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Dataset results
23 results for “support package”
Data package supporting manuscript "Widespread Heterogeneity in Density-Dependent Mortality of Nearshore Fishes"
This repository contains the complete data synthesis and analysis pipeline for a global meta-analysis on density-dependent mortality in reef fishes. We estimated mortality parameters (α and β) from >30 ecological studies and explored how ecological traits, experimental methods, and phylogenetic history explain variation in density dependence. It comprises eight data tables in csv format, three .tre files for phylogenetic trees (see method document for data sources), and the zipped code folder (including 12 R scripts) to ensure transparent, end-to-end reproducibility of data processing, analysis, and visualization. This package supports the manuscript “Widespread Heterogeneity in Density-Dependent Mortality of Nearshore Fishes” by Stier & Osenberg (Ecology Letters).
Supporting Information for 'forceX and forceR: a mobile setup and R package to measure and analyse a wide range of animal closing forces'
<p><strong>Supporting Information of 'forceX and forceR: a mobile setup and R package to measure and analyse a wide range of animal closing forces'</strong></p> <p>This dataset contains the Supporting Information of the publication </p> <p>Rühr PT & Blanke A <strong>(2022)</strong>: 'forceX and forceR: a mobile setup and R package to measure and analyse a wide range of animal closing forces'. doi: <a href="https://doi.org/10.1111/2041-210X.13909">10.1111/2041-210X.13909</a>.</p> <p>It includes</p> <ul> <li>validation measurements the forceX setups (1 Ruehr Blanke 2022 validation measurements.zip)</li> <li>all CAD files to build the forceX setup (3D-printed or metal-turned) (2 Ruehr Blanke 2022 forceX CAD files.zip)</li> <li>forceX assembly instructions in HTML format, including schematics of custom electronics (3 Ruehr Blanke 2022 forceX Assembly instructions.html)</li> <li>forceX assembly instructions as video (4 Ruehr Blanke 2022 forceX assembly video 03.mp4)</li> <li>R code that produced all validation-related figures used in the original publication and that functions as a forceR v.1.0.13 example workflow (5 Ruehr Blanke 2022 forceR_workflow_example.R)</li> <li>Python code to take videos of force measurements using the forceX camera module (6 Ruehr Blanke 2022 forceX_RPi_camera_code.py)</li> <li>bundled version of forceR v.1.0.15 (forceR_1.0.15.tar.gz)</li> </ul> <p>The CAD files and assembly instructions are also available on <a href="https://www.thingiverse.com/thing:4961834">Thingiverse</a>. The forceR package is available on <a href="https://cran.r-project.org/web/packages/forceR/index.html">CRAN</a> (stable version) and <a href="https://github.com/Peter-T-Ruehr/forceR">GitHub</a> (development version).</p>
Dataset supporting the tool 'delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition'
<h2>Purpose</h2> <p><br>These data can be used to test my tool <a href="https://github.com/bricoletc/delfies">delfies </a>on real data, to get a concrete sense of its inputs/outputs and test that it is <br>properly installed.</p> <h2>Description</h2> <h3>Genome</h3> <p>I downloaded the genome of <em>Oscheius onirici</em>, accession: <a href="https://www.ebi.ac.uk/ena/browser/view/GCA_932521025.1">GCA_932521025</a>.</p> <p>I subsampled the genome to the last 2kbp of chromosome I, which contains an elimination breakpoint, <br>using `seqkit` v2.8.2, giving the FASTA file in this release.</p> <h3>Sequencing data</h3> <p>I then downloaded the following sequencing data for *O. onirici*, from the European Nucleotide Archive:</p> <ul> <li>ERR5967937: Illumina NovaSeq 6000 paired end short reads. Reads are 2x150bp with average per-base quality of Q27.</li> <li>ERR10796202: Oxford Nanopore PromethION long reads. Reads have average length 11.9kbp and average per-base quality Q11.4.</li> <li>ERR7979900: Pacific Biosciences (PacBio) Sequel II long reads. Reads have average length 11.1kbp and average per-base quality Q28.<br><br></li> </ul> <p>And aligned them to the above genome with `minimap2` version 2.26-r1175, using the following presets: <br>"map-ont" for the Nanopore data, "map-hifi" for the PacBio data, "sr" for the Illumina data.</p> <p>After sorting with `samtools`, this gives the BAM files in this release.</p> <h3>Running delfies</h3> <p>I then ran `delfies` version 0.6.0 on each BAM and genome, as:</p> <p>```sh<br>delfies --threads 16 \<br> --telo_forward_seq TTAGGC \<br> --breakpoint_type all \<br> --min_mapq 20 \<br> --min_supporting_reads 6 \<br> \${genome} \${bam} \${odirname}<br>```</p> <p>The three resulting output directories are in this release, prefixed with `delfies_`.</p> <p><strong>A single, identical breakpoint is found using all three BAMs</strong> (see files '*breakpoint_locations.bed').</p> <h3>Data source</h3> <p>The above raw data were produced and released by the Wellcome Sanger Institute as part of projects <br><a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB51305">PRJEB51305</a> and <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB59023">PRJEB59023.</a></p>
mapspamc_db: a database with global spatial datasets to support the implementation of the mapspamc R package.
<p>This repository contains the mapspamc database (mapspamc_db), a collection of global spatial datasets to support the implementation of the <a href="https://github.com/michielvandijk/mapspamc">mapspamc</a> R package. The database also includes subnational crop statistics and matching country shapefiles for several country examples. For more information on how to use the mapspamc package in combination with mapspamc_db, see the <a href="https://michielvandijk.github.io/mapspamc/">mapspamc documentation</a>. Detailed information on the contents of mapspam_db, such as the sources of information and pre-processing is described in the mapspamc_db documentation (pdf file) that is part of the repository.</p>
Supporting Data for "Extending GPU-Accelerated Gaussian Integrals in the TeraChem Software Package to f Type Orbitals: Implementation and Applications."
<p>Raw data and output files for "Extending GPU-Accelerated Gaussian Integrals in the TeraChem Software Package to f Type Orbitals: Implementation and Applications."</p>
A Model-Driven, Metrics-Based Approach to Assessing Support for Quality Aspects in MLOps System Architectures: Replication Package
<div> <p><strong>Title:</strong> A Model-Driven, Metrics-Based Approach to Assessing Support for Quality Aspects in MLOps System Architectures: Replication Package</p> <p><strong>Authors:</strong> Stephen John Warnett; Uwe Zdun</p> <p><strong>About:</strong> This is the replication package artefact for the paper entitled "A Model-Driven, Metrics-Based Approach to Assessing Support for Quality Aspects in MLOps System Architectures".</p> <p><strong>Paper Abstract:</strong> In machine learning (ML) and machine learning operations (MLOps), automation serves as a fundamental pillar, streamlining the deployment of ML models and representing an architectural quality aspect. Support for automation is especially relevant when dealing with ML deployments characterised by the continuous delivery of ML models. Taking automation in MLOps systems as an example, we present novel metrics that offer reliable insights into support for this vital quality attribute, validated by ordinal regression analysis. Our method introduces novel, technology-agnostic metrics aligned with typical Architectural Design Decisions (ADDs) for automation in MLOps. Through systematic processes, we demonstrate the feasibility of our approach in evaluating automation-related ADDs and decision options. Our approach can itself be automated within continuous integration/continuous delivery pipelines. It can also be modified and extended to evaluate any relevant architectural quality aspects, thereby assisting in enhancing compliance with non-functional requirements and streamlining development, quality assurance and release cycles.</p> </div>
Generating Evidence for a Support Package to Stabilize Youth Trajectories Out of Homelessness
ClinicalTrials.gov study NCT03277794. IPD Sharing: NO. Countries: 1. Publications: 29.
Supporting dataset for phuEGO PyPI package
<p>This upload contain support dataset for the Python package phuEGO, required for version 1.2.0 onwards and compatible with older version.</p> <p>It is labelled as the "slim" version as it only contains sematic similarity of type "gic".</p> <p>Github: https://github.com/haoqichen20/phuego</p> <p>PyPI: https://pypi.org/project/phuego/</p> <p>Documentation: https://phuego.readthedocs.io/en/latest/</p>
Characterizing Support for a Third-party Library: A Study of External Pull Requests for npm packages
<p>Third-party libraries play a key role in building contemporary software applications. Despite this, most libraries are open source that often rely on volunteer (usually unpaid and overworked) contributions for their sustainability. Our motivation is to understand the extent to which third-party libraries are supported by contributions in the form of Pull Requests (PR) from outside the project team (i.e., External PR). Concretely, we analyze 1,076,123 PRs to investigate the External PR prevalence, bots, and the PR characteristics. Our results show that external contributions are prevalent, with packages receiving a high rate of (median of 73.45%) External PR . Furthermore, contributors are also submitting a high proportion of External PR (median of 87.62%). Results indicate a statistical difference in the acceptance of PRs submitted by bots compared to abandoned or open PRs. Furthermore, comparing external and internal PR, we find that Internal PR are more likely to be accepted. Statistically, we find that submitted patches (i.e., commit and code metrics) submitted by Internal PR are higher than patches submitted by External PR. We find that the External PR and Internal PR both have the same content (i.e., introducing new features and fixing bugs). Differently, External PR have more PRs that relate to documentation content, while Internal PR relates to refactoring-related changes</p>
Replication package for Journal paper title "Supporting the identification of prevalent quality issues in code changes by analyzing reviewers' feedback"
<p>Replication package for the study "Supporting the identification of prevalent quality issues in code changes by analyzing reviewers' feedback"</p> <p> </p>
Supported data for manuscript "Different technology packages to deliver the 1.5°C target for global aluminum smelters"
<p>This is the database of the manuscript "Different technology packages to deliver the 1.5°C target for global aluminum smelters" submitted to Nature Climate Change.</p>
Data from: Randomised controlled trial of an education and support package for stroke patients and their carers
Objective: Tailoring stroke information and providing reinforcement opportunities are two strategies proposed to enhance the effectiveness of education. This study aimed to evaluate the effects of an education package which utilised both strategies on the knowledge, health and psychosocial outcomes of stroke patients and carers. Design: Multisite, randomised trial comparing usual care with an education and support package. Setting: Two acute stroke units. Participants: Patients and their carers (N=138) were randomised (control n=67, intervention n=71) of which data for 119 participants (control n=59, intervention n=60) were analysed. Intervention: The package consisted of a computer-generated, tailored written information booklet and verbal reinforcement provided prior to, and for 3 months following, discharge. Outcome measures: Outcome measures were administered prior to hospital discharge and at 3-month follow-up by blinded assessors. The primary outcome was stroke knowledge (score range: 0–25). Secondary outcomes were: self-efficacy (1–10), anxiety and depression (0–21), ratings of importance of information (1–10), feelings of being informed (1–10), satisfaction with information (1–10), caregiver burden (carers) (0–13) and quality of life (patients) (1–5). Results: Intervention group participants reported better: self-efficacy for accessing stroke information (adjusted mean difference (MD) of 1.0, 95% CI 0.3 to 1.7, p=0.004); feeling informed (MD 0.9, 95% CI 0.2 to 1.6, p=0.008); and satisfaction with medical (MD 2.0, 95% CI 1.1 to 2.8, p<0.001); practical (MD 1.1, 95% CI 0.3 to 1.9, p=0.008), services and benefits (MD 0.9, 95% CI 0.1 to 1.8, p=0.036) and secondary prevention information (MD 1.7, 95% CI 0.9 to 2.5, p<0.001). There was no significant effect on other outcomes. Conclusions: Intervention group participants had improved self-efficacy for accessing stroke information and satisfaction with information, but other outcomes were not significantly affected. Evaluation of a more intensive intervention in a trial with a larger sample size is required to establish the value of an educational intervention that uses tailoring and reinforcement strategies.
Replication package for: (Successful) Democracies Breed Their Own Support
<p>This replication package generates all the tables and figures in the paper "(Successful) Democracies Breed Their Own Support" (Review of Economics Studies, forthcoming) by Acemoglu, Ajzenman, Aksoy, Fiszbein, and Molina, using data from multiple sources (see README for details) and Stata code. </p> <p> </p> <p> </p>
Supporting data for "onlineFDR: an R package to control the false discovery rate for growing data repositories"
<p>Supporting data for the manuscript "onlineFDR: an R package to control the false discovery rate for growing data repositories"</p>
Scale-up of an Evidence-based Adolescent Transition Package to Support Transitional Care Among Youth Living With HIV
ClinicalTrials.gov study NCT06924073. IPD Sharing: YES. Countries: 1. Publications: 0.
Smart Blister Packaging and Mobile Application to Monitor and Support Medication Adherence: a Two-arm Usability Study
ClinicalTrials.gov study NCT07099612. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Randomised controlled trial of an education and support package for stroke patients and their carers
Open the record for dataset details and reuse information.
Adult-caregiver Supported Positive Psychology Intervention to Increase Resilience: Work Package 2
ClinicalTrials.gov study NCT06691711. IPD Sharing: NO. Countries: 1. Publications: 0.
Clinical Application of Nutrition Support Package Before Hepatectomy
ClinicalTrials.gov study NCT04218253. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
HOME Study: a Combination Support Package to Increase Uptake of PrEP and HIV/STI Testing
ClinicalTrials.gov study NCT03138135. IPD Sharing: NO. Countries: 1. Publications: 0.
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.