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7,195 results for “SET”
MetaBAT 2.12.1 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly
Genome binning of the gold standard pooled assembly <br><strong>Software: </strong>MetaBAT<br><strong>SoftwareVersion: </strong>2.12.1<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://bitbucket.org/berkeleylab/metabat<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandUsed:</strong> bowtie2-build anonymous_gsa_pooled.fasta anonymous_gsa_pooled.fasta<br>for i in {0..63}; do bowtie2 -q --threads 30 --fr -x anonymous_gsa_pooled.fasta --interleaved sample_${i}/anonymous_reads.fq -S anonymous_reads_sample_${i}.sam ; done<br>for i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & done<br>for i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; done<br>for i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; done<br>runMetaBat.sh -l anonymous_gsa_pooled.fasta anonymous_reads_sample_*.sorted.bam
Kraken 2.0.8 beta taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>Kraken<br> <strong>SoftwareVersion: </strong>2.0.8 beta<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://ccb.jhu.edu/software/kraken2/<br> <strong>ReferenceDatabase:</strong> built 2019-05-22<br> <strong>Taxonomy:</strong> NCBI 2019-05-22<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> kraken2-build --standard --db kraken2db_std --use-ftp<br> kraken2 --db kraken2db_std --threads 16 --output 19122017_mousegut_scaffolds.kraken --report 19122017_mousegut_scaffolds.kreport anonymous_gsa_pooled.fasta<br> cat 19122017_mousegut_scaffolds | awk '{print $2 "\t" $3}' > 19122017_mousegut_scaffolds.cami</p>
Set de datos y códigos en R para DataViz
<p>Set de datos y código en R para el curso de <em>Tratamiento y visualización de datos en la Humanidades Digitales.</em></p> <p><code>stylometry_sample.csv</code> ha sido extraído de Christof Schöch, <em>Bibliography on Stylometry</em>, 2017, dataset (Version v.0.1.3 10.5281), DOI: <a href="https://doi.org/10.5281/zenodo.835190">10.5281/zenodo.835190</a>.</p> <p> </p>
InterFlex RWTH_WP8 data set_
<p>Within the context of InterFlex project under GA 731289, an agent-based control power scheduling framework for interconnected Local Energy Communities (LECs) has been developed. The interconnection of differnt LECs is inspired by the InterFlex Simris demonstrator. For furhther information, please refer to the respective publications: http://publications.rwth-aachen.de/record/775099; http://publications.rwth-aachen.de/record/751892?ln=de; http://publications.rwth-aachen.de/record/759872/files/759872.pdf; https://cired-repository.org/handle/20.500.12455/640; https://www.cired-repository.org/handle/20.500.12455/480; http://publications.rwth-aachen.de/record/763488;</p>
GC-MS data set for Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana
<p>RAW GC/MS data set for characterization of class II terpene synthases from <em>Callicarpa americana </em></p>
Benchmark set for relative free energy calculations
<p>Created by Christina Schindler and Daniel Kuhn, Merck KGaA, Darmstadt, Germany.</p> <p>December 2018</p> <p>Manuscript in preparation.</p> <p>Previously presented at Alchemical Free Energy Workshop 2019 in Goettingen, Germany.</p> <p>DOI: 10.5281/zenodo.3258925</p> <p> </p> <p>References for datasets used in benchmark</p> <p>CDK8<br> Schiemann, Kai, et al. "Discovery of potent and selective CDK8 inhibitors from an HSP90 pharmacophore." Bioorganic & medicinal chemistry letters 26.5 (2016): 1443-1451.</p> <p>DOI: 10.1016/j.bmcl.2016.01.062</p> <p>c-Met</p> <p>Dorsch, Dieter, et al. "Identification and optimization of pyridazinones as potent and selective c-Met kinase inhibitors." Bioorganic & medicinal chemistry letters 25.7 (2015): 1597-1602.</p> <p>DOI: 10.1016/j.bmcl.2015.02.002<br> Eg5</p> <p>Schiemann, Kai, et al. "The discovery and optimization of hexahydro-2H-pyrano [3, 2-c] quinolines (HHPQs) as potent and selective inhibitors of the mitotic kinesin-5." Bioorganic & medicinal chemistry letters 20.5 (2010): 1491-1495.</p> <p>DOI: 10.1016/j.bmcl.2010.01.110<br> Hif2a</p> <p>Wallace, Eli M., et al. "A small-molecule antagonist of HIF2α is efficacious in preclinical models of renal cell carcinoma." Cancer research 76.18 (2016): 5491-5500.</p> <p>DOI: 10.1158/0008-5472.CAN-16-0473</p> <p>Dixon, Darryl David, et al. "Aryl ethers and uses thereof." U.S. Patent No. 9,908,845. 6 Mar. 2018.</p> <p>URL: Google Patents<br> PFKFB3</p> <p>Boutard, Nicolas, et al. "Discovery and Structure–Activity Relationships of N-Aryl 6-Aminoquinoxalines as Potent PFKFB3 Kinase Inhibitors." ChemMedChem 14.1 (2019): 169-181.</p> <p>DOI: 10.1002/cmdc.201800569<br> SHP2</p> <p>Chen, Ying-Nan P., et al. "Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases." Nature 535.7610 (2016): 148.</p> <p>DOI:10.1038/nature18621</p> <p>Garcia Fortanet, Jorge, et al. "Allosteric inhibition of SHP2: identification of a potent, selective, and orally efficacious phosphatase inhibitor." Journal of medicinal chemistry 59.17 (2016): 7773-7782.</p> <p>DOI: 10.1021/acs.jmedchem.6b00680</p> <p>Chen, Christine Hiu-tung, et al. "1-pyridazin-/triazin-3-yl-piper (-azine)/idine/pyrolidine derivatives and compositions thereof for inhibiting the activity of shp2." U.S. Patent Application No. 15/110,498.</p> <p>URL: Google Patents</p> <p> </p> <p>SYK<br> Currie, Kevin S., et al. "Discovery of GS-9973, a selective and orally efficacious inhibitor of spleen tyrosine kinase." Journal of medicinal chemistry 57.9 (2014): 3856-3873.</p> <p>DOI: 10.1021/jm500228a</p> <p>TNKS2<br> Buchstaller, Hans-Peter, et al. "Discovery and Optimization of 2-Arylquinazolin-4-ones into a Potent and Selective Tankyrase Inhibitor Modulating Wnt Pathway Activity." Journal of medicinal chemistry 62.17 (2019): 7897-7909.</p> <p>DOI: 10.1021/acs.jmedchem.9b00656</p>
Data Set - Laboratory measurement of the wave–induced plastic particles motion: The influence of wave period, plastic size and plastic density
<p><strong>Data set - Laboratory measurement of the wave–induced plastic particles motion: The influence of wave period, plastic size and plastic density</strong></p> <p>This data set describes the wave flume experimental data on the wave-induced plastic particles motion induced by different wave conditions and different plastic particles density and size. A manuscript is currently under review describing the analysis of the data.</p> <p>The data set is divided in two parts:</p> <p>- <strong>Wave flume hydrodynamics</strong>. With measured water surface elevation at different locations within the wave flume. These data are stored in txt files with headings describing the type of measurement, i.e. wave paddle motion, water surface elevation at different sensors, synchronization signal for the video-cameras.</p> <p>- <strong>Lagrangian trajectories. </strong>hdf5 files with information of the particles position, velocity and time (with respect to the synchronization signal in the respective hydrodynamic file) for each experiment. Two tar.gx files have been uploaded with trajectories information:</p> <p> - TOPIOS_Trajectories_FloatingParticles.tar.xz, with information of floating plastic particles and,</p> <p> - TOPIOS_Trajectories_NonfloatingParticles.tar.xz, with information of non-floating plastc particles.</p> <p>An excel file with information of filenames, cross-shore locations of sensors, plastic particles and wave conditions is also uploaded (TOPIOS_Control_exp.xlsx).</p> <p>Any question regarding the data can be addressed at jose.alsina@upc.edu</p>
LRRo: A Lip Reading Data Set for the Under-resourced Romanian Language
<p>Two distinct collections are presented in this repository:</p> <p>(i) wild LRRo data is designed for an Internet in-the-wild, ad-hoc scenario, coming with more than 35 different speakers, 1.1k words, a vocabulary of 21 words, and more than 20 hours;</p> <p>(ii) lab LRRo data, addresses a lab controlled scenario for more accurate data, coming with 19 different speakers, 6.4k words, a vocabulary of 48 words, and more than 5 hours.</p>
The ECHAM/MESSy idealized (EMIL) model set-up: data of reference simulations
<p>This data set contains the data from simulations performed with the ECHAM/MESSy IdeaLized (EMIL) dry dynamical core model, as presented in the GMD(D) publication by Garny et al., available under doi https://doi.org/10.5194/gmd-2019-330. For details, please refer to the enclosed data description file.</p>
Data set | Water- and land-borne geophysical surveys before and after the sudden water-level decrease of two large karst lakes in southern Mexico (v1.1)
<p>This repository contains raw and processed data along with the Matlab scripts used to prepare the visualizations presented in the manuscript</p> <p>Bücker, M., Flores Orozco, A., Gallistl, J., Steiner, M., Aigner, L., Hoppenbrock, J., Glebe, R., Morales Barrera, W., Pita de la Paz, C., García García, E., Razo Pérez, J.A., Buckel, J., Hördt, A., Schwalb, A., and Perez, L. (2020). <strong><em>Water- and land-borne geophysical surveys before and after the sudden water-level decrease of two large karst lakes in southern Mexico</em></strong>. Submitted to Solid Earth.</p> <p>If you find this data useful in your own research, please mention this data set and/or the manuscript.</p>
Geophysical data set for San Ramon Fault master section
<p>This data set is a multivariable analysis carried out in the San Ramon Fault (SRF) along a master section perpendicular to the main fault scarp. These data include: (1) a ~ 1 km long Electrical resistivity tomography (ERT) with a dipolo-dipolo configuration, 48 channels every 20 meters (named as the master section). (2) Differential GPS data with the location of the ERT electrodes and gravity stations. (3) Data of the gravity stations, with a Garmin GPS data. (4) Seismic data of an active experiment of 24 channels every 5 m, with several hammer strikes, which are explained in a text-document inside each seismic file (TRV_seismic_data and SRF_seismic_data). (5) Time-series of the Nakamura stations located along the ERT master profile. (6) The voltage decay curve of a TEM-station in the western edge of the master section, which is ready for modeling.</p> <p> </p>
Data set related to the manuscript "Efficient prediction of Nucleus Independent Chemical Shifts for polycyclic aromatic hydrocarbons"
<p>Input/output files for Gaussian calculations, data sets for all plots shown in the manuscript "Efficient prediction of Nucleus Independent Chemical Shifts for polycyclic aromatic hydrocarbons", C code for the NICS calculations through the dipolar model and python code for the NICS calculations through the tight-binding model described in the manuscript.</p>
Institutional arrangements regarding Minimum Wage Setting in 195 countries
<p>Most countries in the world have country-level policies concerning their minimum wage-fixing machinery. These policies vary widely, and therefore it becomes important to have adequate classifications of these policies. This paper reviews databases that classify country-level policies for determining minimum wages. Several databases - we found twelve - classify countries according to their minimum wage-fixing mechanisms and the coverage of these mechanisms. The mechanisms indicate whether the minimum wages are set by Law, by Collective Bargaining or any policy in between, the coverage indicates whether the minimum wages cover the entire dependent labour force or only one or more sections within the labour force. The twelve databases vary with respect to the years covered, the countries covered and the characteristics coded. We restricted our analysis to the years 2011 to 2015. The number of countries covered in these databases range from 29 to 189, with 195 countries in total. The merged database reveals that countries are not classified similarly across databases. Between 75% and 93% of the countries apply a statutory minimum wage-fixing mechanism across years and databases. Less than one in ten countries relies solely on minimum wage setting by collective bargaining. In the EU28 plus Norway this percentage is relatively high, but in countries outside Europe it is far below 10%. Two ILO conventions refer to minimum wage-fixing mechanisms. Across years and databases roughly three in five countries that apply a statutory minimum wage-fixing mechanism have signed the oldest Convention (C26), whereas roughly one in three has done so with the most recent Convention (C131). Obviously, many more countries could have signed the Conventions. Only a few countries have signed the Conventions but do not have a statutory minimum wage-fixing mechanism. Among others a few EU28 countries rely solely on collective bargaining for minimum wage setting, and consider that as a national wide fixing mechanism. If countries apply a statutory wage-fixing mechanism, does the minimum wage then cover the entire dependent labour force? Globally, more than half of the countries with a statutory minimum wage apply differentiated minimum wages. Most frequently reported breakdowns are by industry or occupation. Countries with multiple minimum wage rates mimic collective bargaining, particularly when they break down the rates by industry or occupation. The aim of this paper is to generate a Minimum Wage Policies Database (MWPDB) from the merged dataset. Using a set of rules for generating data from the source databases, we indicate for almost half of the 195 countries the presence or absence of a statutory minimum wage for all five years from 2011 to 2015. For 16 countries no valid data is available for any year. Particularly for Europe and South America, MWPDB has satisfactory number of observations, whereas the opposite holds for the small islands in Oceania. The MWPDB results show that approximately nine in ten countries do apply a minimum wage policy, and that this is slightly increasing between 2011 to 2015. </p>
MR Spectra from rat hippocampus with LCModel quantification and the corresponding basis set
<p>This folder contains the LCModel quantifications of spectra acquired in hippocampus from 7 rats. The spectra were quntified using six different DKNTMN (spline stiffness) values (0.1, 0.25, 0.4, 0.5, 1, 5). In the folder Control_files_Basis_set you can find all the control files used in this quantification along with the corresponding basis set (metabolites/simulated using NMRScopeB from jMRUI and <em>in vivo </em>parameters + full MM spectrum).</p> <p>Please cite the following manuscript if you are using the data</p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/34268821/">In vivo macromolecule signals in rat brain 1 H-MR spectra at 9.4T: Parametrization, spline baseline estimation, and T2 relaxation times - PubMed (nih.gov)</a><br> </p>
The Set Increment with Limited Views Encoding Ratio (SILVER) Method for Optimizing Radial Sampling of Dynamic MRI: Supporting Data
<p>This data was created to perform the first experiments with the SILVER method of optimizing radial MRI acquisition. The files are mainly .mat files containing the numerical data used to assess the SILVER method using MATLAB (Version R2018b). Instructions on how to use the data and how to reproduce the experiments are available on https://github.com/SophieSchau/SILVER</p>
Enhanced Molecular Spin-Photon Coupling at Superconducting Nanoconstrictions. Open data sets
<p>Includes data relevant for publication with DOI <a href="https://doi.org/10.1021/acsnano.0c03167">10.1021/acsnano.0c03167</a> plus a table with information on how the data were obtained and processed.</p>
Archäologische Chronologie und historische Interpretation: Die Merowingerzeit in Süddeutschland (Correspondence Analysis Data Set)
<p>This data set is a supplement to the book "Archäologische Chronologie und historische Interpretation: Die Merowingerzeit in Süddeutschland" (De Gruyter, 2016) and comprises the archaeological data and the results of the correspondence analysis of Merovingian-period graves from southern Germany and their chronological classification. The data sets for female and male burials can be downloaded as PDF, EXCEL and CSV files.</p>
SMART2: Age-specific social mixing of school-aged children in a US setting using proximity detecting sensors and contact surveys
<p>To increase the evidence base supporting specific methods to measure social interaction, we compared data from self-reported contact surveys and wearable proximity sensors from a cohort of schoolchildren in the Pittsburgh metropolitan area.</p> <p> </p> <p>Enrollment in the Social Mixing and Respiratory Transmission (SMART) study operated on an opt-out basis, and all students registered in a participating school before the start of the study were eligible to participate. Students in kindergarten (typically aged 5 years) to 12<sup>th</sup> grade (typically aged 18 years) from two elementary (K to 4<sup>th</sup> grade, K to 5<sup>th</sup> grade), two middle (5<sup>th</sup> to 6<sup>th</sup> grade, 7<sup>th</sup> to 8<sup>th</sup> grade), two elementary-middle (K to 8<sup>th</sup> grade), and two high (both 9<sup>th</sup> to 12<sup>th</sup> grade) schools were eligible to participate in SMART. Participation rates were high in all schools (82 to 99%). Each school provided aggregate demographic information about the school population, and individual grade and sex of participating students.</p> <p><em>Proximity sensor deployments</em></p> <p>The details of proximity sensor deployments have been described in detail elsewhere (60). In brief, participating students were given proximity sensors in plastic pouches and instructed to wear the pouch around their neck for the duration of the school day without removing or otherwise tampering with the sensor. In six of the eight schools, all participating students were given a sensor; in two schools, the large student population limited the deployment to randomly selected classrooms in each grade. Deployments typically lasted from the first class period (08:00 – 09:00) to the last class period (14:00 – 15:00). Deployment days in each school were chosen to be representative of a typical school day, without any special schoolwide or grade-specific activities that could modify normal contact patterns.</p> <p> </p> <p>We used TelosB wireless sensors (61) programmed in the NesC language to send beacons every 20 seconds (beacon frequency 3 per minute). The receiving sensor recorded the contacting sensor’s identity, an internal time stamp, and a radio strength signal indicator (RSSI). Signal strength provided an estimate of physical proximity, but was highly dependent on the orientation of the two sensors and any obstructions between them and therefore could not be used to define an exact distance between contacts. Based on pilot studies and previous work on effective distances of respiratory virus transmission (29, 62), we chose a signal threshold (-80 dBm) that should correspond to contacts of relevance to respiratory disease transmission.</p> <p> </p> <p>The number of unique proximity sensor contacts recorded for a participant was defined as the total number of other participants with whom their proximity sensor recorded at least one interaction during each deployment. To explore patterns of contacts of varying length, we considered several values of the contact threshold, or the minimum number of recorded interactions between two proximity sensors required to be considered a unique contact. The number of interactions between any given pair of sensors was taken to be the maximum number of interactions recorded by either sensor, to account for battery failure, measurement error, or other malfunctions.</p> <p> </p> <p><em>Contact survey design</em></p> <p>Contact surveys were completed by participants in school under the supervision of project staff and teachers. Each sheet of the paper version allowed for information on up to 30 contacts to be recorded; additional sheets could be requested. Two versions were designed: one for middle- and high-school students, and a simplified version for elementary school students (although some elementary school children completed the middle- and high-school version, upon consultation with school administrators and teachers). Classrooms were randomly selected to participate from each grade, and students of several classrooms completed more than one contact survey over the course of the study period.</p> <p> </p> <p>Participants were asked to report information about any individual they talked with, played with, or touched the previous day, including the contact’s age and sex, whether they attended the same school as the participant, the context in which the contact was made, whether the contact involved direct or indirect (through a shared object) touch, and approximate duration of the contact. Students reported the total number of contacts made in the previous day, without detailed information, and additional demographic information about themselves and their household. The surveys were completed either on paper or by computer, depending on resources available in each school.</p> <p> </p> <p>We defined total survey contacts as the total number of individuals a student reported having interacted with on the day before the survey was completed. Detailed contacts were the subset of total contacts for which the student reported contact age, sex, duration, and context. We considered further subsets of detailed survey contacts, including those occurring within school, those reported to have lasted more than 10 minutes over the course of the day, and those occurring on the same day as a sensor deployment.</p> <p> </p>
SSH data set used for Rossby Wave Analysis, extraction from ORCA12.L46-MJM189 DRAKKAR simulation
<p>This data set corresponds to the Sea Surface Heigh (SSH) silmulated by the NEMO ocean circulation model, under the ORCA12.L46-MJM189 configuration, developped in the frame of the DRAKKAR project. This particular data set is an extraction from the native numerical grid, covering the area between 38N and 40N in the North Altantic ocean, for the period 1970 to 2015. The data are concatenated in a single file with 5-days average of SSH. The corresponding metrics for this sub domain are also present in this netcdf file. This subset was used in Watelet et al. (2020) submitted paper, dealing with Rossby waves analysis.</p>
Animations: Turbulence sets the length scale for planetesimal formation:Local 2D simulations of streaming instability and planetesimal formation
<p>This repository includes three animations discussed in the accepted version of ''Turbulence sets the length scale for planetesimal formation:Local 2D simulations of streaming instability and planetesimal formation" to appear in the Astrophysical Journal. </p> <p>Short descriptions of the animations are as follows:</p> <p>Movie 1: Simulations Ae3L0005 and Ae3L0005. Both use $\St= 0.1$ particles, but only the larger box shows collapse and planetesimal formation. See also: <a href="https://youtu.be/gkHiluqH8HY">https://youtu.be/gkHiluqH8HY</a> </p> <p>Movie 2: The evolution of $\St= 0.1$ pebbles for all 6 different box sizes in Table 1. See also: <a href="https://youtu.be/nA87-9_trUc">https://youtu.be/nA87-9_trUc</a></p> <p>Movie 3: The evolution of $\St= 0.01$ pebbles. See also: <a href="https://youtu.be/CCywDPKVU8w">https://youtu.be/CCywDPKVU8w</a></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.