Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
94
datasets available to search
ShareScore release 0.9.0
Dataset results
94 results for “Training Materials”
Training data for 'Upload data to ENA' (Galaxy Training Material)
<p>The data here is a subset of the data published in 10.5281/zenodo.3732359 to be used in GTN 'Upload data to ENA' tutorial.</p> <p>Human traces have been removed following <a href="https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html">https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html</a></p> <p>We produced consensus sequences (*.fasta) for the Illumina PE data following SARS-CoV-2-PE-Illumina-WGS-variant-calling (https://workflowhub.eu/workflows/113?version=4), SARS-CoV-2-variation-reporting (https://workflowhub.eu/workflows/109?version=5) and COVID-19-consensus-construction (https://workflowhub.eu/workflows/138?version=4) workflows.</p>
Dataset for Training Material - Galaxy Workflow - Analyse unaligned ncRNAs
<p>Input dataset for Galaxy Training Material for the Analyze unaligned ncRNAs workflow.</p> <p>See https://github.com/galaxyproject/training-material for more information.</p>
Supplementary Material for "Advancing quantum technology workforce: industry insights into qualification and training needs" and "Extending the European Competence Framework for Quantum Technologies: new proficiency triangle and qualification profiles"
<p>This is a file collection as supplementary material for the paper <em>Advancing quantum technology workforce: industry insights into qualification and training needs, <a href="https://doi.org/10.1140/epjqt/s40507-024-00294-2">doi 10.1140/epjqt/s40507-024-00294-2</a>.</em> It consists of:</p> <ol> <li>Interview guide: questions and more as guideline for the interviews conducted for the industry needs analysis documented in the publication.</li> <li>Interview transcript extracts: anonymised phrases from the interviews that are given as quotes (in a shortened/liguistically smoothed out form) in the publication as well as further phrases that are refered in the results sections of the publication.</li> <li>Dataset of the follow-up survey</li> </ol> <p>The results of this study were also used to update the <a href="https://doi.org/10.5281/zenodo.10976836" target="_blank" rel="noopener">European Competence Framework for Quantum Technologies Version 2.5</a>, which is documented in <em>Extending the European Competence Framework for Quantum Technologies: new proficiency triangle and qualification profiles, <a href="https://doi.org/10.1140/epjqt/s40507-024-00302-5">doi 10.1140/epjqt/s40507-024-00302-5</a></em>. In an additional sheet, the three draft versions of qualification profile descriptions (v2.1, v2.2, v2.3) are provided.</p>
Training material for ChIP-seq analysis
<p>The data provided here are part of a Galaxy tutorial that analyzes ChIP-seq data from a study published by Wu et al., 2014 (DOI:10.1101/gr.164830.113). The goal of this study was to investigate "the dynamics of occupancy and the role in gene regulation of the transcription factor Tal1, a critical regulator of hematopoiesis, at multiple stages of hematopoietic differentiation." To this end, ChIP-seq experiments were performed in multiple mouse cell types including a G1E cell line and megakaryocytes, the two cell types represented here. The dataset contains biological replicate Tal1 ChIP-seq and input control experiments (*.fastqsanger files). Because of the long processing time for the large original files, we have downsampled the original raw data files to include only reads that align to chromosome 19 and a subset of interesting genomic loci (ChIPseq_regions_of_interest_v4.bed) pulled from the Wu et al. publication. Also included is a gene annotation file (RefSeq_gene_annotations_mm10.bed) with gene names added for viewing in a genome browser.</p>
Training material for de novo transcriptome reconstruction from RNA-seq data
<p>The data provided here are part of a Galaxy tutorial that analyzes RNA-seq data from a study published by Wu et al., 2014 (DOI:10.1101/gr.164830.113). The goal of this study was to investigate "the dynamics of occupancy and the role in gene regulation of the transcription factor Tal1, a critical regulator of hematopoiesis, at multiple stages of hematopoietic differentiation." To this end, RNA-seq libraries were constructed from multiple mouse cell types including G1E - a GATA-null immortalized cell line derived from targeted disruption of GATA-1 in mouse embryonic stem cells - and megakaryocytes. This RNA-seq data was used to determine differential gene expression between G1E and megakaryocytes and later correlated with Tal1 occupancy. This dataset (GEO Accession: GSE51338) consists of biological replicate, paired-end, polyA selected RNA-seq libraries. Because of the long processing time for the large original files, we have downsampled the original raw data files to include only reads that align to chromosome 19 and a subset of interesting genomic loci identified by Wu et al.</p>
Training data for 'Preparing genomic data for phylogeny reconstruction' (Galaxy Training Material)
<p>This data is used for Galaxy Training Network training 'Preparing genomic data for phylogeny reconstruction'. There are four nucleotide sequences from chromosome 5 of four strains of S. cerevisiae. The GenBank annotated sequenced were produced using 'funannotate predict annotation' (Galaxy Version 1.8.9+galaxy2) on the nucleotide sequences sequences. References: DOI: 10.1126/science.274.5287.546; DOI: 10.1126/science.1189015; DOI: 10.1016/j.cell.2016.08.020</p>
gmap - qgis training material: Ingenii Basin (moon)
<p>This dataset part of the Geology and Planetary Mapping Winter School 2022 featuring Ingenii Basin as a study area.<br> Ingenii Basin is located on the lunar farside centred at 33.7°S 163.5°E within the South Pole-Aitken basin. The floor of Ingenii Basin is filled with mare materials with the basin having a diameter of 282 km.<br> We compiled a beginners – intermediate level training package for the area. The package includes the Lunar Reconnaissance Orbiter Camera (LROC) Wide Angle Camera (WAC) global mosaic (Speyerer et al., 2011) as a basemap, the Lunar Orbiter Laser Altimeter (LOLA) and SELenological and Engineering Explorer (SELENE) Kaguya merged lunar digital elevation model (DEM) (Barker et al., 2016) and spectral data in the form of a clementine Ultraviolet/Visible (UVVIS) warped color ratio mosaic (Lucey et al., 2000). The data is cut to the area of interest and a training project is set up for QGIS. </p> <p>The training package is designed as a group exercise with four adjacent tiles covering the entirety of Ingenii basin. For beginners the aim is to create a low scale map of the area where the basin rim is distinguished from the basin floor and mare unit as well as detecting smaller craters that exist in the area. These units should then be put in a stratigraphic relationship based on superposition, degradation state and embayment. For intermediate mappers this task can be extended to include the swirl features and finding potential areas for crater size frequency distribution measurement to determine absolute ages for a more detailed stratigraphy.</p> <p><br> </p> <p> </p>
Galaxy Training Material for Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
<p>This dataset contains the training data for the <strong>Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)</strong> GTN tutorial. It includes 3 GC-[EI+]-HRMS files from seminal plasma samples, the RECETOX Metabolome HR-[EI+]-MS library collected from mostly endogoenous compounds from MetaSci Human Metabolite Library, reference alkanes, sample metadata table, and preprocessed XCMS object.</p>
Training data for 'Exome sequencing data analysis' tutorial (Galaxy Training Material)
<p>The data used in this tutorial are a subset of the data published previously in <a href="https://zenodo.org/record/3243160">Training material for the course "Exome analysis with GALAXY"</a>. Credit for uploading the original data goes to Paolo Uva and Gianmauro Cuccuru!</p> <p>Specifically, you may need the following datasets for following the tutorial:</p> <p><strong>Raw sequencing reads</strong></p> <ul> <li><a href="https://zenodo.org/record/3243160/files/father_R1.fq.gz?download=1">https://zenodo.org/record/3243160/files/father_R1.fq.gz</a></li> <li><a href="https://zenodo.org/record/3243160/files/father_R2.fq.gz?download=1">https://zenodo.org/record/3243160/files/father_R2.fq.gz</a></li> <li><a href="https://zenodo.org/record/3243160/files/mother_R1.fq.gz?download=1">https://zenodo.org/record/3243160/files/mother_R1.fq.gz</a></li> <li><a href="https://zenodo.org/record/3243160/files/mother_R2.fq.gz?download=1">https://zenodo.org/record/3243160/files/mother_R2.fq.gz</a></li> <li><a href="https://zenodo.org/record/3243160/files/proband_R1.fq.gz?download=1">https://zenodo.org/record/3243160/files/proband_R1.fq.gz</a></li> <li><a href="https://zenodo.org/record/3243160/files/proband_R2.fq.gz?download=1">https://zenodo.org/record/3243160/files/proband_R2.fq.gz</a></li> </ul> <p><strong>Premapped sequencing reads</strong></p> <ul> <li><a href="https://zenodo.org/record/3243160/files/mapped_reads_father.bam?download=1">https://zenodo.org/record/3243160/files/mapped_reads_father.bam</a></li> <li><a href="https://zenodo.org/record/3243160/files/mapped_reads_mother.bam?download=1">https://zenodo.org/record/3243160/files/mapped_reads_mother.bam</a></li> <li><a href="https://zenodo.org/record/3243160/files/mapped_reads_proband.bam?download=1">https://zenodo.org/record/3243160/files/mapped_reads_proband.bam</a></li> </ul> <p><strong>Reference sequence (human chromosome 8)</strong></p> <ul> <li><a href="https://zenodo.org/record/3243160/files/hg19_chr8.fa.gz?download=1">https://zenodo.org/record/3243160/files/hg19_chr8.fa.gz</a></li> </ul> <p> </p> <p>If you would just like to play with GEMINI rather than work through the full tutorial, you'll find below a prebuilt GEMINI database (for GEMINI version 0.20.1) for the family trio. You can start exploring this database without having to run GEMINI load and, in fact, without having to install GEMINI's bundled annotation data.</p>
Training data for 'Genome annotation with Maker' tutorial (Galaxy Training Material)
<p>The data provided here are part of a Galaxy Training Network tutorial for genome annotation with Maker.</p> <p>It is based on data used in <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018">another Maker tutorial</a>.</p> <p>The full genome was <a href="https://www.ncbi.nlm.nih.gov/genome/?term=Schizosaccharomyces%20pombe[Organism]&cmd=DetailsSearch">downloaded from NCBI</a>, and mitochondria sequence removed from it for simplicity.</p>
Doctoral Studies as part of an Innovative Training Network (ITN): Early Stage Researcher (ESR) experiences - supplemental material & data
<p>Table and data repository for the manuscript "Doctoral Studies as part of an Innovative Training Network (ITN): Early Stage Researcher (ESR) experiences"</p> <p><strong>Supplemental Tables:</strong></p> <ul> <li>table1_ESIT Project Table</li> <li>table2_TIN-ACT Project Table</li> <li>table3_ITN_tinnitus</li> <li>table4_ITN_other</li> <li>table5_Individual PhDs</li> </ul> <p><strong>Individual-level and de-identified survey data (raw data):</strong></p> <ul> <li>raw_data_ITN_tinnitus (survey results from PhDs as part of an ITN with a focus on tinnitus)</li> <li>raw_data_ITN_other (survey results from PhDs associated to ITNs with another focus)</li> <li>raw_data_Individual_Phds (survey results from PhDs not part of an ITN)</li> </ul>
Training material for small RNA-seq data analysis (Galaxy Training Network tutorial)
<p>The data provided here are part of a Galaxy Training Network tutorial that analyzes small RNA-seq (sRNA-seq) data from a study published by Harrington et al. (DOI:10.1186/s12864-017-3692-8) to detect differential abundance of various classes of endogenous short interfering RNAs (esiRNAs). The goal of this study was to investigate "connections between differential retroTn and hp-derived esiRNA processing and cellular location, and to investigate the potential link between mRNA 3’ end cleavage and esiRNA biogenesis." To this end, sRNA-seq libraries were constructed from triplicate <em>Drosophila</em> tissue culture samples under conditions of either control RNAi or RNAi knockdown of a factor involved in mRNA 3’ end processing, <em>Symplekin</em>. This dataset (GEO Accession: GSE82128) consists of single-end, size-selected, non-rRNA-depleted sRNA-seq libraries. Because of the long processing time for the large original files, we have downsampled the original raw data files to include only reads that align to a subset of interesting transcript features including: (1) transposable elements, (2) <em>Drosophila</em> piRNA clusters, (3) <em>Symplekin</em>, and (4) genes encoding mass spectrometry-defined protein binding partners of <em>Symplekin</em> from Additional File 2 in the indicated paper by Harrington et al. More details on features 1 and 2 can be found here: https://github.com/bowhan/piPipes/blob/master/common/dm3/genomic_features (piRNA_Cluster, Trn). All features are from the <em>Drosophila</em> genome Apr. 2006 (BDGP R5/<em>dm3</em>) release.</p>
HYPERCOG – training material dataset
<p>The Hypercog training pack is aimed at teaching cyberphysical systems to two different types of profiles : </p><p>1) the operators at the 3 industrial sites impacted by the implementation of the HyperCOG solution (Solvay, Sidenor, Çimsa);</p><p> 2) Master students who would like to get familiar with cyberphysical systems.</p><p>The main objective for operators training was to understand the human environment where the solutions are implemented. For students it was to identify the skills needed to become familiar with cyber-physical systems. The ultimate goal was to train operators to overcome the skill gap, so they can use HyperCOG solutions in their daily work, and to produce training materials on cyber-physical systems based on the Hypercog experience, aimed at Master students .</p>
Training material for flye genome assembly (Galaxy Training Network tutorial)
<p>Datasets are subsets of 3 public datasets (Mucor mucedo Fresen. NRRL 3635 Standard Draft genome sequencing with PacBio technology)</p> <p>https://www.ncbi.nlm.nih.gov/sra/SRX5336965[accn]</p> <p>https://www.ncbi.nlm.nih.gov/sra/SRX5336964[accn]</p> <p>https://www.ncbi.nlm.nih.gov/sra/SRX5336963[accn]</p> <p> </p> <p> </p>
Long reads training material for 'Quality Control' tutorial (Galaxy Training Material)
<p>The data provided here are part of a Galaxy Training Network tutorial for reads Quality Control.</p> <p>PacBio HiFi reads were provided by PacBio - GIAB sample HG002 (https://www.pacb.com/smrt-science/smrt-resources/datasets/) and was downsampled using seqtk (https://github.com/lh3/seqtk)</p> <p>Nanopore reads were provided by Tim Kahlke as part of "Long-Read, long reach Bioinformatics Tutorials" (https://timkahlke.github.io/LongRead_tutorials/) and was basecalled using Guppy v5.0.2 (dna_r9.4.1_450bps_sup.cfg).</p>
gmap - qgis training material: Beagle Rupes (Mercury)
<p>This dataset part of the Geology and Planetary Mapping Winter School 2022 featuring Beagle Rupes as a study area.<br> Beagle Rupes is lobate scarp at Mercurys surface with a length of more than 600km cross-cutting an oval shaped crater. <br> We compiled a beginners – intermediate level training package for the area. The package includes several basemaps such as Map Projected Basemap Reduced Data Record (BDR) (Hash 2013a), High-incidence East-illumination Basemap (HIE), Map-projected High-incidence West-illumination (HIW) (Hash 2015a), Map Projected Low-Incidence Angle Basemap Reduced Data Record (LOI) (Hash 2013b), Map Projected Multispectral Reduced Data Record (MDR) Hash 2015b) and digital terrain model (DTM) (Becker et al., 2016). The data is cut to the area of interest and a training project is set up for QGIS. </p> <p>The training package is designed as a group exercise with four adjacent tiles covering the Beagle Rupes area. </p>
Additional Material for Debiasing architectural decision-making: a workshop-based training approach
<p>This additional material was created to enable full replication of the experiment described in the paper:<br> "Klara Borowa, Maria Jarek, Gabriela Mystkowska, Weronika Paszko and Andrzej Zalewski: <strong>Debiasing architectural decision-making: a workshop-based training approach</strong>".<br> The paper was accepted for publication at ECSA 2022 (The 16th European Conference on Software Architecture).<br> <br> The folder contains the following files:<br> Coding-details.xlsx - the coding scheme, as well as coding results. Contains all code counts for each team participating in the experiment.<br> Experiment-meeting-plan.pdf - contains the plan for the 3-hour meeting during which the experiment was conducted, as well as a timetable of when each meeting took place and who organised it.<br> Debiasing-workshop-slides.pdf - slides used during the debiasing workshop.<br> Debiasing-workshop-plan.pdf - detailed instruction for workshop organisers, what should be said and done during the workshop.<br> Participants_questionnaire_and_results.xlsx - questionnaire questions used to obtain information about participants, as well as questionnaire results for all 44 participants.</p>
gmap - qgis training material: Aram Chaos (Mars)
<p>Aram Chaos is a more than 250 km large crater characterized by the presence of Chaotic Terrains forming mesas and knobs, associated with the outflow channel of Ares Vallis. The Chaotic Terrains are unconformably embayed and locally superposed by some layered hydrate minerals-bearing deposits. </p> <p> </p> <p>The training package includes a complete HRSC coverage (including images and DEMs) (Neukum et al., 2004; Jaumann et al., 2007) and selected CTX (Malin et al., 2007), HiRISE (McEwen et al., 2007), and CRISM (Murchie et al., 2007) data. The area has been divided in 8 tiles each of one ‘stand.alone’ in terms of geology but at the same time ready for collaborative mapping purposes.</p>
URL list for downloading training data for 'Maximum Likelihood Phylogeny Reconstruction'' (Galaxy Training Material)
<p>This data is used for Galaxy Training Network (GTN) training 'Maximum Likelihood Phylogeny Reconstruction'. It is a list of Zenodo URL pointers to a dataset of 173 amino acid alignments of orthologs found in chromosome 5 of four strains of S. cerevisiae. Original sequence data (https://zenodo.org/record/6610704) was processed in Galaxy following GTN 'Preparing genomic data for phylogeny reconstruction' training (10.48546/workflowhub.workflow.359.1) to generate alignments of orthologs.</p>
Training data for 'Functional annotation of protein sequences' tutorial (Galaxy Training Material)
<p>The data provided here are part of a Galaxy Training Network tutorial for functional annotation of protein sequences.</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.