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10 results for “Repository Pattern”
Repository for: Patterned invagination prevents mechanical instability during gastrulation
<p>This is the repository for the paper:</p> <p>Vellutini, B. C., Cuenca, M. B., Krishna, A., Szałapak, A., Modes, C. D. & Tomancak, P. Patterned invagination prevents mechanical instability during gastrulation. <em>Nature</em> (2025). doi:<a href="https://10.1038/s41586-025-09480-3">10.1038/s41586-025-09480-3</a></p> <p>Here are all the associated repositories:</p> <ul> <li><strong>Main repository (code and data):</strong> <a href="https://doi.org/10.5281/zenodo.7781947">https://doi.org/10.5281/zenodo.7781947</a></li> <li><strong>Model and simulations (code and data):</strong> <a href="https://doi.org/10.5281/zenodo.7784906">https://doi.org/10.5281/zenodo.7784906</a></li> <li><strong>Lightsheet and in situ experiments (imaging data):</strong> <a href="https://doi.org/10.5281/zenodo.15876638">https://doi.org/10.5281/zenodo.15876638</a></li> <li><strong>Laser perturbation experiments (imaging data):</strong> <a href="https://doi.org/10.5281/zenodo.15876646">https://doi.org/10.5281/zenodo.15876646</a></li> <li><strong>Figures and videos (media files):</strong> <a href="https://doi.org/10.5281/zenodo.7781916">https://doi.org/10.5281/zenodo.7781916</a></li> </ul> <p>The main repository is maintained at <a href="https://github.com/bruvellu/cephalic-furrow">https://github.com/bruvellu/cephalic-furrow</a>.</p>
Repository for: Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning
<p>This repository contains the data and analyses for the manuscript:</p> <p>Vellutini, B. C., Martín-Durán, J. M., Børve, A. & Hejnol, A. <strong>Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning.</strong> BMC Biol. 22, 1–23 (2024). <a href="https://doi.org/10.1186/s12915-024-01988-w" rel="nofollow">https://doi.org/10.1186/s12915-024-01988-w</a></p> <p>The source is maintained at <a href="https://github.com/bruvellu/terebratalia-wnts">https://github.com/bruvellu/terebratalia-wnts</a>.</p>
DataQI.NET: A Framework for Specifying Query Criteria Using the Repository Pattern
<p>During the construction of applications that require integration with databases, developers often dedicate a considerable amount of time writing the data access layer. Although there are some tools that aim at improving that process, it still demands a great amount of (usually default) code, which is error-prone, takes effort and time from the developer, and reduces the code reuse potential. This paper presents the DataQI.NET, a framework that encapsulates the complexity of those tools and makes possible the definition of customized queries through method signatures on interfaces that follow the Repository Pattern, allowing the developer to focus more on the business rules implementation. A comparative study is provided considering the implementation with and without the framework, demonstrating that, by using DataQI.NET, we obtain more homogeneous and standardized query methods that communicate, supporting code reuse and significant reduction on the lines of code and implementation time.</p>
Data repository for "Lockdown impact on age-specific contact patterns and behaviours, France, April 2020"
<p>Aggregated contact matrices associated with the publication "Lockdown impact on age-specific contact patterns and behaviours, France, April 2020" . </p> <p> </p>
Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)
<p>Simulated ONT and PacBio RNA-Seq data for "Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns" paper (Mikheenko et al., Genome Research, 2022). All details can be found in the Methods section of the paper.</p> <p><strong>PacBio.simulated_uniform_coverage.fasta.gz</strong> and <strong>ONT.simulated_uniform_coverage.fasta.gz files</strong> were used in Supplemental Note “Benchmarking of the read-to-isoform assignment algorithm”.</p> <p><strong>ONT.simulated_real_expression.fasta.gz</strong> file and all GTF files were used in the Section "Splice site correction improves transcript discovery precision". <strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> was used as the annotation file for all tools. <strong>mouse.gencode.M26.spatial.15percent.expressed.gtf </strong>contains the set of all expressed isoforms. <strong>mouse.gencode.M26.spatial.15percent.expressed_kept.gtf</strong> contains those of the isoforms that are in presented in the annotation file ("known" transcripts), <strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> contains expressed isoforms that were removed from the annotation ("novel" transcripts).</p>
Design Patterns for AI-based Systems: A Multivocal Literature Review and Pattern Repository
<p>The data for a multivocal literature review on design patterns for AI-based systems.</p> <ul> <li>mlr-search-and-selection.xlsx: the results from the queried databases and search engines, the inclusion/exclusion process, and the backward and forward snowballing results</li> <li>mlr-results.xlsx: the final set of selected resources, the patterns extracted from them, and some analysis</li> <li>query-strings-google-and-google-scholar.txt: the individual terms of the search query (broken up for Google Scholar and Google Search)</li> </ul>
Qualisign: Software Metrics and GoF Design Patterns of the Maven Central Repository
<p>This dataset contains software metric and design pattern data for around 100,000 projects from the Maven Central repository. The data was collected and analyzed as part of my master's thesis "Mining Software Repositories for the Effects of Design Patterns on Software Quality" (https://www.overleaf.com/read/vnfhydqxmpvx, https://zenodo.org/record/4048275).</p> <p>The included qualisign.* files all contain the same data in different formats:<br> - qualisign.sql: standard SQL format (exported using "pg_dump --inserts ..."),<br> - qualisign.psql: PostgreSQL plain format (exported using "pg_dump -Fp ..."),<br> - qualisign.csql: PostgreSQL custom format (exported using "pg_dump -Fc ...").</p> <p>create-tables.sql has to be executed before importing one of the qualisign.* files. Once qualisign.*sql has been imported, create-views.sql can be executed to preprocess the data, thereby creating materialized views that are more appropriate for data analysis purposes.</p> <p>---</p> <p>Software metrics were calculated using CKJM extended:<br> http://gromit.iiar.pwr.wroc.pl/p_inf/ckjm/</p> <p>Included software metrics are (21 total):<br> - AMC: Average Method Complexity<br> - CA: Afferent Coupling<br> - CAM: Cohesion Among Methods<br> - CBM: Coupling Between Methods<br> - CBO: Coupling Between Objects<br> - CC: Cyclomatic Complexity<br> - CE: Efferent Coupling<br> - DAM: Data Access Metric<br> - DIT: Depth of Inheritance Tree<br> - IC: Inheritance Coupling<br> - LCOM: Lack of Cohesion of Methods (Chidamber and Kemerer)<br> - LCOM3: Lack of Cohesion of Methods (Constantine and Graham)<br> - LOC: Lines of Code<br> - MFA: Measure of Functional Abstraction<br> - MOA: Measure of Aggregation<br> - NOC: Number of Children<br> - NOM: Number of Methods<br> - NOP: Number of Polymorphic Methods<br> - NPM: Number of Public Methods<br> - RFC: Response for Class<br> - WMC: Weighted Methods per Class</p> <p>In the qualisign.* data, these metrics are only available on the class level. create-views.sql additionally provides averages of these metrics on the package and project levels.</p> <p>---</p> <p>Design patterns were detected using SSA:<br> https://users.encs.concordia.ca/~nikolaos/pattern_detection.html</p> <p>Included design patterns are (15 total):<br> - Adapter<br> - Bridge<br> - Chain of Responsibility<br> - Command<br> - Composite<br> - Decorator<br> - Factory Method<br> - Observer<br> - Prototype<br> - Proxy<br> - Singleton<br> - State<br> - Strategy<br> - Template Method<br> - Visitor</p> <p>---</p> <p>The code to generate the dataset is available at:<br> https://github.com/jaichberg/qualisign</p> <p>The code to perform quality analysis on the dataset is available at:<br> https://github.com/jaichberg/qualisign-analysis</p>
Code and Data Repository for "Identifying microbiota community patterns important for plant protection using machine learning in synthetic community experiments"
<p>The repository includes data and R code necessary to reproduce all figures and analyses presented in the study titled "Identifying microbiota community patterns important for plant protection using machine learning in synthetic community experiments".</p>
Repository for "Activity-induced polar patterns of filaments gliding on a sphere"
<p>Activity-induced polar patterns of filaments gliding on a sphere (Nature Communications)</p> <p>The structure of this repository is as follows:</p> <p>1. Image.zip -- contains confocal images and equirectangular projections </p> <ul> <li> <p>Confocal_Stacks </p> </li> </ul> <p> contains confocal stacks of Movie S1-S8</p> <ul> <li> <p>Epifluorescence_Projections</p> </li> </ul> <p> contains epifluorescence projections of 100, 150, 300, and 600 nM encapsulated actin concentrations for Figure 1&2</p> <ul> <li> <p>Equirectangular_Projections</p> </li> </ul> <p> contains equirectangular projections of Movie S2, S4-6, S8</p> <p>2. Code.zip -- contains python3 codes and data for MSD and optical flow analysis </p> <ul> <li> <p>MSD</p> </li> </ul> <p> contains codes and data for the MSD analysis in Figure 3f&3g and Figure S5</p> <ul> <li> <p>OpticalFlow</p> </li> </ul> <p> contains codes and data for optical flow analysis in Figure 4b&4c</p> <p> </p>
Github Repository for "Social interactions generate complex selection patterns in virtual worlds"
<p>Repository for <br><strong>"Social interactions generate complex selection patterns in virtual worlds"</strong><br><em>Francesca Santostefano, Maxime Fraser Franco, Pierre Olivier Montiglio</em><br>Journal of Evolutionary Biology 2024</p>
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
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.