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9,097 results for “wild”

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zenodo44/100

Johann Sebastian Wild (w1503)

<b>-- <a href="https://doi.org/10.5281/zenodo.11582199">Documentation</a> --</b><br><br><u>Name</u>: Johann Sebastian Wild<br><u>musiXplora-ID</u>: w1503<br><u>musiXplora-URI</u>: <a href="https://musixplora.de/mxp/w1503">https://musixplora.de/mxp/w1503</a><br><u>Gender</u>: m<br><u>Confessions</u>: römisch-katholisch<br><u>First Mentioned</u>: 1693<br><u>Last Mentioned</u>: 1739<br><u>Sectors</u>: Kirche, Orgelbau<br><u>Professions (Musical)</u>: Orgelbauer<br><u>Main Place of Activity</u>: Walderbach<br><u>Other Places of Activity</u>: Aldersbach, Bamberg, Neunburg/Wald, Straubing<br><br><br><u>Herkunftsfamilie:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>Eltern</td><td>Vater</td><td>Georg Carl Wild</td><td><a href="https://musixplora.de/mxp/w1504">w1504</a></td></tr></tbody></table><br><u>Ausbildung:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>LehrerInnen und AusbilderInnen</td><td>Schüler</td><td>Johann Georg Götz</td><td><a href="https://musixplora.de/mxp/g0446">g0446</a></td></tr><tr><td>LehrerInnen und AusbilderInnen</td><td>Lehrer</td><td>Georg Carl Wild</td><td><a href="https://musixplora.de/mxp/w1504">w1504</a></td></tr></tbody></table><br><u>Arbeitsumfeld:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>KollegInnen</td><td>Kollege</td><td>Georg Carl Wild</td><td><a href="https://musixplora.de/mxp/w1504">w1504</a></td></tr></tbody></table><br><u>Personal:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>Leitungsfunktion</td><td>Mitarbeiter</td><td>Wild</td><td><a href="https://musixplora.de/mxp/3030855">3030855</a></td></tr></tbody></table><br><u>Titel/Medien:</u><br><table><tbody><tr><th>Role</th><th>Sigel</th><th>Title</th><th>mXp-ID</th></tr><tr><td>Related</td><td>Bernhard 2003a</td><td>Orgeldatenbank Bayern</td><td><a href="https://musixplora.de/mxp/5001131">5001131</a></td></tr><tr><td>Related</td><td>Fischer &amp; Wohnhaas 1994</td><td>Lexikon süddeutscher Orgelbauer</td><td><a href="https://musixplora.de/mxp/5001133">5001133</a></td></tr></tbody></table><br><br><u>Changelog</u>:<br>&nbsp;&nbsp;- v0.0.1: Initial Upload.<br>

opencc-by-4.0Jun 2024View details →
zenodo44/100

Georg Carl Wild (w1504)

<b>-- <a href="https://doi.org/10.5281/zenodo.11582199">Documentation</a> --</b><br><br><u>Name</u>: Georg Carl Wild<br><u>musiXplora-ID</u>: w1504<br><u>musiXplora-URI</u>: <a href="https://musixplora.de/mxp/w1504">https://musixplora.de/mxp/w1504</a><br><u>Gender</u>: m<br><u>First Mentioned</u>: 1738<br><u>Last Mentioned</u>: 1746<br><u>Sectors</u>: Kirche, Orgelbau<br><u>Professions (Musical)</u>: Orgelbauer<br><u>Main Place of Activity</u>: Walderbach<br><u>Other Places of Activity</u>: Ensdorf, Falkenstein, Stamsried<br><br><br><u>Herkunftsfamilie:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>Eltern</td><td>Sohn</td><td>Johann Sebastian Wild</td><td><a href="https://musixplora.de/mxp/w1503">w1503</a></td></tr></tbody></table><br><u>Ausbildung:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>LehrerInnen und AusbilderInnen</td><td>Schüler</td><td>Johann Sebastian Wild</td><td><a href="https://musixplora.de/mxp/w1503">w1503</a></td></tr></tbody></table><br><u>Arbeitsumfeld:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>KollegInnen</td><td>Kollege</td><td>Johann Sebastian Wild</td><td><a href="https://musixplora.de/mxp/w1503">w1503</a></td></tr></tbody></table><br><u>Personal:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>Leitungsfunktion</td><td>Mitarbeiter</td><td>Wild</td><td><a href="https://musixplora.de/mxp/3030855">3030855</a></td></tr></tbody></table><br><u>Titel/Medien:</u><br><table><tbody><tr><th>Role</th><th>Sigel</th><th>Title</th><th>mXp-ID</th></tr><tr><td>Related</td><td>Bernhard 2003a</td><td>Orgeldatenbank Bayern</td><td><a href="https://musixplora.de/mxp/5001131">5001131</a></td></tr><tr><td>Related</td><td>Fischer &amp; Wohnhaas 1994</td><td>Lexikon süddeutscher Orgelbauer</td><td><a href="https://musixplora.de/mxp/5001133">5001133</a></td></tr></tbody></table><br><br><u>Changelog</u>:<br>&nbsp;&nbsp;- v0.0.1: Initial Upload.<br>

opencc-by-4.0Jun 2024View details →
zenodo44/100

Johann Wilde (w0664)

<b>-- <a href="https://doi.org/10.5281/zenodo.11582199">Documentation</a> --</b><br><br><u>Name</u>: Johann Wilde<br><u>musiXplora-ID</u>: w0664<br><u>musiXplora-URI</u>: <a href="https://musixplora.de/mxp/w0664">https://musixplora.de/mxp/w0664</a><br><u>Gender</u>: m<br><u>Date of Death</u>: 1770<br><u>Place of Death</u>: Undefined<br><u>First Mentioned</u>: 1748<br><u>Sectors</u>: Instrumentenbau<br><u>Professions (Musical)</u>: Geiger, Instrumentalist, Instrumentenbauer<br><u>Other Places of Activity</u>: St. Petersburg<br><br><br><u>Portfolio:</u><br><table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>Sortimente</td><td>Sortiment</td><td>Pochette</td><td><a href="https://musixplora.de/mxp/2001476">2001476</a></td></tr><tr><td>Sortimente</td><td>Sortiment</td><td>Stockgeige</td><td><a href="https://musixplora.de/mxp/2003686">2003686</a></td></tr></tbody></table><br><u>Titel/Medien:</u><br><table><tbody><tr><th>Role</th><th>Sigel</th><th>Title</th><th>mXp-ID</th></tr><tr><td>Related</td><td>Hader et al. 2000</td><td>Lexikon zur deutschen Musikkultur. Böhmen, Mähren, Sudetenschlesien. Sudetendeutsches Musikinstitut</td><td><a href="https://musixplora.de/mxp/5001127">5001127</a></td></tr><tr><td>Related</td><td>Sachs 1913</td><td>Real-Lexikon der Musikinstrumente. zugleich ein Polyglossar für das gesamte Instrumentengebiet. Mit 200 Abbildungen</td><td><a href="https://musixplora.de/mxp/5040221">5040221</a></td></tr></tbody></table><br><br><u>Changelog</u>:<br>&nbsp;&nbsp;- v0.0.1: Initial Upload.<br>

opencc-by-4.0Jun 2024View details →
zenodo44/100

Multiple DJI drone flights with thermal camera over Lithuanian forests in winter for wild boar detection

<p>5 Flight over multiple days in the evening time for better thermal conditions for boar detection.</p> <p>Flight were conducted with DJI thermal cameras filmed at the speed of about 5m/s.&nbsp;<br>Flights 1, 2, 4 and 5 were filmed at from 90m height with camera pointing straight down.<br>Flight 3 was filmed at 120m height.</p> <p>&nbsp;</p> <p>Link for Dataset download: <a title="Thermal imaging dataset over Lithuanian forests in winter" href="https://art21-icaerus.s3.eu-central-1.amazonaws.com/Boars.zip" target="_blank" rel="noopener">https://art21-icaerus.s3.eu-central-1.amazonaws.com/Boars.zip</a>&nbsp;</p>

opencc-by-4.0Jul 2024View details →
zenodo44/100

CNN Wild Park - Graph Neural Networks for Learning Equivariant Representations of Neural Networks

<p>This repository contains the <strong>CNN Wild Park</strong> dataset from the paper:</p> <blockquote> <p><strong>Graph Neural Networks for Learning Equivariant Representations of Neural Networks</strong><br><a href="https://mkofinas.github.io/">Miltiadis Kofinas</a>*,&nbsp;<a href="https://bknyaz.github.io/">Boris Knyazev</a>, <a href="https://www.cyanogenoid.com/">Yan Zhang</a>,&nbsp;<a href="https://yunlu-chen.github.io/">Yunlu Chen</a>,&nbsp;<a href="https://gertjanburghouts.github.io/">Gertjan J. Burghouts</a>,&nbsp;<a href="https://egavves.com/">Efstratios Gavves</a>,&nbsp;<a href="https://www.ceessnoek.info/">Cees G. M. Snoek</a>,&nbsp;<a href="https://davzha.netlify.app/">David W. Zhang</a>*<br><em>ICLR 2024</em> (oral)<br><a href="https://arxiv.org/abs/2403.12143">https://arxiv.org/abs/2403.12143</a><br><a href="https://github.com/mkofinas/neural-graphs">https://github.com/mkofinas/neural-graphs</a><br>*Joint first and last authors</p> </blockquote> <p>We introduce a new dataset of CNNs, which we term <em>CNN Wild Park</em>.<br>The dataset consists of 117,241 checkpoints from 2,800 CNNs, trained for up to 1,000 epochs on CIFAR10.<br>The CNNs vary in the number of layers, kernel sizes, activation functions, and residual connections between arbitrary layers.</p> <p>More specifically, we construct the CNN Wild Park dataset by training 2,800 small CNNs with different architectures for 200 to 1,000 epochs on CIFAR10. We retain a checkpoint of its parameters every 10 steps and also record the test accuracy. The CNNs vary by:</p> <ul> <li>Number of layers L in [2, 3, 4, 5] (note that this does not count the input layer).</li> <li>Number of channels per layer c_l in [4, 8, 16, 32].</li> <li>Kernel size of each convolution k_l in [3, 5, 7].</li> <li>Activation functions at each layer are one of ReLU, GeLU, tanh, sigmoid, leaky ReLU, or the identity function.</li> <li>Skip connections between two layers with at least one layer in between. Each layer can have at most one incoming skip connection. We allow for skip connections even in the case when the number of channels differ, to increase the variety of architectures and ensure independence between different architectural choices. We enable this by adding the skip connection only to the min(c_n, c_m) nodes.</li> </ul> <p>We divide the dataset into train/val/test splits such that checkpoints from the same run are <strong>not</strong> contained in both the train and test splits.&nbsp;</p> <div>&nbsp;</div> <div>&nbsp;</div>

opencc-by-4.0May 2024View details →
zenodo44/100

Individual-based body sizes of wild bees along elevational gradients on Mt. Kilimanjaro

<p><span>This dataset contains body size measurements of wild bees that were captured along elevational gradients on the southern slopes of Mt. Kilimanjaro (Tanzania) using standardized sampling methods (pan traps, transect walks). The dataset includes bee species identified at the species level as well as morphospecies. The bees were measured individually, meaning that intraspecific differences in body size are also represented. The intertegular distance (ITD) in millimeters was measured as a surrogate for body size.</span></p> <p><span>The KiLi project (2010-2018) is a German Science Foundation (DFG) funded research unit (DFG research unit FOR1246) that focuses on biodiversity and ecosystem processes along altitudinal and disturbance gradients on Mt. Kilimanjaro (Tanzania, Africa), capitalizing on its world-wide unique range of climatic and vegetation zones. The research unit comprises 2 central projects and 7 subprojects from various disciplines. On a total of 60 study sites in both natural and human-disturbed ecosystems biodiversity (e.g. plants, soil arthropods, ants, bees, frogs, lizards, bats, birds), related ecosystem processes (decomposition, seed dispersal, pollination, herbivory, predation), and biogeochemical processes and properties of ecosystems (climate, soil properties and nutrient status, regulation of water and carbon fluxes, trace gas emissions, primary productivity, functional diversity) are analyzed.</span></p>

opencc-by-4.0Jul 2024View details →
zenodo44/100

Herbarium specimen image of Omphalocarpum sphaerocarpum De Wild., part of the collection of Meise Botanic Garden

Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.

opencc-zeroNov 2018View details →
zenodo44/100

Herbarium specimen image of Omphalocarpum mortehanii De Wild., part of the collection of Meise Botanic Garden

Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.

opencc-zeroNov 2018View details →
zenodo44/100

Herbarium specimen image of Omphalocarpum ghesquierei De Wild., part of the collection of Meise Botanic Garden

Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.

opencc-zeroNov 2018View details →
zenodo44/100

Herbarium specimen image of Thomandersia congolana De Wild. & T.Durand, part of the collection of Meise Botanic Garden

Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.

opencc-zeroNov 2018View details →
zenodo44/100

Herbarium specimen image of Vitex seretii De Wild., part of the collection of Meise Botanic Garden

Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.

opencc-zeroNov 2018View details →
zenodo44/100

Herbarium specimen image of Bulbostylis congolensis De Wild., part of the collection of National Museum of Natural History, Paris

Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.

opencc-zeroNov 2018View details →
zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with DHA (POSES 1-4)

<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_DHA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of docosahexaenoic acid (DHA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). &nbsp;</p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis&nbsp;: Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>

opencc-by-4.0Oct 2019View details →
zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 3 and 4)

<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). &nbsp;</p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis&nbsp;: Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>

opencc-by-4.0Sep 2019View details →
zenodo44/100

Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids

<p>This is the &quot;parent&quot; repository for the Data Note : &quot;&shy;Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids&quot; by Abelak, Bishop-Bailey and Nobeli.</p> <p>It contains a document (<strong>Abelak_etal_Methods.pdf</strong>) describing the methods used to produce the data here and the data in all repositories supplementing it.</p> <p>It also contains a shell script (<strong>create_sim4_repeats.sh</strong>)&nbsp;that is typical of those used to set up the molecular dynamics simulations in the&nbsp;repositories supplementing this one.</p> <p>Finally, it contains the results of the homology modelling and docking simulations that formed the starting points for the molecular dynamics simulations in this study.</p> <p>Description of files in this dataset:</p> <p><strong>C2J2_min3_mod_noH.pdb</strong> : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10.</p> <p><strong>docking_wild_type_C2J2.zip</strong> : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2.</p> <p>Details of how this data was produced is available in the Abelak_etal_Methods.docx document.</p>

opencc-by-4.0Sep 2019View details →
zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 1 and 2)

<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). &nbsp;</p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis&nbsp;: Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>

opencc-by-4.0Sep 2019View details →
zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 5 and 6)

<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose). &nbsp;</p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis&nbsp;: Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>

opencc-by-4.0Oct 2019View details →
zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with EPA (POSES 1-4)

<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_wt_CYP2J2_EPA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of&nbsp;eicosapentaenoic acid (EPA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3&nbsp;repeats per pose). &nbsp;</p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis&nbsp;: Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>

opencc-by-4.0Oct 2019View details →
zenodo44/100

Unveiling Web Fingerprinting in the Wild Via Code Mining and Machine Learning

<p>Dataset of Javascripts used for training and testing the fingerprinting algorithms described in&nbsp;</p> <p>Rizzo, Valentino, Stefano Traverso, and Marco Mellia. &quot;Unveiling Web Fingerprinting in the Wild Via Code Mining and Machine Learning.&quot;&nbsp;<em>Proceedings on Privacy Enhancing Technologies</em>&nbsp;2021.1 (2021): 43-63.</p>

opencc-by-4.0Nov 2020View details →
zenodo44/100

Data and code for: Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats, Suricata suricatta

<p>Data and code to go with our publication &quot;Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats, <em>Suricata suricatta&quot;, </em>Nature Communications (2021).</p> <p><strong>FILE DESCRIPTIONS</strong></p> <p><em>****** DATA ******</em></p> <p><strong>meerkat_16S_data.tar.gz</strong>&nbsp;&nbsp;&nbsp; # 16S V4 amplicon sequences&nbsp; sequenced on an Illumina MiSeq platform using primer pair 515F and 806R, including all faecal samples, controls, and sand samples. Sequence identifiers and basic metadata are in <strong>sequence_identifiers.csv.</strong></p> <p><strong>sequence_identifiers.csv&nbsp;&nbsp;&nbsp; </strong># Simple metadata and identifiers for all sequences/samples (what type of sample/sequencing run, etc), required for QIIME2 processing of the raw fasta.gz files contained in meerkat_16S_data.tar.gz. It contains a column for whether the sample was included in the final analysis. Does not include sample biological metadata as generating this data requires access to Kalahari Meerkat Project database. Biological metadata for samples included in the final analysis are instead provided in <strong>processed_data_phyloseq.RDS </strong>and can be accessed via <em>phyloseq::sample_data(processed_data_phyloseq)</em>.</p> <p><strong>processed_data_phyloseq.RDS</strong> # Phyloseq object containing the processed data used in the presented analysis. Contains data for 1109 samples, and includes the ASV table, the taxonomic classification, the phylogenetic tree, and the sample metadata used in the analysis.</p> <p><strong>technical_replicate_data_phyloseq.RDS</strong> # Phyloseq object containing data from the 16 technical replicates.</p> <p><strong>pilot_study_data_phyloseq.RDS</strong> # Phyloseq object containing data from the pilot study on captive meerkats.</p> <p><em>****** CODE ******</em></p> <p><strong>CODE1_QIIME_script.R</strong>&nbsp;&nbsp; # QIIME2 script to generate ASV table, taxonomy, and phylo tree from <strong>meerkat_16S_data.tar.gz. </strong>Requires a reference taxonomy (SILVA) and a reference phylogeny (SEPP) for taxonomic and phylogenetic placements.</p> <p><strong>CODE2_processing_QIIME_output.Rmd</strong>&nbsp; # R markdown script that processes the QIIME2 output generated by <strong>CODE1_QIIME_script.R</strong>. Does not generate meerkat metadata as this requires access to the Kalahari Meerkat Project database. This metadata is provided in <strong>processed_data_phyloseq.RDS.</strong></p> <p><strong>CODE3_data_analysis_script.Rmd </strong># R markdown script that generates data and figures presented in paper, using data from <strong>processed_data_phyloseq.RDS, technical_replicate_data_phyloseq.RDS, </strong>and<strong> pilot_study_data_phyloseq.RDS.</strong></p> <p><em>****** R MARKDOWN REPORTS ******</em></p> <p>The following reports are html files that show the code output for the two RMD files above.</p> <p><strong>RMARKDOWN_data_processing.html </strong># R markdown report for<strong> CODE2_processing_QIIME_output.Rmd</strong></p> <p><strong>RMARKDOWN_data_analysis.html </strong># R markdown report for <strong>CODE3_data_analysis_script.Rmd</strong></p> <p>*****************************</p> <p>For general queries, unexpected errors and/or inconsistencies, please contact riselya@gmail.com.</p> <p>&nbsp;</p>

opencc-by-4.0Aug 2021View details →

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