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376 results for “scalable”
Leveraging the strengths of citizen science and structured surveys to achieve scalable inference on population size
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Data from: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
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Cloud-hosted DBMS Performance, Scalability and Availability Evaluation Data
<p>These data sets contain evaluation data for the evaluation objectives performance, scalability and availability of different cloud-hosted, distributed DBMS. </p> <p>The data sets contain the raw performance metrics, monitoring data and evaluation metadata. For the higher-level evaluation objectives scalability and availability, supportive plots are provided.</p> <p><br> The performance and scalability evaluations have been carried out with the <a href="https://dl.acm.org/doi/10.1145/3297663.3310303">Mowgli framework</a> and the availability evaluation have been carried out with the <a href="https://dl.acm.org/doi/abs/10.1145/3341105.3373968">King Louie framework</a>.</p>
HiSS-Cube: A scalable framework for Hierarchical Semi-Sparse Cube that preserves uncertainties
<p>This dataset is used for our framework HiSS-Cube, available at <a href="https://github.com/nadvornikjiri/HiSS-Cube">GitHub</a>. </p> <p>It includes the data folder, the generated HDF5 file (SDSS_cube_gzip.h5) and a contiguous stream export in FITS that can be visualized for example in TOPCAT (SDSS_cutout_export.fits).</p> <p>The data folder contains spectra and images from the SDSS DR14. The documentation for these can be found on the <a href="https://data.sdss.org/datamodel/files/BOSS_PHOTOOBJ/frames/RERUN/RUN/CAMCOL/frame.html">Frame</a> and <a href="https://data.sdss.org/datamodel/files/BOSS_SPECTRO_REDUX/RUN2D/spectra/PLATE4/spec.html">Spectra</a> pages, respectively.</p> <p>The SDSS_cube_gzip.h5 file contains a copy of the data ingested from the data folder optimized for both visualization and stream-lined contiguous access required for example by machine learning algorithms. The purpose is to visualize or run machine learning on combined spectra and images.</p> <p>The SDSS_cube_export.fits contains joined spectra with their respective image cutouts flattened to a table where every row represents one image pixel or spectral "pixel". To visualize these in TOPCAT, choose the 3D Cube plot and RA for X axis, Dec for Z axis and Wavelength or Time for Y axis. Go to the Form tab and choose the "aux" where you can enter either the Mean or Sigma axis as auxiliary.</p> <p> </p>
Replication Package for: Theodolite: Scalability Benchmarking of Distributed Stream Processing Engines in Microservice Architectures
<p>This repository contains a replication package and experimental results for our study <em>Theodolite: Scalability Benchmarking of Distributed Stream Processing Engines in Microservice Architectures</em>.</p> <p>The following description can also be found in the README.md file.</p> <p><strong>Repeating Benchmark Execution</strong></p> <p><em><strong>The following introduction describes how to repeat our scalability experiments. If you plan to conduct your own studies, we suggest to use the latest version of <a href="https://github.com/cau-se/theodolite">Theodolite</a> with significantly enhanced usability.</strong></em></p> <p>The Apache Kafka Streams scalability experiments of our study were executed with <a href="https://github.com/cau-se/theodolite/tree/v0.1.2">Theodolite v0.1.2</a>. To repeat our Kafka Streams experiments:</p> <ol> <li>Clone and install <a href="https://github.com/cau-se/theodolite/tree/v0.1.2">Theodolite v0.1.2</a> according to the official documentation located in <code>execution</code>.</li> <li>Copy the file <code>repeat-kstream.sh</code> into Theodolite's <code>execution</code> directory.</li> <li>Run the repetition file with <code>./repeat-kstream.sh</code> from within the <code>execution</code> directory.</li> </ol> <p>Our Apache Flink benchmark implementations are currently migrated to the latest version of Theodolite. <a href="https://github.com/cau-se/theodolite/tree/apache-flink">Theodolite's <code>apache-flink</code> Branch</a> provides the basis for our Flink scalability experiments. To repeat them:</p> <ol> <li>Clone <a href="https://github.com/cau-se/theodolite/tree/apache-flink">Theodolite's <code>apache-flink</code> Branch</a> and install Theodolite according to the official documentation located in <code>execution</code> (should be identical to the installation for Kafka Streams (see above)).</li> <li>Copy the files <code>repeat-flink-without-checkpointing.sh</code> and <code>repeat-flink-with-checkpointing.sh</code> into Theodolite's <code>execution</code> directory.</li> <li>Switch to the <code>execution</code> directory.</li> <li>Run the first repetition file with <code>./repeat-flink-with-checkpointing.sh</code>.</li> <li>Disable checkpointing by reconfiguring the Kubernetes resources <code>jobmanager-job.yaml</code> and <code>taskmanager-job-deployment.yaml</code> for each benchmark (<code>uc{1,2,3,4}-application</code>) by setting the environment variable <code>CHECKPOINTING</code> to <code>"false"</code>.</li> <li>Run the second repetition file with <code>./repeat-flink-without-checkpointing.sh</code>.</li> </ol> <p><em>Please note that the naming of our benchmarks recently changed. While our publication already uses the new naming, the corresponding Theodolite versions are is still using the old one. Specifically, this means that UC1 in the publication is UC1 in Theodolite, UC2 in the publication is UC3 in Theodolite, UC3 in the publication is UC4 in Theodolite, and UC4 in the publication is UC2 in Theodolite.</em></p> <p><strong>Raw Measurements</strong></p> <p>The results of above benchmark execution can be found in the <code>measurements</code> directory. These are CSV files, containing the measured lag trend over time for a certain subexperiment. Theodolite creates a bunch of additional files, which serve for debugging and preliminary interpretation. As these files are not required for replication, we do not included them in this package.</p> <p>The CSV files are named according to the schema <code>exp{id}_{uc}_{load}_{inst}_totallag.csv</code>, where <code>{id}</code> represents the experiment ID, assigned by Theodolite, <code>{uc}</code> the benchmark name, <code>{load}</code> the generated load, and <code>{inst}</code> the number of evaluated instances.</p> <p>The CSV table <code>experiments.csv</code> provides an overview about the configurations used in each experiment.</p> <p><strong>Reproducing Scalability Analysis</strong></p> <p><em><strong>The following introduction describes how to repeat our scalability analysis, either with our measurements or with your own. If you plan to conduct your own studies, we suggest to use the latest version of <a href="https://github.com/cau-se/theodolite">Theodolite</a> with significantly enhanced usability.</strong></em></p> <p>Analyzing the Theodolite's measurements is done using two Jupyter notebooks. In general, these notebooks should be runnable by any Jupyter server. Python 3.7 or 3.8 is required (e.g., in a virtual environment) as well as some Python libraries, which can be installed via: <code>pip install -r requirements.txt</code>. See the <a href="https://github.com/cau-se/theodolite/tree/master/analysis">Theodolite documentation</a> for additional installation guidance.</p> <p><strong>Obtaining a Scalability Graph as a CSV File</strong></p> <p>The <code>scalability-graph.ipynb</code> notebook combines the measurements (i.e., the <code>totallag.csv</code> files) of one experiment. It produces a CSV file, which provides a mapping of load intensities to minimum required resources for that load (i.e., the scalability graph). The CSV files are named according to the schema <code>exp{id}_min-suitable-instances.csv</code>, where <code>{id}</code> represents the experiment ID. Additional guidance is provided in the notebook.</p> <p><strong>Resulting Scalability Graph CSV Files</strong></p> <p>The <code>results</code> directory provides the scalability graphs for all our executed experiments.</p> <p><strong>Visualization of the Scalability Graph</strong></p> <p>The <code>scalability-graph-plotter.ipynb</code> notebook creates PDF plots of a scalability graph and allows to combine multiple scalability graphs in one plot. It can be adjusted to match the desired visualization.</p> <p><strong>Acknowledgments</strong></p> <p>This research is funded by the German Federal Ministry of Education and Research (BMBF) under grant no. 01IS17084 and is part of the <a href="https://www.industrial-devops.org">Titan project</a>.</p>
Experimental data for the paper "Scalable Fine-Grained Proofs for Formula Processing"
<p>We provide here the binary, options and experimental data for our CADE paper and the companion report.</p> <p><strong>Setup</strong></p> <p>The tarball containing the source code of veriT used in our experiments is available here. The command line parameters of veriT used in each of the configurations described in the paper are:</p> <ul> <li>Basic: "--old-processing --disable-sym --disable-simp --disable-unit-simp --disable-unit-subst-simp --disable-ackermann --disable-bclause"</li> <li>Extended: "--old-processing --disable-sym --disable-unit-simp --disable-unit-subst-simp --disable-ackermann --disable-bclause"</li> <li>Complete: "--old-processing"</li> <li>with proofs: "--proof=/dev/null --proof-with-sharing"</li> <li>with new code: remove parameter "--old-processing"</li> </ul> <p>The benchmarks are from the SMT-LIB categories QF_ALIA, QF_AUFLIA, QF_IDL, QF_LIA, QF_LRA, QF_RDL, QF_UF, QF_UFIDL, QF_UFLIA, QF_UFLRA, AUFLIA, AUFLIRA, UF, UFIDL, UFLIA, and UFLRA.</p> <p>Our experiments were conducted on servers equipped with two Intel Xeon E5-2630 v3 processors, with eight cores per processor, and 126 GB of memory. The time limit was set to 30 s.</p>
Dataset for Article: "Citizen Science Provides a Reliable and Scalable Tool to Track Disease-Carrying Mosquitoes"
<p>This is the dataset used for the analysis in Citizen Science Provides a Reliable and Scalable Tool to Track Disease-Carrying Mosquitoes, by John R.B. Palmer, Aitana Oltra, Francisco Collantes, Juan Antonio Delgado, Javier Lucientes, Sarah Delacour, Mikel Bengoa, Roger Eritja, and Frederic Bartumeus. </p> <p> </p> <p>Copyright &copy; 2017 John R.B. Palmer, Aitana Oltra, Francisco Collantes, Juan Antonio Delgado, Javier Lucientes, Sarah Delacour, Mikel Bengoa, Roger Eritja, and Frederic Bartumeus.</p> <p><br> Dataset for Article: "Citizen Science Provides a Reliable and Scalable Tool to Track Disease-Carrying Mosquitoes" by John R.B. Palmer, Aitana Oltra, Francisco Collantes, Juan Antonio Delgado, Javier Lucientes, Sarah Delacour, Mikel Bengoa, Roger Eritja, and Frederic Bartumeus is licensed under a Creative Commons Attribution 4.0 International License.</p>
Data from "FICTURE: Scalable segmentation-free analysis of sub-micron resolution spatial transcriptomics"
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Performance Measurement Dataset of the HPC Benchmarks FASTEST, Kripke, LULESH, MiniFE, Quicksilver, and RELeARN for Scalability Studies with Extra-P
<p>This dataset contains performance measurements of the HPC benchmarks FASTEST, Kripke, LULESH, MiniFE, Quicksilver, and RELeARN intended to be used for scalability studies with Extra-P (https://github.com/extra-p/extrap). The datasets contains measurements of various application configurations considering several model parameters, e.g., the number of MPI ranks and the input problem size, using weak scaling for each benchmark.</p>
Building a realistic, scalable memory model with independent engrams using a homeostatic mechanism
<p>Code and data for our paper:</p> <p><a href="doi.org/10.3389/fninf.2024.1323203">Building a realistic, scalable memory model with independent engrams using a homeostatic mechanism</a><br>Marvin Kaster, Fabian Czappa, Markus Butz-Ostendorf, Felix Wolf</p>
msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis
<p>This record contains example and result data of msiFlow.</p> <p>msiFlow is a collection of automated workflows for reproducible and scalable multimodal mass spectrometry imaging (MSI) and immunofluorescence microscopy (IFM) data processing and analysis. Using an experimental mouse model for urinary tract infection, induced by uropathogenic E.coli (UPEC), we generated data by</p> <ul> <li>matrix-assisted laser desorption ionisation mass spectrometry imaging with laser-induced postionisation (MALDI-2 MSI) using the Bruker timsTOFfleX instrument</li> <li>transmission-mode MALDI-2 MSI (t-MALDI-2)</li> <li>immunofluorescence microscopy (IFM) using the MACSima system from Miltenyi </li> </ul> <p>msiFlow was tested on MALDI-2 MSI, t-MALDI-2 MSI and IFM data of control and UPEC-infected mouse bladder sections. In IFM we used Ly6G and actin for staining neutrophils and the muscle layer. We validated msiFlow on MALDI MSI data of bone marrow (BM)-derived neutrophils. Tentative lipid annotations were validated by MALDI DDA MSI and MALDI MS/MS. All data used and results generated by msiFlow are included in this dataset (besides the intermediate results of the MALDI-2 preprocessing due to data size).</p> <p>The dataset contains the following zip files:</p> <table> <tbody> <tr> <td><strong>zip file</strong></td> <td><strong>description</strong></td> </tr> <tr> <td>ly6g_heterogeneity.zip</td> <td>example and result data (Ly6G clusters) for molecular_heterogeneity_flow</td> </tr> <tr> <td>if_segmentation.zip</td> <td>example and result data (Ly6G segmentation) for if_segmentation_flow</td> </tr> <tr> <td>ly6g_heterogeneity_signatures.zip</td> <td>example and result data (lipids for Ly6G clusters) for molecular_signatures_flow</td> </tr> <tr> <td>ly6g_molecular_signatures.zip</td> <td>example and result data (lipids for Ly6G) for molecular_signatures_flow</td> </tr> <tr> <td>msi_if_registration.zip</td> <td>example and result data for msi_if_registration_flow</td> </tr> <tr> <td>msi_segmentation.zip</td> <td>example and result data (segmented MSI bladder data) for msi_segmentation_flow</td> </tr> <tr> <td>region_group_analysis.zip</td> <td>example and result data (regulated lipids in different bladder tissue regions) for region_group_analysis_flow</td> </tr> <tr> <td>macsima.zip</td> <td>raw IFM data of UPEC-infected bladders containing Ly6G, actin and autofluorescence images</td> </tr> <tr> <td>maldi-bm-neutrophils.zip</td> <td>raw and pre-processed MALDI MSI data of BM-derived neutrophils</td> </tr> <tr> <td>t-maldi-2.zip</td> <td>raw t-MALDI-2 MSI data of a UPEC-infected bladder section</td> </tr> <tr> <td>maldi-2-<em>group-sampleno</em>.zip</td> <td>raw MALDI-2 MSI data of a control/UPEC bladder section</td> </tr> <tr> <td>MALDI_DDA_MSI.zip</td> <td>raw MALDI MSI data acquired in DDA mode</td> </tr> <tr> <td>TIMS_MS_MS.zip</td> <td>raw MALDI TIMS MS/MS data</td> </tr> </tbody> </table> <p> </p>
Replication Package for: A Configurable Method for Benchmarking Scalability of Cloud-Native Applications
<p>This repository contains a replication package and experimental results for our study <em>A Configurable Method for Benchmarking Scalability of Cloud-Native Applications</em>.</p> <p>It provides benchmark execution files for repeating our experiments as well as the collected data from our experiments and Jupyter notebooks for reproducing our analysis.</p> <p>Instructions for repeating our experiments and reproducing our analysis can be found in the Readme.md file.</p>
Master Thesis Replication Package for: Empirical Scalability Evaluation of Hopping Window Aggregation Methods in Distributed Stream Processing
<p>Master Thesis Replication Package for: Empirical Scalability Evaluation of Hopping Window Aggregation Methods in Distributed Stream Processing</p> <p>A detailed description can be found in the <em>README.md</em>.</p>
MIntO: a Modular and Scalable Pipeline for Microbiome Metagenomic and Metatranscriptomic Meta-omics Data Integration
<p>To illustrate the use of MIntO, a set of 91 human fecal metagenomes from the Inflammatory Bowel Disease Multi’omics Database was selected (IBDMDB). We selected six participants diagnosed as non-IBD (P6018 (nIBD1), M2072 (nIBD2)); Crohn’s disease (H4006 (CD1) and H4020 (CD2)); and ulcerative colitis (H4019 (UC1) and H4035 (UC2)) that were followed for one year each. </p> <p>Here, we present the results from the <em>genome-based assembly-dependent</em> mode, where we used 91 metagenomic high-quality reads<strong> </strong>to recover 163 high-quality MAGs, which constituted a set of non-redundant genomes.</p>
Supporting data and software for the article "Comprehensive and scalable quantification of splicing differences with MntJULiP"
<p>Supporting data and software for the publication "Comprehensive and scalable quantification of splicing differences with MntJULiP".</p>
Artifact for the Scalability Study of the STTT Paper "Analyzing Neural Network Behavior through Deep Statistical Model Checking"
<p>Scripts and infrastructure for the scalability study on DSMC published in the STTT paper "Analyzing Neural Network Behavior through Deep Statistical Model Checking".</p>
Code and data for N Le et. al "Scalable and robust quantum computing on qubit arrays with fixed coupling"
<p>Simulation code and data used in N Le et. al "Scalable and robust quantum computing on qubit arrays with fixed coupling."</p>
Front Data for Scalable GPU-Enabled Creation of Three Dimensional Weather Fronts
<p>Frontal Polylines for 2016 created with the network described in:</p> <p>https://doi.org/10.5194/wcd-3-113-2022</p> <p> </p> <p>The work is supported by the project ``Big Data in Atmospheric Physics<br>(BINARY)'', funded by the Carl Zeiss Foundation (grant P2018-02-003).</p>
Data supporting "A real-time, scalable, fast and resource-efficient decoder for a quantum computer"
<p>Data includes the circuits (stim_circuits.zip) used to create samples to benchmark CC decoder across different noise rates and code sizes. The resulting accuracy and cycle data is in fpga_accuracy_data.csv. The memory footprint (in KB) of the algorithm for different code sizes is in fpga_memory_data.csv.</p> <p>Weights of syndromes for different noise rates for both phenomenological and circuit-level noise at distance d=23 and d=21 are in noise_rate_sampling_full_d23.csv and noise_rate_sampling_full_d21.csv respectively.</p>
Datasets for evaluating SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data
<p>This resource contains pre-processed A. thaliana root , the H. sapiens aortic valve datasets, PBMC Covid atlas and public 10x datasetse used in the paper, SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data. The raw datasets provided in the links below are pre-processed for quality control with respect to both cells and genes. </p> <p>A. thaliana datasets are sourced from the following locations at <a href="https://www.ebi.ac.uk/gxa/sc/home">Single-cell Gene expression Atlas </a>and <a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression Omnibus (GEO)</a>:</p> <ol> <li>E-GEOD-121619 : <a title="E-GEOD-121619" href="https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-121619/results">https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-121619/results</a></li> <li>E-GEOD-152766 : <a href="https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-152766/results">https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-152766/results</a></li> <li>E-GEOD-158761 : <a href="https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-158761/results">https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-158761/results</a></li> <li>E-GEOD-123013 : <a href="https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-123013/results">https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-123013/results</a></li> </ol> <p>H. sapiens datasets are obtained from the NCBI database : <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562645/">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562645/ </a></p> <ol> <li>GSE152766: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152766">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152766</a></li> <li>GSE158761: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158761">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158761</a></li> </ol> <p>All COVID atlas datasets are from: <a href="http://covid19.cancer-pku.cn">http://covid19.cancer-pku.cn</a> . covid_atlas_data1.zip contains the h5ad files and covid_atlas_data2.zip contains the Seurat rds files.</p> <p>PBMC datasets are from the following public sources:</p> <table> <tbody> <tr> <td>Dataset Name</td> <td>Chemistry Version</td> <td>Web Link</td> </tr> <tr> <td>10k Human PBMCs, 3' v3.1, Chromium X</td> <td>v3.1</td> <td><a href="https://www.10xgenomics.com/datasets/10k-human-pbmcs-3-ht-v3-1-chromium-x-3-1-high">https://www.10xgenomics.com/datasets/10k-human-pbmcs-3-ht-v3-1-chromium-x-3-1-high</a></td> </tr> <tr> <td>20k Human PBMCs, 3' HT v3.1, Chromium X</td> <td>v3.1</td> <td><a href="https://www.10xgenomics.com/datasets/20-k-human-pbm-cs-3-ht-v-3-1-chromium-x-3-1-high-6-1-0">https://www.10xgenomics.com/datasets/20-k-human-pbm-cs-3-ht-v-3-1-chromium-x-3-1-high-6-1-0</a></td> </tr> <tr> <td>10k Human PBMCs, 3' v3.1, Chromium Controller</td> <td>v3.1</td> <td><a href="https://www.10xgenomics.com/datasets/10k-human-pbmcs-3-v3-1-chromium-controller-3-1-high">https://www.10xgenomics.com/datasets/10k-human-pbmcs-3-v3-1-chromium-controller-3-1-high</a></td> </tr> <tr> <td>Healthy PBMC Chromium Connect (channel 1)</td> <td>v3.1</td> <td><a href="https://www.10xgenomics.com/datasets/peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-chromium-connect-channel-1-3-1-standard-3-1-0">https://www.10xgenomics.com/datasets/peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-chromium-connect-channel-1-3-1-standard-3-1-0</a></td> </tr> <tr> <td>Healthy PBMC Chromium Connect (channel 5)</td> <td>v3.1</td> <td><a href="https://www.10xgenomics.com/datasets/peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-chromium-connect-channel-5-3-1-standard-3-1-0">https://www.10xgenomics.com/datasets/peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-chromium-connect-channel-5-3-1-standard-3-1-0</a></td> </tr> <tr> <td>10k PBMCs from a Healthy Donor (v3 chemistry)</td> <td>v3.0</td> <td><a href="https://www.10xgenomics.com/datasets/10-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0">https://www.10xgenomics.com/datasets/10-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0</a></td> </tr> <tr> <td>1k PBMCs from a Healthy Donor (v2 chemistry)</td> <td>v2.0</td> <td><a href="https://www.10xgenomics.com/datasets/1-k-pbm-cs-from-a-healthy-donor-v-2-chemistry-3-standard-3-0-0">https://www.10xgenomics.com/datasets/1-k-pbm-cs-from-a-healthy-donor-v-2-chemistry-3-standard-3-0-0</a></td> </tr> <tr> <td>1k PBMCs from a Healthy Donor (v3 chemistry)</td> <td>v3.0</td> <td><a href="https://www.10xgenomics.com/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0">https://www.10xgenomics.com/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0</a></td> </tr> <tr> <td>Fresh 68k PBMCs (Donor A)</td> <td>v1.0</td> <td><a href="https://www.10xgenomics.com/datasets/fresh-68-k-pbm-cs-donor-a-1-standard-1-1-0">https://www.10xgenomics.com/datasets/fresh-68-k-pbm-cs-donor-a-1-standard-1-1-0</a></td> </tr> <tr> <td>Frozen PBMCs (Donor A)</td> <td>v1.0</td> <td><a href="https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-a-1-standard-1-1-0">https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-a-1-standard-1-1-0</a></td> </tr> <tr> <td>Frozen PBMCs (Donor B)</td> <td>v1.0</td> <td><a href="https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-b-1-standard-1-1-0">https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-b-1-standard-1-1-0</a></td> </tr> <tr> <td>Frozen PBMCs (Donor C)</td> <td>v1.0</td> <td><a href="https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-c-1-standard-1-1-0">https://www.10xgenomics.com/datasets/frozen-pbm-cs-donor-c-1-standard-1-1-0</a></td> </tr> <tr> <td>PBMCs from a Healthy Donor: Whole Transcriptome Analysis</td> <td>v3.1</td> <td><a href="https://www.10xgenomics.com/datasets/pbm-cs-from-a-healthy-donor-whole-transcriptome-analysis-3-1-standard-4-0-0">https://www.10xgenomics.com/datasets/pbm-cs-from-a-healthy-donor-whole-transcriptome-analysis-3-1-standard-4-0-0</a></td> </tr> <tr> <td>PBMC 600K</td> <td>v1</td> <td><a href="https://www.ebi.ac.uk/gxa/sc/experiments/E-HCAD-4/downloads">https://www.ebi.ac.uk/gxa/sc/experiments/E-HCAD-4/downloads</a></td> </tr> <tr> <td>GSM4560071</td> <td>v2.0</td> <td><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560071">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560071</a></td> </tr> <tr> <td>GSM4560074</td> <td>v2.0</td> <td><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560074">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560074</a></td> </tr> <tr> <td>GSM4560070</td> <td>v2.0</td> <td><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560070">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4560070</a></td> </tr> </tbody> </table> <p>References for the Datasets :</p> <ol> <li>H. sapiens dataset: Kang Xu, Shangbo Xie,Yuming Huang,Tingwen Zhou, Ming Liu, Peng Zhu, Chunli Wang, Jiawei Shi, Fei Li,Frank W. Sellke and Nianguo Dong (2020) Cell-Type Transcriptome Atlas of Human Aortic Valves Reveal Cell Heterogeneity and Endothelial to Mesenchymal Transition Involved in Calcific Aortic Valve Disease.</li> <li>E-GEOD-152766: Shahan R, Hsu C, Nolan TM, Cole BJ, Taylor IW et al. (2020) A single cell Arabidopsisroot atlas reveals developmental trajectories in wild type and cell identity mutants.</li> <li>E-GEOD-121619: Jean-Baptiste K, McFaline-Figueroa JL, Alexandre CM, Dorrity MW, Saunders L et al. (2019) Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana.</li> <li>E-GEOD-123013: Ryu KH, Huang L, Kang HM, Schiefelbein J. (2019) Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells.</li> <li>E-GEOD-158761: Gala HP, Lanctot A, Jean-Baptiste K, Guiziou S, Chu JC et al. (2020) A single cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana.</li> <li>COVID Atlas Reference: Xianwen Ren, Wen Wen, Xiaoying Fan et.al. (2021) COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas</li> <li>PBMC data are downloaded from respective links</li> </ol>
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.