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650 results for “Workflow”
Workflow Trace Archive workflowhub_montage_ti01-971107n_degree-4-0_osg_schema-0-2_montage-4-0-osg-run009 trace
Workload downloaded from WorkflowHub, see http://workflowhub.isi.edu/.
Workflow Trace Archive Pegasus_P4 trace
Trace description unavailable.
Workflow Trace Archive workflowhub_montage_dataset-02_degree-2-0_osg_schema-0-2_montage-2-0-osg-run007 trace
Workload downloaded from WorkflowHub, see http://workflowhub.isi.edu/.
Workflow Trace Archive workflowhub_montage_dataset-02_degree-4-0_osg_schema-0-2_montage-4-0-osg-run009 trace
Workload downloaded from WorkflowHub, see http://workflowhub.isi.edu/.
Workflow Trace Archive alibaba2018 trace
Trace description unavailable.
Replication Package for "Catching Smells in the Act: A GitHub Actions Workflow Investigation" - Thesis
Open the record for dataset details and reuse information.
Code to reproduce the data analysis performed in the study "EXCRETE workflow enables deep proteomics of the microbial extracellular environment"
Open the record for dataset details and reuse information.
Data supporting publication: MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics
<p>MiFoDB (Microbial Foods Database) is a workflow and primary reference database which includes 675 assembled MAGs and RefSeq bacterial, yeast, fungal, and substrate genomes from fermented foods.</p>
Figure 1 from: Haston E, Cubey R, Pullan M, Atkins H, Harris D (2012) Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach. ZooKeys 209: 93-102. https://doi.org/10.3897/zookeys.209.3121
Figure 1 - Diagrammatic overview of the digitisation workflows at the Royal Botanic Garden Edinburgh (RBGE)
Figure 2 from: Tulig M, Tarnowsky N, Bevans M, Kirchgessner A, Thiers B (2012) Increasing the efficiency of digitization workflows for herbarium specimens. ZooKeys 209: 103-113. https://doi.org/10.3897/zookeys.209.3125
Figure 2 - NYBG imaging station consisting of a Canon Eos 5D Mark II digital camera body, a Canon EF 50mm f/2.5 Macro lens, Photo e-Box Plus 1419 from MK Direct, and Kaiser RS 1 copystand.
Figure 6 from: Vohland K, Hoffmann A, Underwood E, Weatherdon L, Bonet F, Häuser C, Wetzel F (2016) 3rd EU BON Stakeholder Roundtable (Granada, Spain): Biodiversity data workflow from data mobilization to practice. Research Ideas and Outcomes 2: e8622. https://doi.org/10.3897/rio.2.e8622
Figure 6 - Participants of the 3rd EU BON Stakeholder Roundtable discussing details of the workflow (credits: Katrin Vohland).
Figure 2 from: Vohland K, Hoffmann A, Underwood E, Weatherdon L, Bonet F, Häuser C, Wetzel F (2016) 3rd EU BON Stakeholder Roundtable (Granada, Spain): Biodiversity data workflow from data mobilization to practice. Research Ideas and Outcomes 2: e8622. https://doi.org/10.3897/rio.2.e8622
Figure 2 - Simplified workflow from data mobilization via processing to stakeholders from the practice.
Figure 1 from: Vohland K, Hoffmann A, Underwood E, Weatherdon L, Bonet F, Häuser C, Wetzel F (2016) 3rd EU BON Stakeholder Roundtable (Granada, Spain): Biodiversity data workflow from data mobilization to practice. Research Ideas and Outcomes 2: e8622. https://doi.org/10.3897/rio.2.e8622
Figure 1 - EU BON Work Packages (WP) with the three sections (a) Data Sources and Infrastructure, (b) Science and Application and (c) Policy and Dialogue. The Stakeholder Roundtables are a specific task in the WP 6 that targets the stakeholder engagement and science-policy dialogue (credits: Pensoft).
Figure 5 from: Vohland K, Hoffmann A, Underwood E, Weatherdon L, Bonet F, Häuser C, Wetzel F (2016) 3rd EU BON Stakeholder Roundtable (Granada, Spain): Biodiversity data workflow from data mobilization to practice. Research Ideas and Outcomes 2: e8622. https://doi.org/10.3897/rio.2.e8622
Figure 5 - Some exemplified results from the questionnaire send around in advance. Left: provision of data. right: Data requirements. N=20 (Florian Wetzel, MfN, 2015).
Kraken2 mini standard database for baargin workflow
<p>This is a minimal nucleotide database for Kraken2 to be used with the baargin workflow: https://github.com/jhayer/baargin</p> <p>It was build as a standard database but with maximum size of 4Gb, in February 2023.</p> <p>The compressed archive is 2.9Gb, and the size of the folder after decompression is 4Gb.</p>
Data for "A massively parallel double selection workflow for the evolution of molecular switches based on surface-display in Escherichia coli" by Givelet, et al., 2023
<p>Data related to a publication on "A massively parallel double selection workflow for the evolution of molecular switches based on surface-display in Escherichia coli"</p> <p> </p> <p>The data contains</p> <p>- FACS data for the images (organized in folders)<br> - images (tiff and jpg)<br> - sequence data (fasta)<br> - one video (mov)</p>
Bioinformatics workflow for the detection of eQTL in the cattle genome using Nextflow DSL2
<p>The <em>in silico</em> detection of expression quantitative trait loci (eQTL) demands high throughput processing from hundreds of samples, which is often a challenge to handle and run such large datasets. In order to focus on the core analysis, it is convenient to have simple coding and hassle-free installation of different software tools required for the bioinformatics workflow. In this context, the newly available technologies like workflow managers and software containers enabled to develop workflows with less complexity. In this study, we developed an eQTL bioinformatics pipeline with the workflow manager Nextflow and docker container software, for coding and installing the required software tools. This workflow can be portable to a different computer environment, and the results are reproducible. We tested the functionality of our workflow with a sample dataset and the runtime estimates from this demo run will provide important information in planning future analyses with much larger datasets.</p>
Supplementary material 2 from: Lumbierres M, Kissling WD (2023) Important first steps towards designing the freshwater, marine and terrestrial Essential Biodiversity Variable (EBV) workflows for the European Biodiversity Observation Network. Research Ideas and Outcomes 9: e109120. https://doi.org/10.3897/rio.9.e109120
Agenda of EuropaBON virtual workshop on EBV workflows
Supplementary material 1 from: Lumbierres M, Kissling WD (2023) Important first steps towards designing the freshwater, marine and terrestrial Essential Biodiversity Variable (EBV) workflows for the European Biodiversity Observation Network. Research Ideas and Outcomes 9: e109120. https://doi.org/10.3897/rio.9.e109120
EuropaBON list of Essential Biodiversity Variables
Supplementary material 1 from: Thompson KM, Birch JL (2023) Mapping the Digitisation Workflow in a University Herbarium. Research Ideas and Outcomes 9: e106883. https://doi.org/10.3897/rio.9.e106883
MELU Digitisation Workflow - Whole picture
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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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.