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ShareScore release 0.9.0
Dataset results
650 results for “Workflow”
DLC networks from: Application of a novel deep learning based 3D videography workflow to bat flight data
<p>Studying the detailed biomechanics of flying animals relies on producing accurate three-dimensional coordinates for key anatomical landmarks. Traditionally, this is achieved through manual digitization of animal videos, a labor-intensive task that grows more so with increasing frame rates and numbers of cameras. In this study, we present a workflow that combines deep learning-powered automatic digitization with intelligent filtering and correction of mislabeled points using 3D information. We tested our workflow using a particularly challenging scenario – bat flight. First, we documented bats flying steadily in a wind tunnel. We compared the results from manually digitizing bats with markers applied to anatomical landmarks against using our automatic workflow on the same bats without markers. In our second test case, we compared manual digitization against our automated workflow for bats exhibiting complex maneuvers in a large flight arena. We found that the variation between the 3D coordinates from our workflow and those from manual digitization was less than a millimeter larger than the variation between 3D coordinates resulting from two different human digitizers. The reduced reliance on manual digitization stemming from this work has the potential to significantly increase the scalability of studies into the detailed biomechanics of animal flight.</p>
Knime workflow and data files to calculate a lead-likeness evaluation function 'Λ' for small molecule compounds
<p class="RSCB01COMAbstract"><span class="06CHeading"><span>A simple and rational method to rank molecules' lead-likeness using continuous evaluation functions was developed to support epigenetic drug discovery. This strategy proved to be highly effective on model chemical libraries and finally helped driving synthetic efforts towards candidates of interest for epigenetic applications towards HDAC6, BRD4 and EZH2.</span></span></p> <p>Here we provide sample data and the knime workflow for generatating lead-like chemical probes for epigenetics. This tool and example data set will enable researchers to establish this workflow in their own laboratories and apply it to new synthetic scaffolds for medicinal chemistry.</p>
Passive Fit of Implant-Supported Complete-Arch Prostheses Using Digital Workflows
ClinicalTrials.gov study NCT07315620. IPD Sharing: NO. Countries: 1. Publications: 30.
DLC networks from: Application of a novel deep learning based 3D videography workflow to bat flight data
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Data from: Detection of the endangered European weather loach (Misgurnus fossilis) via water and sediment samples: testing multiple eDNA workflows.
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Open‐source workflow approaches to passive acoustic monitoring of bats
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Knime workflow and data files to calculate a lead-likeness evaluation function 'Λ' for small molecule compounds
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Data from: Ortho2Web: A workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae
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Demo dataset for: SPACEc, a streamlined, interactive Python workflow for multiplexed image processing and analysis
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MALDI-MS dataset for use with open-source untargeted metabolomic workflow for complex biological samples
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Data from: Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: A multicentre clinical study of two end-to-end commercial workflows
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Acute pseudo-landmarking and Constellation homologies: A generalized workflow to identify and track segmented structures in plant time series images
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Figure 19 in Additional new species of Grouvellinus Champion 1923 (Insectaı Coleopteraı Elmidae) discovered by citizen scientists and DNA barcoded in the field applying a novel MinIONbased workflow
Figure 19. Statistical parsimony network of mtDNA haplotypes produced by TCS based on CO1 partial sequences (654 bp). High numbers of 'missing haplotypes' are indicated by their respective count. Coloured circles represent existing haplotypes from the sample set.
Figure 18 in Additional new species of Grouvellinus Champion 1923 (Insectaı Coleopteraı Elmidae) discovered by citizen scientists and DNA barcoded in the field applying a novel MinIONbased workflow
Figure 18. Map of Sabah and Brunei (Borneo) with collecting site of Grouvellinus species with new species record in red fonts.
Figures 2–5 in Additional new species of Grouvellinus Champion 1923 (Insectaı Coleopteraı Elmidae) discovered by citizen scientists and DNA barcoded in the field applying a novel MinIONbased workflow
Figures 2–5. Habitus of the Grouvellinus species collected from the Tawan Hills Park. 2: G. andrekuipersi; 3: G. nigerquadratus, sp. nov. (paratype male from Tawau River); 4: G. nigerquadratus, sp. nov. (male from Lucia River); 5: G.cruxniger, sp. nov. (paratype male from Lucia River). Scale: 1 mm.
Figure 17 in Additional new species of Grouvellinus Champion 1923 (Insectaı Coleopteraı Elmidae) discovered by citizen scientists and DNA barcoded in the field applying a novel MinIONbased workflow
Figure 17. Grouvellinus borneensis, sp. nov. (paratypes): (a) aedeagus, lateral; (b) aedeagus, ventral; (c) ovipositor (half), ventral. Scale bar = 0.1 mm.
Figure 16 in Additional new species of Grouvellinus Champion 1923 (Insectaı Coleopteraı Elmidae) discovered by citizen scientists and DNA barcoded in the field applying a novel MinIONbased workflow
Figure 16. Grouvellinus borneensis, sp. nov. (paratypes): (a) anteriodorsal aspect with pronotum and elytra; (b) ventral aspect with prosternum and mesoventrite; (c) posteriodorsal aspect with metaventrite and ventrites 1–5.
Figure 14 in Additional new species of Grouvellinus Champion 1923 (Insectaı Coleopteraı Elmidae) discovered by citizen scientists and DNA barcoded in the field applying a novel MinIONbased workflow
Figure 14. Grouvellinus luciaensis, sp. nov. (paratypes): (a) anteriodorsal aspect with pronotum; (b) anterioventral aspect with head and prosternum; (c) ventral aspect with prosternum and mesoventrite, (d) posterioventral aspect with metaventrite and ventrites 1–5.
Figure 12 in Additional new species of Grouvellinus Champion 1923 (Insectaı Coleopteraı Elmidae) discovered by citizen scientists and DNA barcoded in the field applying a novel MinIONbased workflow
Figure 12. Grouvellinus cruxniger, sp. nov. (paratypes): (a) anteriodorsal aspect with pronotum and elytra; (b) ventral aspect with prosternum, meso-, metaventrite, and ventrites 1–5.
Test data for running snakePipes : WGBS workflow
<p><strong>Test files for running snakePipes workflows</strong></p> <p><strong>snakePipes</strong> are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to <a href="https://snakepipes.readthedocs.io/en/latest/">this link</a> for further information on snakePipes.</p> <p>This folder contains test files that can be used to run the WGBS workflow under snakePipes. To test the workflow, follow the following steps : </p> <ul> <li>Download or prepare genome fasta, indices and annotations for the mouse (<strong>GRCm38</strong>) genome.</li> <li>Download and install snakePipes via `conda create -n snakePipes -c mpi-ie -c bioconda -c conda-forge snakePipes`</li> <li>Update <a href="https://snakepipes.readthedocs.io/en/latest/content/running_snakePipes.html#genome-configuration-file">Genome configuration file</a> with path to indices and annotations.</li> <li>Move to this repository and run the example <strong>command.sh</strong></li> </ul>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.