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59 results for “sketches”
Fig. 2. Sketches illustrating anomiid and trace morphology. A in Centrichnus eccentricus revisited: A new view on anomiid bivalve bioerosion
Fig. 2. Sketches illustrating anomiid and trace morphology. A. Shell exterior of left valve. B. Shell interior of right valve. C. Morphological features and measured dimensions of Centrichnus eccentricus. D. Schematic cross section of a living anomiid attached to the substrate illustrating the position of etching traces (modified after Yamaguchi 1998).
Figure 1. Professor M in Maria Guiomar Nates-Parra: Biographical sketch and summary of contributions to the melittological knowledge of Colombia
Figure 1. Professor M. Guiomar Nates-Parra in 2006 showing a collection of orchid bees in her lab (Photograph courtesy of M.L. Bueno).
Text-fig. 1. Location of Ivanovce Pliocene primate site in Slovakia within the wider area of the Carpathians-Pannonian Basin (white circle). The northern wall of the former limestone quarry at Ivanovce near Trenčín in western Slovakia. Several karst fillings provided a rich early Pliocene vertebrate assemblage. a: schematic sketch of the site showing the location of different karst fillings, b: photo of the same site during the palaeontological research in 1960s. in Allosorex Stenodus Fejfar, 1966 (Eulipotyphla, Soricidae): Re-Description Of Type Material And Re-Interpretation Of Its Fossil Record
Text-fig. 1. Location of Ivanovce Pliocene primate site in Slovakia within the wider area of the Carpathians-Pannonian Basin (white circle). The northern wall of the former limestone quarry at Ivanovce near Trenčín in western Slovakia. Several karst fillings provided a rich early Pliocene vertebrate assemblage. a: schematic sketch of the site showing the location of different karst fillings, b: photo of the same site during the palaeontological research in 1960s.
Text-fig. 1. Geological sketch-map of the Ludvíkovice quarry area (adopted from the on-line geological map 1: 50 000 scale of the Czech Geological Survey – https://mapy.geology.cz/ geocr50/). in A New Oligocene Flora From Ludvíkovice Near Děčín (České Středohoří Mts., The Czech Republic)
Text-fig. 1. Geological sketch-map of the Ludvíkovice quarry area (adopted from the on-line geological map 1: 50 000 scale of the Czech Geological Survey – https://mapy.geology.cz/ geocr50/).
Text-fig. 1. Sketch map of the Devonian of the Prague Basin, and generalised stratigraphy of the Koněprusy Limestone (Pragian), Suchomasty Limestone (Upper Emsian), Acanthopyge Limestone (Eifelian) and the top of the Acanthopyge Limestone and the Srbsko Formation (transition Eifelian-Givetian) in the Koněprusy area (with marked neptunian dykes and approximate positions of Calceola-bearing limestone beds). Modified after Chlupáč et al. (1986), Hladil et al. (1992) and Mergl (2014). in Trilobite Assemblage Of Calceola -Bearing Beds In Acanthopyge Limestone (Choteč Formation, Middle Devonian, Eifelian, Prague Basin, The Czech Republic)
Text-fig. 1. Sketch map of the Devonian of the Prague Basin, and generalised stratigraphy of the Koněprusy Limestone (Pragian), Suchomasty Limestone (Upper Emsian), Acanthopyge Limestone (Eifelian) and the top of the Acanthopyge Limestone and the Srbsko Formation (transition Eifelian-Givetian) in the Koněprusy area (with marked neptunian dykes and approximate positions of Calceola-bearing limestone beds). Modified after Chlupáč et al. (1986), Hladil et al. (1992) and Mergl (2014).
Mash Sketch of RefSeq Bacterial Representative Genomes v217
<p>This was created to get a new mash reference that was current. The script to create this uses ncbi datasets and mash (https://github.com/UPHL-BioNGS/Grandeur/blob/main/bin/new_mash_ref.sh)<br> <br> This was created on April 27, 2023, and is RefSeq v217<br> <br> ```bash</p> <p>#/bin/bash<br> out=mash_db<br> <br> mkdir $out</p> <p>cd $out</p> <p>datasets summary genome taxon bacteria --reference --as-json-lines | \</p> <p>dataformat tsv genome --fields accession,assminfo-refseq-category,organism-name --elide-header | \</p> <p>grep representative | \</p> <p>tee representative_genomes.txt | \</p> <p>cut -f 1 > genome_ids.txt</p> <p>echo "$(date): Downloading genomes for ids"</p> <p>datasets download genome accession --inputfile genome_ids.txt --filename rep-genomes.zip</p> <p>echo "$(date): Decompressing zip file"</p> <p>unzip rep-genomes.zip</p> <p>echo "$(date): Creating file for mash"</p> <p>cat ncbi_dataset/data/*/*.fna | sed 's/ /_/g' | sed 's/,//g' > rep-genomes.fasta</p> <p>echo "$(date): Skeching rep-genomes.fasta"</p> <p>mash sketch -i -p 20 rep-genomes.fasta -o rep-genomes</p> <p>############################################################</p> <p>echo "$(date): File preparation is complete"</p> <p>ls -alh rep-genomes.fasta</p> <p>ls -alh rep-genomes.msh<br> <br> ```</p>
Sketch of the experiment with movable plasma collector
<p>1 – magnetic coils, 2 – expander tank, 3 – end plate, 4 – movable plasma collector with embedded probes, 5 – limiter</p>
Mash Sketch of RefSeq Bacterial Reference Genomes
<p>The mash reference that can be downloaded from <a href="https://mash.readthedocs.io/en/latest/data.html">the mash documentaion</a> is for RefSeq version 70.</p> <p>I do not inherently have a problem with RefSeq version 70, but RefSeq is well past version 200 now. </p> <p>RefSeq updates four times year, and I needed an easy way to create and distribute a mash sketch file of the representative bacterial/prokaryotic genomes.<br><br>This is intended to be a place to hold the mash sketches from <a href="https://github.com/erinyoung/update_mash_dist">https://github.com/erinyoung/update_mash_dist</a>.<br><br>The mash sketch file from erinyoung/update_mash_dist requires git lfs to be installed when cloning the repository, which is cumbersome for some users.<br><br>The update requency is intended to mirror that of RefSeq (i.e. 4 time a year), but... is likely to be less frequent than that.<br><br>Don't hesitate to <a href="https://github.com/erinyoung/update_mash_dist/issues">submit an issue</a> if this needs to get updated.<br><br>I do have some prior zenodo repositories (https://zenodo.org/records/10519852 , https://zenodo.org/records/7887021 , and https://zenodo.org/records/7348463 ) which hold the same mash sketch reference, but the refseq version is in the title. I'd rather have one repository that gets updated rather than create new repositories each time.<br><br>This is how the mash reference file was created:<br><br></p> <pre><code># Step 1. Download Datasets and Dataformat </code></pre> <pre><code>wget https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets wget https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat chmod +x datasets dataformat</code></pre> <pre><code> # Step 2. Download Mash <br></code></pre> <pre><code> wget https://github.com/marbl/Mash/releases/download/v2.3/mash-Linux64-v2.3.tar tar -xvf mash-Linux64-v2.3.tar </code></pre> <pre><code><br> # Step 3. Get a list of all the genomes # Note: this also changes how some of the names are represented datasets summary genome taxon bacteria --reference --as-json-lines | \ dataformat tsv genome --fields accession,organism-name --elide-header | \ sed 's/\[//g' | \ sed 's/\]//g' | \ sed 's/["'\'']//g' | \ sed 's/endosymbiont of /endosymbiont_of_/g' > \ ids.txt # Step 4. Download the reference files and sketch them # Note: Since this is done in Github Actions (GA), I need to keep everything below 30G. # The best way to do this is to download the process each reference file individually, and then combine it to the whole. # This obviously does not need to be followed if not under those same limitations. while read line do id=$(echo $line | awk '{print $1}') ge=$(echo $line | awk '{print $2}') if [ ! -n "$ge" ] ; then ge="unknown" ; fi sp=$(echo $line | awk '{print $3}') if [ ! -n "$sp" ] ; then sp="unknown" ; fi datasets download genome accession $id unzip ncbi_dataset.zip cp ncbi_dataset/data/*/*_genomic.fna ${ge}_${sp}_${id}.fasta if [ ! -f RefSeqSketches_${version}.msh ] then mash sketch ${ge}_${sp}_${id}.fasta -o RefSeqSketches_${version} else mash sketch ${ge}_${sp}_${id}.fasta -o ${ge}_${sp}_${id} mv RefSeqSketches_${version}.msh tmp.msh mash paste RefSeqSketches_${version} tmp.msh ${ge}_${sp}_${id}.msh rm tmp.msh ${ge}_${sp}_${id}.msh fi rm ${ge}_${sp}_${id}.fasta rm -rf ncbi_dataset/ rm ncbi_dataset.zip rm README.md rm md5sum.txt done < ids.txt</code></pre> <pre><br><br>To use</pre> <pre><code># download file wget <insert url for file> mask sketch sample.fasta RefSeqSketches_<version>.msh > mash_results.txt # These results are unsorted, so many find it useful to sort them. sort -gk3 mash_results.txt > sorted_mash_results.txt</code></pre> <p> <br>The should look like the following:</p> <pre><code>2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_pyogenes_GCF_900475035.1.fasta 0.0116661 0 643/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_dysgalactiae_GCF_016128095.1.fasta 0.0782587 0 107/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_canis_GCF_900636575.1.fasta 0.132399 2.34894e-153 32/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_agalactiae_GCF_001552035.1.fasta 0.164662 1.32611e-72 16/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_castoreus_GCF_000425025.1.fasta 0.174408 2.34302e-58 13/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_didelphis_GCF_000380005.1.fasta 0.182269 8.30736e-49 11/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_uberis_GCF_900475595.1.fasta 0.186761 5.62934e-44 10/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_iniae_GCF_000831485.1.fasta 0.191731 3.33152e-39 9/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_ictaluri_GCF_000188015.2.fasta 0.197292 1.75608e-34 8/1000 2024CK-00429-UT-M03999-240412_contigs.fa Streptococcus_phocae_GCF_001302265.1.fasta 0.203604 2.46548e-30 7/1000</code></pre> <pre> </pre>
CIA Memory Sketch Of The Kalashnikov Rifle
A simple and ugly as sin looking model based on an interesting document from the CIA. In the year in 1953 in Leningrad and Novgorod oblasts (administrative division) certain soldiers were spotted by US CIA spies carrying yet unseen weapons, a new gas operated service rifle later to be known to them as the AK47. But as the said agents did not have the time nor the ability to examine the newly spotted weapon systems closely they had to instead rely on their sight and memory of the rifle when reporting about their finding back to the US. https://www.thefirearmblog.com/blog/wp-content/uploads/2018/03/CIA-First-Memory-Sketch-of-the-Kalashnikov-Rifle-2.jpg As the sketch was solely based on memory it looks really nothing at all like what the actual AK47 would have looked like, even the memorized sketch of the supposed cartridge that the AK47 would have fired was nearly completely wrong. More info on the sketch here https://www.thefirearmblog.com/blog/2018/03/13/cia-first-memory-sketch-of-the-kalashnikov-rifle/ Source: Objaverse 1.0 / Sketchfab
Single-cell datasets for distribution-based sketching
<p>Contains preprocessed single-cell data for sketching single-cell samples. Preprocessed adata objects can be accessed using the 'read_h5ad' function in Scanpy.</p> <ul> <li>The HIV Vaccine Trials Network (HVTN) Flow Cytometry dataset (hvtn_preprocessed.h5ad) was originally downloaded from the Flow Repository under Repository ID FR-FCM-ZZZV (<a href="http://flowrepository.org/id/FR-FCM-ZZZV">http://flowrepository.org/id/FR-FCM-ZZZV</a>).</li> <li>The preeclampsia CyTOF dataset (preeclampsia_preprocessed.h5ad) was originally downloaded from the Flow Repository under Repository ID FR-FCM-ZYRQ (<a href="http://flowrepository.org/id/FR-FCM-ZYRQ">http://flowrepository.org/id/FR-FCM-ZYRQ</a>).</li> <li>The NK-Cell CyTOF dataset (nk_cell_preprocessed.h5ad) from Ref. (<a href="https://www.nature.com/articles/ncomms14825">https://www.nature.com/articles/ncomms14825</a>) was originally downloaded from (<a href="https://github.com/eiriniar/CellCnn">https://github.com/eiriniar/CellCnn</a>).</li> <li>The multiple sclerosis (MS) single-cell RNA sequencing dataset of peripheral blood samples (ms_preprocessed.h5ad) from Ref. (<a href="https://www.nature.com/articles/s41467-019-14118-w">https://www.nature.com/articles/s41467-019-14118-w</a>) was originally accessed from the Gene Expression Omnibus using the accession code GSE138266 (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138266">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138266</a>).</li> </ul>
Linking Sketches and Diagrams to Source Code Artifacts — Supplementary Material
<p>Sketches and diagrams play an important role in the daily work of software developers. If they are archived, they are often detached from the source code they document, because there is no adequate tool support to assist developers in capturing, archiving, and retrieving sketches related to certain source code artifacts. We implemented <em>SketchLink</em> to increasing the value of sketches and diagrams created during software development by supporting developers in these tasks. Our prototype implementation provides a web application that employs the camera of smartphones and tablets to capture analog sketches, but can also be used on desktop computers to upload, for instance, computer-generated diagrams. We also implemented a plugin that embeds the links in Javadoc comments and visualizes them in situ in the source code editor as graphical icons for the IntelliJ Java IDE. Besides being a useful software documentation tool, SketchLink also enables developers to navigate through their source code using the linked sketches and diagrams.</p> <p>This dataset contains:</p> <ul> <li>The source code of the <em>SketchLink</em> server, web application, and IntelliJ plugin.</li> <li>A demo video.</li> <li>Recordings of the user study sessions (audio removed due to confidentiality).</li> <li>The questionnaire and task list used for the plugin study sessions.</li> </ul>
Fig. 7. Sketch profile from the locality 10 in New Stratigraphic Data from the Erlian Basin: Implications for the Division, Correlation, and Definition of Paleogene Lithological Units in Nei Mongol (Inner Mongolia)
Fig. 7. Sketch profile from the locality 10 miles southwest of the Camp Margetts (Granger, 1930).
DrawMon: A Distributed System for Detection of Atypical Sketch Content in Concurrent Pictionary Games
<p>Dataset for training CanvasNet, a model for detecting atypical sketch instances. CanvasNet processes the rendered image as input and outputs a list of atypical activities (if any) along with associated meta-information (atypical content category, 2-D spatial location).</p> <p>For more details, visit our page https://drawm0n.github.io/.</p>
Sketch of The Lalindloch Palace (College of Agriculture, Vellayani) drawn by Noor Fidha P. K. V.
<p>Sketch of The Lalindloch Palace (College of Agriculture, Vellayani) drawn by Noor Fidha P. K. V. </p>
Handmade Data for Sketch Map Creation
<p>Handmade data created for automatic sketch map creation.</p>
Ebutius Dilemma characters and other sketches
<p>Graphics for Ebutius, Calle, and Callum characters created for the onsite and virtual verson of EMOTIVE project Ebutius's Dilemma experience, created for the Antonine Wall Gallery of the Hunterian Museum. More information can be found here: https://emotiveproject.eu/index.php/what-we-do/experiences/</p>
Country Mark Digital Sketch
Source: Objaverse 1.0 / Sketchfab
Optrode Holder Technical Sketch
<p>Technical sketch of an optrode holder, now featured in our published protocol 'Simultaneous recordings of pupil size variation and locus coeruleus activity in mice' (available at <a href="https://star-protocols.cell.com/protocols/3209#article-info" target="_new">https://star-protocols.cell.com/protocols/3209#article-info</a>). This resource enable researchers to replicate and utilize our custom-built optrode holder for various applications, including the one described in our protocol. </p>
Kaveh Zahak Sketch Fab
concept for ancient history shahnameh warriors Source: Objaverse 1.0 / Sketchfab
Sketch Terminology for ArCo CQs
<p>Terminology extracted from the CQs of ArCo by using Sketch as keyword extraction service.</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.