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650 results for “Workflow”
Workflow Run RO-Crate capturing provenance from WSI conversion
<p>Example of <a href="https://www.researchobject.org/workflow-run-crate/profiles/">Workflow Run RO-Crate</a> capturing provenance data from an execution of the <a href="https://github.com/crs4/fair-crcc-img-convert/tree/main">fair-crcc-img-convert</a> workflow on a whole-slide image from the <a href="https://doi.org/10.7937/25T7-6Y12">Cancer Moonshot Biobank - Prostate Cancer Collection (CMB-PCA)</a>.</p><ul><li>Slide ID: MSB-02917-01-02, generated by Natasha Honomichl</li><li>Image License: <a href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a></li></ul><p>Note that the license for the RO-Crate is CC BY 4.0, except for the workflow, which is licensed under the <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPL-3.0</a>.</p>
Data from: "Navigating through Complexity: Optimizing Cathodes for Organic Electrohydrogenation through Coherent Workflows"
<p>The data used in "<strong>Navigating through Complexity: Optimizing Cathodes for Organic Electrohydrogenation through Coherent Workflows</strong>". </p>
Digital Preservation for the Masses: Creating Workflows for Institutions & Under-Resourced Organisations
<p>Digital preservation for the masses: Creating and publishing workflows and guidelines for institutions and smaller organisations interested in digital preservation, data management, and archiving</p> <p>Presentation given by Julia Colleen Miller at the Language Documentation and Archiving conference</p> <p>Creating public documentation is a crucial step in providing transparency of archiving processes, helping maintain consistent institutional knowledge, and making available resources for those wanting to know about digital preservation, archiving or data management. To this end, PARADISEC's pre-existing archiving workflows have been reworked and new technical workflows and archiving help-guides [1] have been developed and made available on GitHub.</p> <p>These resources can provide guidance for other archives, but perhaps more importantly, to empower smaller communities with fewer available resources wishing to preserve their own cultural materials. The archiving guides discuss topics such as data management and metadata. Technical workflows include digitising audio tapes, creating high-resolution photographs of manuscripts and notebooks, and processing born-digital audio and video files, closely following specifications [2] set out by the International Association for Sound and Audiovisual Archives and refined with input from holding institutions such as The National Library of Australia, The National Film and Sound Archive and The Language Archive based at the Max Planck Institute for Psycholinguistics.</p> <p>Cultural institutions including the Australian Institute of Aboriginal and Torres Strait Islander Studies and the National Film and Sound Archive have discussed their concerns to get their magnetic tape holdings digitised by 2025- a deadline beyond which access to functioning digitising equipment will become increasingly difficult and costly [3], [4]. Collaboration and capacity building will bring us closer to preserving at-risk cultural material before it is too late.</p> <p>References: [1] Miller, JC (2021) PARADISEC archiving workflows. https://paradisec-archive.github.io/PARADISEC_workflows/. [2] Prentice, W. and Gaustad, L. (2017) The Safeguarding of the Audiovisual Heritage: Ethics, Principles and Preservation Strategy (web edition). IASA. https://www.iasa-web.org/iasa-publications. [3] Campbell, L. (16 November 2021) Deadline 2025, the need to preserve First Nations community collections. AIATSIS. https://aiatsis.gov.au/publication/117747. [4] National Film and Sound Archive (27 October 2015) Deadline 2025. NFSA. https://www.nfsa.gov.au/corporate-information/publications/deadline-2025</p>
Recording provenance of workflow runs with RO-Crate (RO-Crate and mapping)
<p>RO-Crate for the manuscript that describes Workflow Run Crate, includes mapping to PROV using SKOS/SSSOM.</p>
BioFlow-Insight Workflow Corpus Open License
<p>This corpus describes a collection of open license Nextflow workflows which we're gathered from Github in February 2024.</p>
Supporting data for "The benefit of in silico predicted spectral libraries in data-independent acquisition data analysis workflows"
Open the record for dataset details and reuse information.
Analysis workflow and dataset for Maxillary palps of tephritidae are tuned to food rather than oviposition volatiles and converge on ecology
<p>In this repository all data and scripts for generating the figure in the manuscript "Maxillary palps of tephritidae are tuned to food rather than oviposition volatiles and converge on ecology" can be found. <br><br>Data is found under /Data with recording for each fruit and the combined lure can be found under its respective name.</p> <p>In Data/sample GC-EPD .pptx there are also sample traces.</p> <p>In workflow most of the script needed to generate the figure that ends up in Output is available</p>
Data for article: Robust characterization of forest structure from airborne laser scanning – a systematic assessment and sample workflow for ecologists
<p><strong>### Update 03/02/2025: the most up to date version of the processing pipeline presented here, also working on Linux, is available on github: https://github.com/fischer-fjd/GCA/tree/main, and a worked example with open data from the Dutch AHN surveys is available on Zenodo: https://zenodo.org/records/14722001 ###<br></strong></p> <p>This is a collection of scripts and research data to assess the robustness of forest structure characterization from airborne laser scanning (ALS). It accompanies the article "Robust characterization of forest structure from airborne laser scanning – a systematic assessment and sample workflow for ecologists" (accepted in Methods in Ecology and Evolution on 25/08/2024). </p> <p>In the article, we assess the derivation of canopy height models (CHMs) from point cloud data, how sensitive CHM algorithms are to point cloud degradation (pulse density thinning, large scan angles, loss of higher-order returns) and how uncertainties and biases propagate to commonly used forest structure metrics. In addition, we provide a standardized processing pipeline in R to convert point clouds into CHMs. </p> <p>The main data source for this study are ALS point clouds from nine Australian research sites belonging to the Terrestrial Ecosystem Research Network (TERN, 5 km x 5 km extent each). The underlying data can be found here: https://portal.tern.org.au/metadata/TERN/4ff0b4c9-cfa0-4d09-9520-b5402adc583f. For one site (Robson Creek), we also used field data to assess the sensitivity of aboveground biomass estimates to ALS point cloud characteristics. Data are available here: https://portal.tern.org.au/metadata/supersite.174. </p> <p>To characterize climatic/environmental differences between sites, we used climatic data from the CHELSA/BIOCLIM+ climatology 1981-2010 (Brun et al. 2022: Global climate-related predictors at kilometer resolution for the past and future. Earth System Science Data, 14(12), 5573–5603. https://doi.org/10.5194/essd-14-5573-2022; Karger et al. 2017: Climatologies at high resolution for the earth's land surface areas. Scientific Data, 4(1), 170122. https://doi.org/10.1038/sdata.2017.122). </p> <p>We note that the enormous size of the full set of manipulated point clouds (original + thinned + individual flightlines: ~400 GB) and the derived raster products (~200 GB) by far exceeds limits on data storage in Zenodo. However, all analyses can be recreated from scratch from the openly available data and the R code in this repository. In addition, we include derived products for the nine study sites that allow to replicate results in the main text without any point cloud processing (CHMs and other rasters across thinned point clouds + summary statistics). </p> <p>The different data layers are:</p> <p><strong>01_rscripts.zip:</strong></p> <ul> <li>contains a sample script to test the processing pipeline (<em>test.processing.R</em>) as well as a collection of helper functions (<em>ALS_processing_helperfunctions_v40.R</em>); the script can be run directly after unzipping the folder, but an installation of LAStools (https://rapidlasso.de) is necessary (path_lastools = "PATH/TO/LASTOOLS/BIN"); we note that the script was developed on Windows PCs, its application with the recent Linux distribution of LAStools has not yet been tested</li> <li>contains the full set of scripts necessary to reproduce the analyses, including point cloud manipulations and derivation of CHMs from the raw data (<em>create.CHMs.R)</em> as well as the overall robustness analysis (<em>analyze.CHMs.R</em>); to replicate the processing of the raw point clouds step by step, .laz files should be downloaded from the TERN repository (cf. citation above) and placed in a "data" folder, with subfolders for each site and with the same naming conventions as in this repository (e.g., "/data/Alice Mulga")</li> </ul> <p><strong>02_reference.zip</strong></p> <ul> <li>contains reference digital surface models (DSMs), canopy height models (CHMs) and digital terrain models (DTMs) for all nine TERN sites, based on the original ALS point clouds</li> <li>note that these reference layers are produced with the "CHMhighest" algorithm, which provides an easily interpretable canopy description as long as pulse densities are high (>= 20 shots per squaremetre)</li> </ul> <p><strong>03_climate.zip</strong></p> <ul> <li>contains site coordinates</li> <li>contains the climate layers from the CHELSA climatology (cf. citation above, only used to evaluate climatic ranges of sites)</li> </ul> <p><strong>04_robson_additional.zip</strong></p> <ul> <li>contains biomass estimates for Robson Creek</li> <li>contains shapefiles for large trees at Robson Creek (only used for visualization purposes)</li> </ul> <p><strong>05_downsampling_pulse_[Site name].zip</strong></p> <ul> <li>[Site name] is a stand-in for the nine TERN sites (e.g., "Alice Mulga.zip", "Credo.zip", etc.)</li> <li>contains the data necessary to reproduce results in the main text of the study, i.e. DSMs, CHMs, and DTMs for all nine TERN sites, and at different pulse density levels (from 16 down to 0.5 laser shots per squaremetre)</li> <li>also contains calculated summary statistics for each site</li> </ul> <p>All zip files should be extracted into the same folder, except for 05_downsampling_pulse_[Site name].zip which should all be moved to a subfolder called "downsampling_pulse".</p>
Mesh used for Robust Discontinuity Indicators workflows
<p>Mesh used in the paper "Robust Discontinuity Indicators for High-Order Reconstruction of Piecewise Smooth Functions."<br>We have three types of spherical meshes: cubed-sphere (CS), quasi-uniform Voronoi (ICOD), and regionally refined (RRM) grids of the CS and ICOD types. They are NetCDF (.nc) meshes. Spherical meshes have different levels, from coarse to fine. All spherical meshes do not contain any function information.<br>We also uploaded the general surfaces of the plane, cylinder, and reamer bit. They are VTK meshes. The grids in the general surfaces are the same, but they contain different function values and generated RDI information.</p>
Dataset for "Feature-Count Table Normalization" workflow
<p>This dataset is associated with the Galaxy workflow "Feature-Count Table Normalization".</p>
Test Data for iwc Pre-curation PretextMap generation workflow
Open the record for dataset details and reuse information.
Test data for mapseq-to-ampvis2 workflow on Galaxy iwc
Open the record for dataset details and reuse information.
Rock physics models of gas hydrate bearing sediments – the classification, simulation workflow, and challenges
<p>This study reviews the rock physics models for simulating the elastic properties of gas hydrate bearing sediments. Considering that it is confusing to select the appropriate model for a specific study from the various models, we classify the models into five categories according to different principles. We also summarize a general workflow of the modeling process, elaborate the possible models in each step and bring up the potential sources of uncertainties. Besides, we explicate the general problems of the current models and raise several potential research directions. This study provides us a clear view of the rock physics models, the associated uncertainties, as well as the general modeling workflow of gas hydrate bearing sediments, and also provides some implications for future studies.</p>
Workflow notebooks for deriving parameter of SUEWS v2020 based on FLUXNET2015 dataset
<p>This archive includes all supportive files (processing and simulation scripts and derived parameters) for revision of <a href="https://doi.org/10.5194/gmd-2020-148">GMD-2020-148</a>.</p> <p>1. ana.zip: scripts for parameter derivation and and result analysis.</p> <p>2. data.zip: preprocessed FLUXNET data and derived parameters.</p> <p>3. sim.zip: scripts for conducting SUEWS simulations.</p> <p>Please note: due to the Zenodo upload restriction, the simulation results are archived separately at: </p>
Complete workflow for the prediction of the secretome of Fusarium oxysporum f. sp. albedinis, the causal agent of palm dieback
<p>Custom scripts for mining the secretome of <em>Fusarium oxysporum</em> f. sp. <em>albedinis</em>, the causal agent of date palm dieback disease. </p>
Test data for GUNC+BUSCO filtering workflow
<p>Test data for running GUNC+BUSCO filtering workflow, as described on <a href="https://github.com/trajkovski-lab/Quality-filtering">this GitHub page.</a></p>
Nurses' experience of using video consultation in a digital care setting and its impact on their workflow and communication
<p>The dataset contains transcription of 15 interviews performed with nurses working in a digital care setting. It also includes the consent form which were sent to the participants in the study. The study aimed to explore nurses' experience of using video consultation in a digital care setting and its impact on their workflow and communication. All interviews were performed in Sweden. </p>
Data from: A data-driven geospatial workflow to map species distributions for conservation assessments
<p>We developed a geospatial workflow that refines the distribution of a species from its extent of occurrence (EOO) to area of habitat (AOH) within the species range map. The range maps are produced with an inverse distance weighted (IDW) interpolation procedure using presence and absence points derived from primary biodiversity data (GBIF and eBird hotspots respectively). Here we provide sample data to run the geospatial workflow for nine forest species across Mexico and Central America.</p>
Test data for Imputation Workflow
<p>Test data for Imputation Workflow</p>
VGP workflows datasets
<p>VGP workflow test data.</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.