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Dataset results
5 results for “Multithreading”
PSnpBind: A database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow
<p>A key concept in drug design is how natural variants, especially the ones occurring in the binding site of drug targets, affect the inter-individual drug response and efficacy by altering binding affinity. These effects have been studied on very limited and small datasets while, ideally, a large dataset of binding affinity changes due to binding site single-nucleotide polymorphisms (SNPs) is needed for evaluation. However, to the best of our knowledge, such a dataset does not exist. Thus, a reference dataset of ligands binding affinities to proteins with all their reported binding sites’ variants was constructed using a molecular docking approach. Having a large database of protein-ligand complexes covering a wide range of binding pocket mutations and a large small molecules’ landscape is of great importance for several types of studies. For example, developing machine learning algorithms to predict protein-ligand affinity or a SNP effect on it requires an extensive amount of data. In this work, we present PSnpBind: A large database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. It provides a web interface to explore and visualize the protein-ligand complexes and a REST API to programmatically access the different aspects of the database contents. PSnpBind is freely available at <a href="https://psnpbind.org">https://psnpbind.org</a>.<strong> </strong>The source code of the tools used in constructing PSnpBind is available on <a href="https://github.com/ammar257ammar/PSnpBind-Build">GitHub</a>.</p>
MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification
<p>These files provide supplementary data underlying the article <a title="https://doi.org/10.1093/bioinformatics/btae601" href="https://doi.org/10.1093/bioinformatics/btae601" target="_blank" rel="noopener noreferrer nofollow">doi.org/10.1093/bioinformatics/btae601</a> (see Figure 1 in the article):</p> <ul> <li>37345_filtered_training_and_test_genomes_list.txt: Refseq assembly sequence filenames of the 37345 filtered training and test genomes</li> <li>taxonomy_37345_filtered_training_and_test_genomes.txt: Taxonomy file for all 37345 filtered training and test genomes</li> <li>Uniform_reference_database_31991_training_genomes_assemblyID_list.txt: Refseq assembly accessions of the 31991 training genomes in the uniform reference database</li> <li>uniform_reference_database.tar.gz_1 to uniform_reference_database.tar.gz_10: Merge them into a single file using the <em>cat</em> command. The folder produced by decompressing this file is the uniform reference database.</li> <li>taxonomy_uniform_reference_database.txt: Taxonomy file for the uniform reference database (i.e. the 31991 training genomes)</li> <li>5354_test_genomes_assemblyID_list.txt: Refseq assembly accessions of the 5354 test genomes</li> <li>testReads_NextSeq_C0.05.fasta.gz: 6562565 150bp-long positive reads randomly generated from the 5354 test genomes, simulating reads sequenced by NextSeq (0.05 coverge)</li> <li>testReads_MiSeq_C0.05.fasta.gz: 3282728 300bp-long positive reads randomly generated from the 5354 test genomes, simulating reads sequenced by MiSeq (0.05 coverge)</li> <li>testReads_Nanopore_C0.05.fasta.gz: 181912 positive reads of normally distributed 1kb-10kb lengths randomly generated from the 5354 test genomes, simulating reads sequenced by Nanopore (0.05 coverge)</li> <li>negaReads_NextSeq_C0.05.fasta.gz: 10143 150bp-long negative reads randomly generated from Chromosome 1 of the Arabidopsis Thaliana reference genome, simulating reads sequenced by NextSeq (0.05 coverge)</li> <li>negaReads_MiSeq_C0.05.fasta.gz: 5072 300bp-long negative reads randomly generated from Chromosome 1 of the Arabidopsis Thaliana reference genome, simulating reads sequenced by MiSeq (0.05 coverge)</li> <li>negaReads_Nanopore_C0.05.fasta.gz: 277 negative reads of normally distributed 1kb-10kb lengths randomly generated from Chromosome 1 of the Arabidopsis Thaliana reference genome, simulating reads sequenced by Nanopore (0.05 coverge)</li> <li>CAMI2_reference_database_16864_genomes_list.txt: Refseq assembly sequence filenames of the 16864 genomes and chromosomes in the reference database for CAMI2</li> <li>taxonomy_CAMI2_reference_database.txt: Taxonomy file for the CAMI2 reference database</li> </ul> <p><strong>Tip</strong>: To directly use the taxonomy file "taxonomy_uniform_reference_database.txt", please use version v1.1 or earlier of the MNBC tool. If using later versions it needs regenerating with the "MNBC taxonomy" program.</p>
MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification
<p>These files provide supplementary data underlying the article <a title="https://doi.org/10.1093/bioinformatics/btae601" href="https://doi.org/10.1093/bioinformatics/btae601" target="_blank" rel="noopener noreferrer nofollow">doi.org/10.1093/bioinformatics/btae601</a>:</p> <ul> <li>CAMI2_reference_database.tar.gz_1 to CAMI2_reference_database.tar.gz_6: Merge them into a single file using the <em>cat</em> command. The folder produced by decompressing this file is the reference database for CAMI2 (RefSeq sequence filenames are in the file CAMI2_reference_database_16864_genomes_list.txt at <a href="https://dx.doi.org/10.5281/zenodo.10568965">https://dx.doi.org/10.5281/zenodo.10568965</a>).</li> </ul> <p> </p>
MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification
<p>These files provide supplementary data underlying the article <a title="https://doi.org/10.1093/bioinformatics/btae601" href="https://doi.org/10.1093/bioinformatics/btae601" target="_blank" rel="noopener noreferrer nofollow">doi.org/10.1093/bioinformatics/btae601</a> (see Figure 1 of the article):</p> <ul> <li>37345_filtered_training_and_test_genomes_sequence_files.tar.gz_1 to 37345_filtered_training_and_test_genomes_sequence_files.tar.gz_6: Merge them into a single file using the <em>cat</em> command. The folder produced by decompressing this file contains the filtered RefSeq sequence files of all 37345 training and test genomes, which were used to build the uniform reference database and generate the test reads (The filenames are in the file 37345_filtered_training_and_test_genomes_list.txt at <a href="https://dx.doi.org/10.5281/zenodo.10568965">https://dx.doi.org/10.5281/zenodo.10568965</a>).</li> </ul>
Artifacts for the FDL21 Paper: In-Vivo Stack Overflow Detection and Stack Size Estimation for Low-End Multithreaded Operating Systems using Virtual Prototypes
<p>Artifacts for the evaluation of the paper <em>In-Vivo Stack Overflow Detection and Stack Size Estimation for Low-End Multithreaded Operating Systems using Virtual Prototypes</em> which will be published as part of <a href="http://www.fdl-conference.org">FDL21</a>. The artifacts provided here use pre-compiled binaries and pre-generated stack usage databases. Based on these provided files, the stack size estimation and performance evaluation performed in the paper can be replicated. Various README.md files, which provide more information on individual artifacts, are also included.</p> <p>The software used in conjunction with these artifacts is also freely available on GitHub:</p> <ul> <li>https://github.com/agra-uni-bremen/fdl21-stackuse-vp</li> <li>https://github.com/agra-uni-bremen/stack-usage-db</li> </ul>
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.