ago2-RNA complex in different force fields

This set of simulations contains 2us of Ago2-RNA complex in Amber ff14SB + OL3, ff19SB + OL3 and Desmond OPLS4 force fields. The polarizable force field AMOEBA has two simulation sets of 10*10ns and 2*100ns. The trajectories have been wrapped in the periodic box, centered around the protein atoms and the water molecules have been stripped out to conserve space using cpptraj. The trajectories are presented in Gromacs xtc-format which can be opened with the corresponding pdb file in multiple software tools such as VMD, PyMol or CaverAnalyst. The simulations are based on the crystal structure PDB ID 4W5O, where the missing loops were modeled using the Schrödinger Suite and missing nucleotides added manually.

Analysis Data, "Drivers and Determinants of Strain Dynamics Following Fecal Microbiota Transplantation"

This package contains datasets in `Rdata` format that underlie the analyses presented in the study, "Drivers and Determinants of Strain Dynamics Following Fecal Microbiota Transplantation" by Schmidt, Li et al.   Corresponding code, referring to these datasets, is available via `github`: https://github.com/grp-bork/fmt_metastudy   The study is available as a preprint: https://www.biorxiv.org/content/10.1101/2021.09.30.462010v1   The present package contains processed/derived data. Metagenome-Assembled Genomes generated for the same study are available via `Zenodo` under: https://zenodo.org/record/5534163#.YpoRFy8RrzA doi: 10.5281/zenodo.5534163

Application of X‑ray Microcomputed Tomography for the Static and Dynamic Characterization of the Microstructure of Oleofoams

Raw, greyscale image stacks collected during a X-Ray tomography analysis on cocoa butter-based oleofoams. The dataset is divided into three subsets: aeration, storage and heating, which contain samples that have been aerated for different amounts of time, samples that have been stored for 3 and 15 months at 20 °C, and finally samples that have been heated to the melting point of the stabilizing crystals, respectively. The dataset contains instructions and the scripts for ImageJ and MATLAB (as text files) to process and measure the bubble size distribution, and the thickness of the continous phase.

Simulation data for "Nonlinear electron phase-space dynamics in spontaneous excitation of falling-tone chorus" submitting to Geophysical Research Letters

Simulation data for "Nonlinear electron phase-space dynamics in spontaneous excitation of falling-tone chorus" submitting to Geophysical Research Letters. Including the simulation input parameter file and the necessary output data for analysis described in the article. The output data consists of waveform data, wave intensity profile, binned phase space distribution, etc. A detailed guide to load the output data is included in the zipped file as well.

Dataset for Surrogate Model Benchmarking for Dynamic Climate Impact Models

The data represents time series of seasonal weather forecasts for rainfall and temperature. The dataset contains 10 forecasts of 6-month horizon from, two per year, from 2017 to 2021; start dates January 1 and July 1, respectively. Each forecast comprises 50 ensemble members. In total, this sums up to 91300 data points, each containing daily average rainfall, temperature. Each sample (row) comprises following features (columns): <ul> <li>datetime: Date of the forecast sample.</li> <li>forecast: Identifier of the ensemble member, i.e. integer between 1 and total number of ensemblemembers.</li> <li>precip: Averaged daily rainfall forecast in millimeters.</li> <li>temp: Averaged daily temperature forecast in degree Celsius.</li> </ul> Dataset created by The Weather Company, an IBM business. This service is based on data and products of the European Center for Medium-range Weather Forecasts (ECMWF-Archive and ECMWF-RT). Generated using Copernicus Climate Change Service information [2019 and ongoing]. ECMWF Archive data published under a Creative Commons Attribution 4.0 International (CC BY 4.0): https://creativecommons.org/licenses/by/4.0/ Disclaimer: Neither the European Commission nor ECMWF is responsible for any use that may be made of the information it contains.