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The North Pacific Eukaryotic Gene Catalog: Raw assemblies from Gradients 1, 2 and 3
<p>The North Pacific Eukaryotic Gene Catalog consolidates eukaryotic metatranscriptome data from three latitudinal transects of the North Pacific transition zone and one cruise in the subtropical gyre. Metatranscriptomes were gathered from latitudinally-resolved surface samples, and diel-resolved temporal studies, with samples taken in triplicate or duplicate and collected on 0.2-100 μm, 0.2-3 μm, and 3 μm-100 or 200 μm size fractions. These metatranscriptome data were <em>de novo</em> assembled into 175 independent assemblies, totalling 182 million clustered nucleotide contigs. Assemblies were annotated by taxonomy and function. This catalog provides assembled environmental contigs, their translated peptide sequences, and their taxonomic and functional annotations with the aim of facilitating continued discoveries about the molecular ecology of microbial eukaryotes in the North Pacific.<br><br>A full description of this data is published in Scientific Data, available here: <a href="https://www.nature.com/articles/s41597-024-04005-5" target="_blank" rel="noopener">The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations</a>. Please cite this publication if your research uses this data:<br><br>Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. <em>Scientific Data</em>, <em>11</em>(1), 1161.</p> <div> <p>This dataset repository is associated with a codebase and documentation repository:<br><a href="https://github.com/armbrustlab/NPac_euk_gene_catalog" target="_blank" rel="noopener">https://github.com/armbrustlab/NPac_euk_gene_catalog</a><br>Please see this code repository for additional data and project updates<br><br>Translated and processed protein sequences and their annotations are available in this repository: <br><a href="../doi/10.5281/zenodo.10472589">https://zenodo.org/doi/10.5281/zenodo.10472589</a><br><br>99% identity clustered nucleotide sequences and kallisto enumerations are available here:<br><a href="../doi/10.5281/zenodo.10570448">https://zenodo.org/doi/10.5281/zenodo.10570448</a></p> </div> <div> <p>File contents: this repository contains five .tar.gz compressed tarballs with raw de novo Trinity assemblies of poly-A selected metatranscriptomes from the Gradients 1 through 3 cruises, and a plain-text file with the custom spike-in mRNA standards (CustomStandardSequences.txt)</p> </div> <div> <p><strong><br>Gradients1.KOK1606.PA.assemblies.tar.gz</strong><br>- Link to <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/tree/main/projects/G1PA" target="_blank" rel="noopener">G1PA project github page</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/KOK1606" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/KOK1606</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G1PA.process_short_reads.sh" target="_blank" rel="noopener">G1PA.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G1PA.trinity_assemblies.sh" target="_blank" rel="noopener">G1PA.trinity_assemblies.sh</a></p> </div> <div> <p><strong><br>Gradients2.MGL1704.PA.assemblies.tar.gz</strong><br>- Link to <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/tree/main/projects/G2PA" target="_blank" rel="noopener">G2PA project github page</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/MGL1704" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/MGL1704</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G2PA.process_short_reads.sh" target="_blank" rel="noopener">G2PA.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G2PA.trinity_assemblies.sh" target="_blank" rel="noopener">G2PA.trinity_assemblies.sh</a></p> </div> <div> <p><strong><br>Gradients3.KM1906.PA.assemblies.tar.gz</strong><br>- Link go <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/tree/main/projects/G3PA" target="_blank" rel="noopener">G3PA project github page</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/KM1906" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/KM1906</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G3PA_UW.process_short_reads.sh" target="_blank" rel="noopener">G3PA_UW.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G3PA_UW.trinity_assemblies.sh" target="_blank" rel="noopener">G3PA_UW.trinity_assemblies.sh</a></p> </div> <div> <p><strong><br>G3_diel.KM1906.PA.assemblies.tar.gz</strong><br>- Link go <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/tree/main/projects/G3PA" target="_blank" rel="noopener">G3PA project github page</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/KM1906" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/KM1906</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G3PA_diel.process_short_reads.sh" target="_blank" rel="noopener">G3PA_diel.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G3PA_diel.trinity_assemblies.sh" target="_blank" rel="noopener">G3PA_diel.trinity_assemblies.sh</a></p> </div> <div> <p><strong><br>CustomStandardSequences.txt<br></strong>- Plain-text FASTA file with the spike-in standards used during mRNA extraction and sequencing prep<br>- Link to publication of spike-in standards methods: <a href="https://www.nature.com/articles/s41564-019-0507-5" target="_blank" rel="noopener">https://www.nature.com/articles/s41564-019-0507-5</a></p> </div> <div> <p>The 2015 SCOPE Diel metatranscriptome raw assemblies have been released in a previous Zenodo repository, and are not included again in this deposition. We provide the links to the Diel1 resources here:<br>- Diel1 raw metatranscriptome assembly Zenodo repository: <a href="../records/5009803" target="_blank" rel="noopener">https://zenodo.org/records/5009803</a><br>- Dataset DOI: <a href="https://doi.org/10.5281/zenodo.5009803" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.5009803</a><br>- Associated publication: <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2021.682651/full" target="_blank" rel="noopener">https://www.frontiersin.org/articles/10.3389/fmicb.2021.682651/full</a><br>- Codebase: <a href="https://github.com/armbrustlab/diel_eukaryotes" target="_blank" rel="noopener">https://github.com/armbrustlab/diel_eukaryotes</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/KM1513" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/KM1513</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/D1PA.process_short_reads.sh" target="_blank" rel="noopener">D1PA.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/D1PA.trinity_assemblies.sh" target="_blank" rel="noopener">D1PA.trinity_assemblies.sh</a></p> </div> <p><br><br></p>
RMTable Consolidated Catalog of Faraday Rotation Measures of Astronomical Radio Sources
<p>This is a catalog of Faraday rotation measures (and other related properties) of astronomical radio sources, consolidated from many published catalogs in the astronomical literature from 1980 to the present day. These catalogs have been converted to the RMTable standard and stored in 3 formats: FITS binary table, tab-seperated-value ASCII, and VOTable XML.</p> <p>These catalog files can be read by any suitable reader, but we have created a Python module, RMTable (https://github.com/CIRADA-Tools/RMTable), which streamlines the process of interacting with and creating new RMTables.</p>
Tabular Data for "A Comprehensive Catalog of UVIT Observations I: Catalog Description and First Release of Source Catalog (UVIT DR1)"
<p>The first comprehensive catalog of UVIT includes the sources from the observations between 2016 and 2017. </p> <p>The catalog is formatted according to the machine-readable format used by the AAS Journals and CDS/VizieR. Specific information on the structure of MRT files can be found at:</p> <p><span> </span>AAS: <a href="https://journals.aas.org/mrt-overview/"><span>https://journals.aas.org/mrt-overview/</span></a></p> <p><span> </span>CDS: <a href="http://cds.u-strasbg.fr/doc/catstd.htx"><span>http://cds.u-strasbg.fr/doc/catstd.htx</span></a></p> <p><span> </span>These files can be read in python using the astropy package<span> </span>or with the most recent version of TOPCAT (> Version 4.8)</p>
Catalog of stool metagenome-assembled genomes from patients with different cancer types
<p><strong>A non-redundant catalog of 3,816 genomes with at least 75% completeness and no more than 15% contamination assembled from metagenomes. Samples of 976 metagenomes were obtained from patients receiving immunotherapy for the treatment of different types of cancers.</strong></p>
Coastal and Marine Ecological Classification Standard (CMECS) Catalog
<p>The <strong>Coastal and Marine Ecological Classification Standard (CMECS) Catalog</strong> is the authoritative collection of ecological units (terms + definitions) and unit relationships (the CMECS classification framework).</p> <p>The CMECS Catalog is the complete representation of the CMECS classification. It contains all units that are or have been members of the CMECS classification throughout its lifecycle, as well as various annotations that provide metadata for each unit that enable Findability, Accessibility, Interoperability, and Reuse (FAIR, <a href="https://www.go-fair.org/fair-principles/" rel="nofollow">https://www.go-fair.org/fair-principles/</a>). The CMECS Catalog (cmecs.owl) file is stored and managed in a Git repository; authoritative versions are publicly released via <a href="https://github.com/NOAA-OCM/cmecs" target="_blank" rel="noopener">the NOAA-OCM/cmecs GitHub</a> as changes are made. Version releases also include the CMECS Catalog in CSV and XLSX formats. A browsable text output of the CMECS Catalog ecological units and implementation guidance, the <a href="https://github.com/NOAA-OCM/cmecs/wiki/CMECS-Thesaurus-Quick-Link"><strong>CMECS Thesaurus</strong></a>, is also available in PDF and MD formats.</p> <p>This release includes changes to the Substrate Component Unit Codes and fixes to Biotic Component typographical errors. Details are available on the <a href="https://github.com/NOAA-OCM/cmecs/releases/tag/v1.1.1" target="_blank" rel="noopener">CMECS GitHub v1.1.1 Release Page.</a></p> <p><strong>Questions? Please contact the CMECS Implementation Group at ocm.cmecs-ig@noaa.gov</strong></p> <p>For more information about the CMECS Catalog, see the <a href="https://github.com/NOAA-OCM/cmecs/wiki">https://github.com/NOAA-OCM/cmecs/wiki.</a></p> <p>For more information about CMECS, including technical guidance and classification examples, visit the <a href="https://iocm.noaa.gov/standards/cmecs-home.html" rel="nofollow">NOAA Integrated Ocean and Coastal Mapping (IOCM) team's CMECS webpage</a>.</p> <p>CMECS follows a Dynamic Standard Process to review and adopt changes that are proposed by the CMECS user community when necessary. More information about CMECS maintenance can be found on the <a href="https://www.ncei.noaa.gov/products/coastal-marine-ecological-classification-standard" rel="nofollow">NOAA National Centers for Environmental Information (NCEI) CMECS webpage</a> under the <strong>Vocabulary Maintenance</strong> section, along with instructions for proposing revisions to CMECS and a form for submitting proposals.</p>
A Catalog of Natural Channelrhodopsins
<p>This repository is an appendix to the publication <a href="https://doi.org/10.1016/j.cub.2020.09.056">[Rozenberg20](10.1016/j.cub.2020.09.056)</a>, "Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses", that is intended to keep the list of the channelrhodopsins (ChRs) presented there as a constantly updated resource that includes updates to the old records, addition of novel unpublished entries, entries from newly published experiments and corrections to the previously published sets.</p> <p>Most of the credit belongs to the projects that generated and assembled the data that ultimately contained the ChRs (especially, <a href="https://doi.org/10.1371/journal.pbio.1001889">[MMETSP_Keeling14](10.1371/journal.pbio.1001889)</a> and <a href="https://doi.org/10.1038/s41586-019-1693-2">[1KP_initiative19](10.1038/s41586-019-1693-2)</a>) and to the experimentalists who took the challenge of characterizing them. The catalog currently focuses mostly but not exclusively on proteins from cultured organisms.</p> <p>Although the format might eventually change, the current version of the catalog is composed of two xlsx spreadsheets:</p> <ul> <li>Channelrhodopsins_Original_List.xlsx that represents the original ChR list with additional metadata, but without changes to the sequences and additions and without changing the classification of the ChRs. This file will remain unchanged throughout releases. It contains the following fields: <ul> <li>ID - integer index</li> <li>Sequence name - unique name of the sequence</li> <li>Is outgroup (not ChR) - flag indicating whether the sequence is not a ChR (a small number of rhodopsins inherited from <a href="https://dx.doi.org/10.1038%2Fnmeth.2836">[Klapoetke14](10.1038/nmeth.2836)</a> belonged to different families)</li> <li>Symbol - gene symbol, short alias</li> <li>Species - source species/strain</li> <li>Taxonomic group - taxonomic affiliation of the species</li> <li>ChR group - clade name, if empty indicates clades unknown back then</li> <li>Bioproject - NCBI bioproject for the sequence</li> <li>Sequence source - initiative/database/publication the gene nucleotide sequence was part of</li> <li>Activity - activity confirmed for the exact sequence (potentially, a shorter version or in rare cases an allelic variant thereof). In the original list, selectivity (cation/anion) was indicted for all ChRs with demonstrated channel activity even if selectivity could not be or was not assessed experimentally.</li> <li>Reference - publication(s) where the activity was demonstrated</li> <li>Full-length 98%-identity clustering: <ul> <li>Representative - representative sequence for the cluster with an identity of 98%</li> <li>Cluster - cluster number</li> <li>Identity - identity % to the reference</li> </ul> </li> <li>Rhodopsin-domain 100%-identity clustering: <ul> <li>Representative - representative sequence for the cluster with an identity of 100% after the 98%-identity clusters were aligned and trimmed to include only the rhodopsin domain</li> <li>Cluster - cluster number</li> </ul> </li> <li>Sequence - full protein sequence for the entry (this might be the complete sequence of the gene, partial sequence of the gene that was not recovered entirely in the assembly or sequence of a specific construct used for expression)</li> <li>Is partial sequence - flag indicating whether the rhodopsin domain is truncated</li> <li>Has indels - flag indicating whether the rhodopsin domain contains indels (unspliced introns in transcripts, gene annotation artifacts)</li> <li>Sequence completeness comment - comments about the nature of the indels</li> </ul> </li> <li>Channelrhodopsins_Updated_List.xlsx includes amended ChR sequences, manually added entries and novel expressed or otherwise published proteins. In this release all of the sequences with complete rhodopsin domains are assigned to a family (some families have only provisional names). The spreadsheet is structured differently from the first one and focuses more on the unique complete sequences by separating genes from constructs that are derived from them. The redundancy of the dataset was further reduced by combining identical sequences. Highly similar sequences are treated mostly separately. In some cases they have been downgraded to allelic or splice variants, but this is not yet consistent. There are now three sheets: <ul> <li>full_channelrhodopsins - full ChR sequences</li> <li>fragmented_channelrhodopsins - ChR sequences with incomplete rhodopsin domains</li> <li>not_channelrhodopsins - additional proteins that have been mentioned in ChR datasets that are not from the ChR family</li> </ul> </li> <li>The sheets have the following fields: <ul> <li>ID - integer index corresponding to the record (new records have IDs >875).</li> <li>Sequence name - this is the chosen sequence name for the longest version of the sequence</li> <li>Version - sequence version. Sequences get updated and increment their versions in the following cases: <ul> <li>the correct start codon was identified</li> <li>a full sequence for the gene was found in an alternative database</li> <li>a full sequence for the gene has been obtained or corrected from the raw data</li> <li>gene annotation artifacts have been corrected manually based for the genomic sequence</li> <li>unspliced introns were found and removed</li> </ul> </li> <li>Reviewed - a somewhat arbitrary flag indicating whether the complete sequence has been manually reviewed</li> <li>Constructs - NCBI protein accessions of constructs overlapping with the gene indicating the overlapping region. Note that construct are allowed to overlap multiple full-length genes even from nominally different species.</li> <li>Symbol - short gene alias</li> <li>Species - species from which the longest representative sequence belongs</li> <li>Taxonomic group</li> <li>ChR group - ChR affiliation based on phylogeny</li> <li>ChR supergroup - ChR supergroup (A: ACRs and green algal CCRs, B: "bacteriorhodopsin-like" CCRs, D: the clade of dinoflagellate and related colpodellid ChRs)</li> <li>Bioproject - bioproject accession(s) for the data from which the sequence is derived</li> <li>Sequence source - one or multiple sources for the sequence, preference is given to earlier released publications</li> <li>Source type - the kind of source(s) (e.g. genome/transcriptome) the sequence comes from</li> <li>First mention - reference for the source where the gene was first indicated as a ChR. Notice that with highly similar sequences this is sometimes tricky.</li> <li>Currents - channeling activity. This differentiates between confirmed and unconfirmed selectivities: square brackets specify the likely but unconfirmed selectivity</li> <li>Cation selectivity - further details on selectivity of cation ChRs</li> <li>Currents reference</li> <li>Absorption maximum, nm</li> <li>Action maximum, nm</li> <li>Spectra references</li> <li>Spectra comment</li> <li>Representative sequence from [Rozenberg20] - representative highly similar sequence (this is inherited from the from the original file: full-length 98% clustering > rhodopsin domain 100% clustering)</li> <li>Sequence - the amino acid sequence</li> <li>Superseded identical sequences - identical sequences included in the same record (with species/strain indicated if different)</li> <li>Splice variants - putative minor splice variants from the same species/strain</li> <li>Allelic variants - putative minor allelic variations from the same species/strain</li> <li>Superseded included sequences - shorter sequences included in the record</li> <li>Superseded incorrect sequences - other sequences that are different due to artifacts</li> <li>Version comments - brief version history</li> <li>Other comments</li> </ul> </li> </ul> <p>Starting from version 2.0, the repository also contains:</p> <ul> <li>Channelrhodopsins_Alphafold3_structures.zip - raw alphafold3 structures of all of the complete ChRs with retinal.</li> </ul> <p>This is work in progress, use with care. If a formal citation is needed, please cite <a href="https://doi.org/10.1016/j.cub.2020.09.056">[Rozenberg20](10.1016/j.cub.2020.09.056)</a>, "Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses" and <a href="https://www.science.org/doi/10.1126/sciadv.add7729">[Vierock22](10.1126/sciadv.add7729)</a>, "WiChR, a highly potassium selective channelrhodopsin for low-light one- and two-photon inhibition of excitable cells". For the most recent phylogeny of ChRs see <a href="https://doi.org/10.7554/eLife.90100.1">[Oppermann23](10.7554/eLife.90100.1)</a>, "Robust optogenetic inhibition with red-light-sensitive anion-conducting channelrhodopsins", and <a href="https://github.com/BejaLab/ACRs">https://github.com/BejaLab/ACRs</a>.</p>
VTSCat: The VERITAS Catalog of Gamma-Ray Observations
<p><strong>VTSCat</strong> is the catalog of high-level data products from all publications of the <a href="https://veritas.sao.arizona.edu/">VERITAS collaboration</a>.</p> <p><strong>Most recent versions of VTSCat are available through https://doi.org/10.5281/zenodo.6988967</strong></p> <p>The <strong>VTSCat</strong> data collection contains:</p> <ul> <li>high-level data like spectral flux points, light curves, spectral fits in human- and machine-readable yaml and ecsv file format</li> <li>tabled data like upper limits tables from dark matter searches or results on the extragalactic background in ecsv file format</li> <li>sky maps (wherever available) in FITS file format</li> </ul> <p>The data collection contains results from gamma-ray measurements only. This is a pre-release for testing and early publications.</p> <p>A forthcoming research note will provide more details on the catalog. Please check the README file and all documentation linked to the README.</p> <p>VTSCat supplements the HEASARC catalogue of VERITAS results (to be published). VTSCat is inspired and derived from <a href="https://github.com/gammapy/gamma-cat">gamma-cat</a>.</p> <p>If you are a previous VERITAS author and would like to be associated with this repository, please send an email to G. Maier.</p> <p><strong>Access</strong>:</p> <ul> <li>GitHub: <a href="https://github.com/VERITAS-Observatory/VERITAS-VTSCat">https://github.com/VERITAS-Observatory/VERITAS-VTSCat</a></li> </ul> <p><strong>References</strong>:</p> <ul> <li>VERITAS: <a href="https://veritas.sao.arizona.edu/">https://veritas.sao.arizona.edu/</a></li> <li>VER Dictionary of Nomenclature: <a href="https://cds.u-strasbg.fr/cgi-bin/Dic-Simbad?/17350620">https://cds.u-strasbg.fr/cgi-bin/Dic-Simbad?/17350620</a></li> </ul>
Interactive Visualizations for: "Virgo Filaments II: Catalog and First Results on the Effect of Filaments on galaxy properties"
<p>This deposit includes 13 HTML 3D interactive visualizations of filaments and galaxies investigated in the accepted article, "<em>Virgo Filaments II: Catalog and First Results on the Effect of Filaments on galaxy properties</em>" by Castignani et al. (accepted, 20-Oct-2021).</p> <p>The specific files correspond to the filaments listed in Table 2 of the accepted manuscript:</p> <table align="left"> <caption>Tabulated HTML files and filaments</caption> <thead> <tr> <th scope="col">HTML File</th> <th scope="col">Filament (Table 2)</th> </tr> </thead> <tbody> <tr> <td> <p>SG_cube_Virgo_Serpens_Filament.html</p> </td> <td> <p>Serpens F.</p> </td> </tr> <tr> <td> <p>SG_cube_Virgo_Coma_Berenices_Filament.html</p> </td> <td> <p>Coma Berenices F.</p> </td> </tr> <tr> <td> <p>SG_cube_VirgoIII_Filament.html</p> </td> <td> <p>VirgoIII F.</p> </td> </tr> <tr> <td> <p>SG_cube_Ursa_Major_Cloud.html</p> </td> <td> <p>Ursa Major Cloud</p> </td> </tr> <tr> <td> <p>SG_cube_NGC5353_4_Filament.html</p> </td> <td> <p>NGC5353/4 F.</p> </td> </tr> <tr> <td> <p>SG_cube_Leo_Minor_Filament.html</p> </td> <td> <p>Leo Minor F.</p> </td> </tr> <tr> <td> <p>SG_cube_LeoII_B_Filament.html</p> </td> <td> <p>LeoII B F.</p> </td> </tr> <tr> <td> <p>SG_cube_Canes_Venatici_Filament.html</p> </td> <td> <p>Canes Venatici F</p> </td> </tr> <tr> <td> <p>SG_cube_W-M_Sheet.html</p> </td> <td> <p>W-M Sheet</p> </td> </tr> <tr> <td> <p>SG_cube_Virgo_Draco_Filament.html</p> </td> <td> <p>Draco F.</p> </td> </tr> <tr> <td> <p>SG_cube_Virgo_Bootes_Filament.html</p> </td> <td> <p>Bootes F.</p> </td> </tr> <tr> <td> <p>SG_cube_Leo_Minor_B_Filament.html</p> </td> <td> <p>Leo Minor B F.</p> </td> </tr> <tr> <td> <p>SG_cube_LeoII_A_Filament.html</p> </td> <td> <p>LeoII A F.</p> </td> </tr> </tbody> </table> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p>For each visualization galaxies within 2 Mpc are color-coded by the 3D local density, and galaxies with separations greater than 2 Mpc are shown with the grey points. The filament spine is shown with the black curve.</p> <p>The files were created with plotly.js v1.58.4.</p> <p> </p>
GWTC-2.1: Deep Extended Catalog of Compact Binary Coalescences Observed by LIGO and Virgo During the First Half of the Third Observing Run - Data Quality Products for GW Searches
<p>This material is part of several data products associated with GWTC-2.1, the deep extended catalog of compact binary coalescences observed by the <a href="https://www.ligo.org/">LIGO</a> Scientific Collaboration and the <a href="https://www.virgo-gw.eu/">Virgo</a> Collaboration during the first half of the third observing run. For further information, see the paper (<a href="https://dcc.ligo.org/LIGO-P2100063/public">dcc.ligo.org/LIGO-P2100063/public</a>), the related material linked from this page, and the GWTC-2.1 data release documentation (<a href="https://www.gw-openscience.org/GWTC-2.1/">www.gw-openscience.org/GWTC-2.1/</a>).</p> <p>This release contains data quality products that are used by search analyses to help mitigate non-Gaussian noise in the detector data.</p> <p><strong>Renormalized iDQ timeseries</strong></p> <p>This release contains the renormalized iDQ timeseries data quality product used within the GstLAL search to generate results for GWTC-2.1 as described in <a href="https://arxiv.org/abs/2010.15282">Goodwin <em>et al</em>. 2020</a>. This data product was found to be statistically helpful in improving data quality within the GstLAL search. For further information about iDQ see <a href="https://iopscience.iop.org/article/10.1088/2632-2153/abab5f">Essick <em>et al</em>. 2020</a>.</p> <p>The file </p> <ul> <li>H1L1-IDQ_TIMESERIES-1238166018-15843600.h5</li> </ul> <p>contains a time series for each LIGO detector related to the probability of a glitch in the strain data given the behavior in the analyzed auxiliary channels which monitor the behavior of the detectors and their environment.</p> <p>The HDF5-formatted file contains two groups, H1 and L1, corresponding to LIGO Hanford and LIGO Livingston, respectively. Each group contains several datasets; the data dataset corresponds to the renormalized iDQ log-likelihoods, as described in Godwin <em>et al</em>. 2020, and the time dataset corresponds to the times associated with the renormalized iDQ log-likelihoods in the data dataset.</p> <p> </p> <p>For more general background on gravitational-wave data quality, try the materials from a <a href="https://www.gw-openscience.org/workshops/">GW Open Data Workshop</a> or the guide to <a href="https://doi.org/10.1088/1361-6382/ab685e">LIGO-Virgo data analysis</a>.</p>
GWTC-2.1: Deep Extended Catalog of Compact Binary Coalescences Observed by LIGO and Virgo During the First Half of the Third Observing Run - Parameter Estimation Data Release
<p>This material is part of several data products associated with GWTC-2.1, an update to the second Gravitational-Wave Transient Catalog from the <a href="https://www.ligo.org/">LIGO</a> Scientific Collaboration, the <a href="https://www.virgo-gw.eu/">Virgo</a> Collaboration, and the <a href="https://gwcenter.icrr.u-tokyo.ac.jp/en/">KAGRA</a> Collaboration. For more information, see the paper (<a href="https://dcc.ligo.org/LIGO-P2100063/public">https://dcc.ligo.org/LIGO-P2100063/public</a>), the related material linked from this page, and the GWTC-2.1 data release documentation (<a href="https://www.gw-openscience.org/GWTC-2.1/">https://www.gw-openscience.org/GWTC-2.1/</a>).</p> <p><strong>Parameter estimation data release</strong></p> <p>This data release contains posterior samples (*.h5) for gravitational-wave candidates through the first part of the third observing run (O3a). We provide results for the 44 candidates that have a probability of astrophysical origin of over 0.5 from O3 as well as the 10 previously-reported binary-black-hole candidates from GWTC-1 (this excludes GW170817). There are two .h5 files per event</p> <ul> <li> <p>Cosmologically reweighted (*cosmo.h5)</p> </li> <li> <p>Not cosmologically reweighted (*nocosmo.h5)</p> </li> </ul> <p>The cosmologically reweighted posteriors are reweighted to have a luminosity-distance prior that has a uniform merger rate in the source's comoving frame. Each .h5 file contains samples for multiple runs with keys C01:RUN_NAME, where RUN_NAME is the waveform used for the run (and additional prior-choice information if necessary) or Mixed, indicating an equal mixture of samples from runs with similar physics if they exist. In cases where only one waveform was used, the Mixed dataset is simply a resampling of those results . GW190425 does not have Mixed samples. See the <a href="https://dcc.ligo.org/LIGO-P2100063/public">paper</a> appendices for further information. In addition to containing the posterior samples, the .h5 files also contain metadata about the analyses including the configuration files (which specify details such as the detector data analyzed), noise power spectral densities (potentially for a superset of the detectors used in the analysis) and calibration uncertainty envelopes.</p> <p>The python notebook explains how to use the posterior samples. This data release also contains .FITS skymap files, which can be read with <a href="https://lscsoft.docs.ligo.org/ligo.skymap/#">ligo.skymap</a>, and skymap statistics in *.txt files.</p> <p>The inference of the source parameters were performed with <a href="https://lscsoft.docs.ligo.org/bilby/">Bilby</a>, <a href="https://lscsoft.docs.ligo.org/parallel_bilby/">Parallel Bilby</a> and <a href="https://git.ligo.org/richard-oshaughnessy/research-projects-RIT/tree/temp-RIT-Tides">RIFT</a>. The results are formatted using <a href="https://lscsoft.docs.ligo.org/pesummary/">PESummary</a>.</p> <p><a href="https://zenodo.org/record/5546663#.YnAAcvPMKqC">A similar release has been made to accompany GWTC-3</a> for results from the second part of the third observing run.</p> <p><strong>How to download all files from this page</strong></p> <p>If you would like to download all files on this page, we recommend <a href="https://gitlab.com/dvolgyes/zenodo_get">zenodo_get</a>:</p> <pre><code class="language-bash">pip install zenodo_get zenodo-get RECORD_ID_OR_DOI </code></pre> <p>where the record ID for the most recent version of this page is 5117702 and IDs for other versions can be found in the Versions section at the side of this page.</p> <p>For more general background on gravitational-wave parameter estimation, try the materials from a <a href="https://www.gw-openscience.org/workshops/">GW Open Data Workshop</a> or the <a href="https://doi.org/10.1088/1361-6382/ab685e">guide to LIGO–Virgo data analysis</a>.</p>
Relocated Seismicity Catalogs on the Discovery Transform Fault, 4S on the East Pacific Rise
<p>Two relocated earthquake catalogs are provided for the Discovery Transform Fault located at 4ºS on the East Pacific Rise. There is a microseismicity catalog representing one year of activity recorded during a 2008 ocean bottom seismometer deployment, which includes 12,635 events with local magnitudes, M<sub>L</sub>, between 0 and 4.1. The second catalog includes 24 years (1 January 1990 - 1 April 2013) of earthquakes obtained from the global Centroid Moment Tensor (CMT) catalog, a total of 15 events, with seismic moment magnitudes, M<sub>W</sub>, between 5.4 and 6.0.</p> <p>Microseismicity was relocated using the HypoDD relocation algorithm (Waldhauser, 2001), while the CMT events were relocated using a teleseismic surface-wave cross-correlation technique (McGuire, 2008). The 15 CMT events all relocated into one of five distinct rupture patches on the Discovery Transform Fault. In general, microseismicity was found to be reduced within these large, repeating rupture patches.</p> <p>A more detailed description of the methodology used to relocate both catalogs, as well as a discussion on the correlation between seismic behavior and fault structure on the Discovery Transform Fault is provided in:</p> <p>Wolfson-Schwehr, M., Boettcher, M. S., McGuire, J. J., & Collins, J. A. (2014). The relationship between seismicity and fault structure on the Discovery transform fault, East Pacific Rise. <em>Geochemistry, Geophysics, Geosystems, </em>15(9), 3698–3712. <a href="https://doi.org/10.1002/2014GC005445">https://doi.org/10.1002/2014GC005445</a></p> <p>Seismic Catalogs:</p> <ul> <li>Discovery_CMT_relocated_seismicity_1990_2013.csv</li> <li>Discovery_relocated_microseismicity_2008.csv</li> </ul> <p>Additional References:</p> <p>1. McGuire, J. J. (2008). Seismic cycles and earthquake predictability on East Pacific Rise transform faults. <em>Bulletin of the Seismological Society of America</em>, 98(3), 1067-1084. <a href="https://www.whoi.edu/cms/files/McGuire_BSSA_2008_48643.pdf">https://www.whoi.edu/cms/files/McGuire_BSSA_2008_48643.pdf</a></p> <p>2. Waldhauser, F. (2001). hypoDD--A program to compute double-difference hypocenter locations. <br> <a href="https://academiccommons.columbia.edu/doi/10.7916/D8SN072H">https://academiccommons.columbia.edu/doi/10.7916/D8SN072H</a></p>
Gaia EDR3 Catalogs of Machine-Learned Radial Velocities
<p><strong>Gaia EDR3 Catalogs of Machine-Learned Radial Velocities</strong></p> <p>Spatially complete Test-Set and Machine-Learned Radial Velocity (ML-RV) Catalogs described in Dropulic et al., arXiv:<a href="https://arxiv.org/abs/2205.12278">2205.12278</a>. The spatially complete Test-Set Catalog contains a total of 4,332,657 stars, while the spatially complete ML-RV Catalog contains 91,840,346 stars. We provide Gaia EDR3 Source IDs, the network-predicted line-of-sight velocity in km/s, and the network-predicted uncertainty in km/s. </p> <p>We have included a simple Jupyter notebook demonstrating how to import the data, and make a simple histogram with it.</p> <p>If you find this catalog useful in your work, please cite Dropulic et al. arXiv:<a href="https://arxiv.org/abs/2205.12278">2205.12278</a>, as well as Dropulic et al. <a href="https://doi.org/10.3847/2041-8213/ac09ef">ApJL 915, L14 (2021)</a> arXiv:<a href="https://arxiv.org/abs/2103.14039">2103.14039</a>. </p>
SDSS-IV Cosmic Web Catalog
<p>This repository contains the cosmic web catalog data released in the paper "Cosmic Web Catalog on SDSS-IV Data with SCONCE" (preparing).</p> <p>The catalog is constructed on the SDSS-IV galaxies and quasars (QSO) using our proposed Directional Subspace Constrained Mean Shift (DirSCMS) algorithm. We release both the cosmic filaments and local modes (i.e., local maxima of the estimated galaxy/QSO density field, which serves as candidates of galaxy clusters) within 325 thin redshift slices, each of which spans 20Mpc under the Planck15 cosmology. The entire catalog covers the redshift range from <span class="math-tex">\(z=0\)</span> to <span class="math-tex">\(z=3\)</span>.</p> <p> 1. "<strong>Cosmic_filaments_2D_DirSCMS_new1</strong>": The file contains some discrete realizations of the estimated cosmic filaments in some particular redshift slices. The meaning of each column in the file is described as follows:</p> <ul> <li><strong>RA</strong> -- right ascension.</li> <li><strong>DEC</strong> -- declination.</li> <li><strong>z_low</strong> -- lower limit of the redshift slice.</li> <li><strong>z_high</strong> -- upper limit of the redshift slice.</li> <li><strong>comov_dist_low</strong> -- lower limit of the comoving distance in the redshift slice under the Planck15 cosmology.</li> <li><strong>comov_dist_high</strong> -- upper limit of the comoving distance in the redshift slice under the Planck15 cosmology.</li> <li><strong>bw</strong> -- smoothing bandwidth parameter for the DirSCMS algorithm in the redshift slice.</li> <li><strong>unc_meas</strong> -- uncertainty measure of the filamentary point by the nonparametric bootstrap techinque.</li> <li><strong>density</strong> -- (proportional) estimated galaxy/QSO density value at the filamentary point.</li> <li><strong>grad_Dir1</strong> -- (Riemannian) gradient of the estimated density field (first direction).</li> <li><strong>grad_Dir2</strong> -- (Riemannian) gradient of the estimated density field (second direction).</li> <li><strong>grad_Dir3</strong> -- (Riemannian) gradient of the estimated density field (third direction).</li> <li><strong>knot_label</strong> -- indicator of whether the filamentary point is a knot (i.e., the intersection of several filaments) or not.</li> </ul> <p> 2. "<strong>Cosmic_local_modes_2D_DirMS_unique1</strong>": The file contains some discrete realizations of the estimated local modes in some particular redshift slices. The columns are subsumed by the ones in the cosmic filament file and has been described above.</p> <p><em>Additional notes: We provide both the "csv" and "fits" format for each of the above file.</em></p> <p> </p> <p>Please cite the paper when using the data in this repository.</p> <p>► Pure catalog data:</p> <p>[1] <strong>Cosmic Web Catalog on SDSS-IV Data with SCONCE</strong>. (In preparation)</p> <p>►Methodology:</p> <p>[1] Yikun Zhang, Rafael S. de Souza, and Yen-Chi Chen (2022). <strong>SCONCE: A Cosmic Web Finder for Spherical and Conic Geometries</strong>. <em>arXiv preprint arXiv:2207.07001</em></p> <p>[2] Yikun Zhang and Yen-Chi Chen (2022) <strong>Linear Convergence of the Subspace Constrained Mean Shift Algorithm: From Euclidean to Directional Data</strong>. <em>Information and Inference: A Journal of the IMA</em>, iaac005, <a href="https://doi.org/10.1093/imaiai/iaac005">https://doi.org/10.1093/imaiai/iaac005</a></p> <p>[3] Yikun Zhang and Yen-Chi Chen (2021) <strong>Kernel Smoothing, Mean Shift, and Their Learning Theory with Directional Data</strong>. <em>Journal of Machine Learning Research</em> <strong>22</strong>(154): 1-92.</p>
Images and catalogs of HST and JWST images in the SMACS-0723 field
<p>This repository is a first-pass reduction of the HST and JWST images of the SMACS-0723 lensing cluster field. </p> <p>All images have been processed with the <a href="https://github.com/gbrammer/grizli">grizli</a> software pipeline. Further documentation will be provided by Brammer et al. (in prep).</p>
Catalog of microseismicity related to the Alto-Tiberina Fault
<p>This template matching catalog contains information about new detected seismicity as the origin time (ot), latitude (lat_temp), longitude (lon_temp), depth (depth_tep), magnitude (mag), origin time of the template that can be used as the event_id (ot_template), the ratio between the average correlation coefficient (CC) and the daily median absolute deviation of the averaged CCs, as an indication for the quality of a detection (cc_mad_ratio), and an indication about the origin as some of the detection's seem to be related to human induced activity (hum_ind). Detailed information about the template matching processing can be gained from <strong>Spatio-temporal evolution of the</strong><strong> Seismicity in the Alto Tiberina Fault System revealed by a High-Resolution Template Matching Catalog</strong> by Essing & Poli (2022)</p> <p> </p>
Catalog of PAM and MBON cell types
<p>A catalog of some of the published anatomical findings on DAN PAM and MBON cell types in the mushroom body of <em>Drosophila melanogaster.</em> Major source is the major table in Aso <em>et al. </em>2014 (https://doi.org/10.7554/eLife.04577). Also includes results from other papers and combines into a single spreadsheet.</p>
UNCOVER Photometric Catalog
<p><a href="https://jwst-uncover.github.io/DR2.html#PhotometricCatalogs">UNCOVER Data Release 3: The Photometric Catalog</a> </p> <p>Photometry and redshifts for 74,000 sources over Abell 2744<br>Authors: John R. Weaver, Wren Suess, Sam Cutler, Richard Pan, Kate Whitaker, and Lukas Furtak</p> <p>The catalogs are selected from a long-wavelength (LW) F277W+F356W+F444W detection image with photometry measured on the 27 available HST and JWST bands over 56 sq. arcmin of Abell 2744 contributed by several major surveys including UNCOVER, MegaScience, and GLASS. Five choices of color aperture are available, although we recommend using the 'super' catalog where photometry from the most suitable aperture per object is reported. Redshift estimates and basic properties are computed with EAzY. See the dedicated readme file and preprint for details.</p> <p>If you use this catalog, please cite the corresponding papers:<br>Suess et al. 2024 (<a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240413132S/abstract">https://ui.adsabs.harvard.edu/abs/2024arXiv240413132S/abstract</a>),<br>Weaver et al. 2023 (<a href="https://ui.adsabs.harvard.edu/abs/2023arXiv230102671W/abstract">https://ui.adsabs.harvard.edu/abs/2023arXiv230102671W/abstract</a>),<br>Bezanson et al. 2024 (<a href="https://ui.adsabs.harvard.edu/abs/2022arXiv221204026B/abstract">https://ui.adsabs.harvard.edu/abs/2022arXiv221204026B/abstract</a>). </p>
Catalog of relocated seismic sequences in Irpinia
<p>This catalog contains the hypocenter coordinates and the source parameters estimations for the enhanced catalogs of seismic sequences in Southern Apennines obtained in Scotto di Uccio et al. (2023)</p>
A comprehensive catalog of exact short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38
<p>To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of exact repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,233,959 TR intervals, covering 0.783306% (24.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta). </p>
FENIKS UDS Catalogs
<p><a href="https://www.zaidikumail.com/feniks-uds-catalogs" target="_blank" rel="noopener">FENIKS UDS Catalogs: Version 1.1 (v1.1)</a></p> <p>Catalogs produced by the FENIKS collaboration in the UDS field, including the multi-wavelength PSF-matched photometric catalog, the catalogs of photometric redshifts and stellar population properties, as well as other high-level products. </p> <p> </p> <p>The catalog construction is described in detail in the accompanying paper <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240103107Z/abstract" target="_blank" rel="noopener">(Zaidi et al. 2024)</a>. Briefly, the catalogs were constructed by combining data in 24 photometric bands covering optical to mid-IR wavelengths ranging from 0.38 microns (MegaCam-uS band) to 8 microns (Spitzer-IRAC ch4 band). The catalog covers a footprint of ~ 0.9 square degrees with full coverage in most of the bands, and close to full coverage in the rest (see the accompanying paper for footprint details).</p> <p> </p> <p>When using these products, please cite <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240103107Z/abstract" target="_blank" rel="noopener">Zaidi et al. 2024</a> and use the following acknowledgment:</p> <p>"This work is based on data and catalog products from the FENIKS survey, funded by the National Science Foundation under grants AST-2009442 and AST-2009632"</p> <p> </p> <p>Please email <a title="mailto:kumail.zaidi@tufts.edu?subject=Notifcation of UDS FENIKS catalogs" href="mailto:kumail.zaidi@tufts.edu?subject=Notifcation%20of%20UDS%20FENIKS%20catalogs">kumail.zaidi at tufts.edu</a> or <a title="mailto:danilo.marchesini@tufts.edu?subject=Notifcation of UDS FENIKS catalogs" href="mailto:danilo.marchesini@tufts.edu?subject=Notifcation%20of%20UDS%20FENIKS%20catalogs">danilo.marchesini at tufts.edu</a> to communicate any published papers that used the data from this release</p> <p> </p> <p>v1.1 release update:</p> <p>The multiplicative factors to apply to color aperture fluxes to get total fluxes, the 'aper_to_tot_corr' column in the photometry catalogs, <span>feniks_uds_v1.1.cat and </span><span>feniks_uds_v1.1_zpcor.cat have been fixed.</span></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.