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3,363 results for “Replication”
Data for "Highly-Automated, High-Throughput Replication of Yeast-based Logic Circuit Design Assessments"
<p>Flow Cytometry and plate reader data from "High Throughput Experimentation to replicate Yeast Gates Experiment," accompanied with jupyter noteboooks to replicate the analyses. Sequencing data is <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA784977">available separately</a>.</p> <p>Files named <code>flow_cytometrya<em>x</em></code> should be concatenated: they are individual slices of a gzipped tar file. Concatenate them and then extract with <code>tar xzf <em>filename</em></code>.</p> <p>The paper is available on <a href="https://biorxiv.org/cgi/content/short/2022.05.31.493627">Biorxiv</a>.</p> <p>The Jupyter notebooks used to analyze this data for the paper are <a href="https://github.com/rpgoldman/replication-paper-data-analysis">available on GitHub</a>.</p>
Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon - Pre-computed features for replication
<p>Machaon's computed features that were used in the structural comparisons with Spike protein.</p> <p>DATA_PDBS_vir_whole_1-3.zip files are parts of a single folder.</p> <p> </p>
Replication Data for: Geometric Transformers for Protein Interface Contact Prediction
<p>This dataset contains replication data for the paper titled "Geometric Transformers for Protein Interface Contact Prediction". The dataset consists of pickled Python dictionaries containing pairs of DGLGraphs that can be used to train and validate protein interface contact prediction models. It also contains our best model checkpoints saved as PyTorch LightningModules. Our GitHub repository, DeepInteract, linked in the "Additional notes" metadata section below provides more details on how we use these files as examples for cross-validation.</p>
Pajala fireball replication data
<p>This dataset contains the Pajala 2020-12-04 fireball replication data. It contains:</p> <p>- The Andenes meteor radar raw voltage</p> <p>- The Sodankyla meteor radar raw voltage</p> <p>- Video recording of the fireball from Skibotn</p> <p>- Video recording of the fireball from Sørreisa</p> <p>- The sodankyla ionosonde measurements of the fireball echoes</p>
Replication data [The who, what and how of the current research at the Brazilian Symposium on Software Engineering]
<p>Replication Data for the SBES paper <em>"The who, what and how of the current research at the Brazilian Symposium on Software Engineering"</em></p> <p>Dataset containing analysis (who, what and how) of 90 SBES papers: 27 from SBES’19, 43 from SBES’20, and 20 from SBES’21.</p>
Party control, intra-party competition and the substantive focus of women's parliamentary questions: evidence from Belgium (replication data)
<p>Replication data for B. de Vet & R. Devroe, (2022). Party Control, Intraparty Competition, and the Substantive Focus of Women's Parliamentary Questions: Evidence from Belgium. <em>Politics & Gender,</em> 1-25. doi:10.1017/S1743923X21000490</p>
Replication material for 'The impact of local identities on voting behaviour: A Scouse case study'
<p>This holds the replication material for the paper 'The impact of local identities on voting behaviour: A Scouse case study'</p>
Perceptions on the utility of community question and answer websites like Stack Overflow to software developers (Replication package)
<p>Interview Questions on the perception of the utility of CQAs like Stack Overflow to software developers. In this study, we focused on the questions highlighted in yellow.</p>
In-depth Tissue-Level Dimerization Analysis of AtLEA proteins from Arabidopsis thaliana - Replicate 2
<p>Post 48-hour infiltration, leaves were examined utilizing a 3I Mariana Spinning Disc Confocal microscope equipped with a Zeiss Observer Z.1 Inverted base and a fluorescence spinning disk. In each experimental run, four plants were analyzed, each expressing one of three specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (encompassing the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (comprising the C-terminal region of AtLEA4-5),pYFN-4-2/pYFC-4-2 (full length AtLEA4-2 protein), or pYFN-pYFC (serving as the control condition). Observations were conducted using a 20X—/0.8 NA air lens from Zeiss, under illumination provided by a pre-centered fiber illuminator from Intelligent Imaging Innovations, Inc. The detection of YFP fluorescence was facilitated by a 515 nm excitation laser and a 542/27 nm emission filter. Images were captured using an Andor Ixon 3 EMCCD camera (Model: DU-897E-CS0-#BV), adhering to protocols defined in SlideBook software version 6. Images were captured at specified intervals with exposure times ranging from 400 to 700 milliseconds. Each image consisted of a plane with a pixel size of 0.8 microns, spaced at 2 micrometer intervals. A total of 16 planes, correlating to an estimated depth of 32 micrometers per z-plane, were scrutinized. From each plant, up to three leaves were examined. The analysis included over 50 volumetric scenes per plant, with each scene encompassing a volume of 100 x 100 x 25 mm³. Image stacks were exported as *.tif </p> <p>Notation:</p> <p><strong> </strong></p> <p>Exp2_PYF: Replicate2 expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>45: Fused to the full length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>4H: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>RC: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>control: The control condition (pYFN-pYFC).</p> <p>42: Fused to the full length AtLEA4-2 protein (pYFN-4-2/pYFC-4-2).</p> <p> </p>
In-depth Tissue-Level Dimerization Analysis of AtLEA proteins from Arabidopsis thaliana - Replicate 1
<p>Post 48-hour infiltration, leaves were examined utilizing a 3I Mariana Spinning Disc Confocal microscope equipped with a Zeiss Observer Z.1 Inverted base and a fluorescence spinning disk. In each experimental run, four plants were analyzed, each expressing one of three specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (encompassing the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (comprising the C-terminal region of AtLEA4-5),pYFN-4-2/pYFC-4-2 (full length AtLEA4-2 protein), or pYFN-pYFC (serving as the control condition). Observations were conducted using a 20X—/0.8 NA air lens from Zeiss, under illumination provided by a pre-centered fiber illuminator from Intelligent Imaging Innovations, Inc. The detection of YFP fluorescence was facilitated by a 515 nm excitation laser and a 542/27 nm emission filter. Images were captured using an Andor Ixon 3 EMCCD camera (Model: DU-897E-CS0-#BV), adhering to protocols defined in SlideBook software version 6. Images were captured at specified intervals with exposure times ranging from 400 to 700 milliseconds. Each image consisted of a plane with a pixel size of 0.8 microns, spaced at 2 micrometer intervals. A total of 16 planes, correlating to an estimated depth of 32 micrometers per z-plane, were scrutinized. From each plant, up to three leaves were examined. The analysis included over 50 volumetric scenes per plant, with each scene encompassing a volume of 100 x 100 x 25 mm³. Image stacks were exported as *.tif </p> <p><strong> </strong>Notation:</p> <p>Exp1_PYF: Replicate1 expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>45: Fused to the full length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>4H: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>RC: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>control: The control condition (pYFN-pYFC).</p> <p>42: Fused to the full length AtLEA4-2 protein (pYFN-4-2/pYFC-4-2).</p> <p> </p>
In-depth Tissue-Level Dimerization Analysis of AtLEA proteins from Arabidopsis thaliana - Replicate 4
<p> Post 48-hour infiltration, leaves were examined utilizing a 3I Mariana Spinning Disc Confocal microscope equipped with a Zeiss Observer Z.1 Inverted base and a fluorescence spinning disk. In each experimental run, four plants were analyzed, each expressing one of three specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (encompassing the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (comprising the C-terminal region of AtLEA4-5),pYFN-4-2/pYFC-4-2 (full length AtLEA4-2 protein), or pYFN-pYFC (serving as the control condition). Observations were conducted using a 20X/0.8 NA air lens from Zeiss, under illumination provided by a pre-centered fiber illuminator from Intelligent Imaging Innovations, Inc. The detection of YFP fluorescence was facilitated by a 515 nm excitation laser and a 542/27 nm emission filter. Images were captured using an Andor Ixon 3 EMCCD camera (Model: DU-897E-CS0-#BV), adhering to protocols defined in SlideBook software version 6. Images were captured at specified intervals with exposure times ranging from 400 to 700 milliseconds. Each image consisted of a plane with a pixel size of 0.8 microns, spaced at 2 micrometer intervals. A total of 16 planes, correlating to an estimated depth of 32 micrometers per z-plane, were scrutinized. From each plant, up to three leaves were examined. The analysis included over 50 volumetric scenes per plant, with each scene encompassing a volume of 100 x 100 x 25 mm³. Image stacks were exported as *.tif </p> <p>Notation:</p> <p>Exp1_PYF: Replicate 4 expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>45: Fused to the full length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>4H: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>RC: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>control: The control condition (pYFN-pYFC).</p> <p>42: Fused to the full length AtLEA4-2 protein (pYFN-4-2/pYFC-4-2).</p>
In-depth Tissue-Level Dimerization Analysis of AtLEA proteins from Arabidopsis thaliana - Replicate 3
<p>Post 48-hour infiltration, leaves were examined utilizing a 3I Mariana Spinning Disc Confocal microscope equipped with a Zeiss Observer Z.1 Inverted base and a fluorescence spinning disk. In each experimental run, four plants were analyzed, each expressing one of three specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein: pYFN-4-/5pYFC-4-5 (representing the complete AtLEA4-5 protein), pYFN-4-51-77/pYFC-4-51-77 (encompassing the N-terminal region of AtLEA4-5), pYFN-4-578-158/pYFC-4-578-158 (comprising the C-terminal region of AtLEA4-5),pYFN-4-2/pYFC-4-2 (full length AtLEA4-2 protein), or pYFN-pYFC (serving as the control condition). Observations were conducted using a 20X—/0.8 NA air lens from Zeiss, under illumination provided by a pre-centered fiber illuminator from Intelligent Imaging Innovations, Inc. The detection of YFP fluorescence was facilitated by a 515 nm excitation laser and a 542/27 nm emission filter. Images were captured using an Andor Ixon 3 EMCCD camera (Model: DU-897E-CS0-#BV), adhering to protocols defined in SlideBook software version 6. Images were captured at specified intervals with exposure times ranging from 400 to 700 milliseconds. Each image consisted of a plane with a pixel size of 0.8 microns, spaced at 2 micrometer intervals. A total of 16 planes, correlating to an estimated depth of 32 micrometers per z-plane, were scrutinized. From each plant, up to three leaves were examined. The analysis included over 50 volumetric scenes per plant, with each scene encompassing a volume of 100 x 100 x 25 mm³. Image stacks were exported as *.tif </p> <p> </p> <p>Notation:</p> <p> </p> <p>Exp3_PYF: Replicate 3 expressing one of four specific genetic constructs fused to complementary fragments of Yellow Fluorescent Protein.</p> <p>45: Fused to the full length AtLEA4-5 protein (pYFN-4-/5pYFC-4-5).</p> <p>4H: Fused to the N-terminal region of AtLEA4-5 (pYFN-4-51-77/pYFC-4-51-77).</p> <p>RC: Fused to the C-terminal region of AtLEA4-5 (pYFN-4-578-158/pYFC-4-578-158).</p> <p>control: The control condition (pYFN-pYFC).</p> <p>42: Fused to the full length AtLEA4-2 protein (pYFN-4-2/pYFC-4-2).</p> <p> </p> <p> </p>
Dataset and code from the ATLAS phone survey to replicate analysis of HIVST positivity rates and linkage to confirmatory testing
<p>This dataset and code allow to replicate the analysis presented in the paper entitled "HIV self-testing positivity rate and linkage to confirmatory testing and care: a telephone survey in Côte d'Ivoire, Mali and Senegal" by Arsène Kra Kouassi et al. Preprint available at <a href="https://doi.org/10.1101/2023.06.10.23291206">https://doi.org/10.1101/2023.06.10.23291206</a></p><p>The data was collected within the ATLAS project, funded by Unitaid and coordinated by Solthis and IRD.</p><p>ATLAS website: <a href="https://atlas.solthis.org/">https://atlas.solthis.org/</a></p><p>ATLAS presentation on Ceped website: <a href="https://www.ceped.org/atlas">https://www.ceped.org/atlas</a></p><p>ATLAS publications portal: <a href="https://hal.science/ATLAS_ADVIH/">https://hal.science/ATLAS_ADVIH/</a></p><p> </p><p> </p>
Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (replicate 1)
<p>Replicate simulation 1/4</p> <p>Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation. </p> <p>Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.</p>
Replication data for Global variation in the preferred temperature for recreational outdoor activity
<p><strong>Description</strong></p> <p>This dataset contains the processed data used for the statistical analysis in Linsenmeier, M. (2024): <a href="https://doi.org/10.1016/j.jeem.2024.103032">Global variation in the preferred temperature for recreational outdoor activity</a>, published in the Journal of Environmental Economics and Management.</p> <p>The main data on temperature and rainfall are from ERA5 reanalysis (Hersbach et al. 2018). Data on mobile phone activity are from the Google Mobility Reports. Data on GDP per capita are from the World Bank.</p> <p><strong>Acknowledgements</strong></p> <p>The data contain modified Copernicus Climate Change Service information 2020. Neither the European Commission nor ECMWF is responsible for any use that may be made of the Copernicus information or data it contains.</p> <p><strong>Bibliography</strong></p> <ul> <li>Hersbach, H., Bell, B., Berrisford, P., Biavati, G., Horányi, A., Muñoz Sabater, J., Nicolas, J., Peubey, C., Radu, R., Rozum, I., Schepers, D., Simmons, A., Soci, C., Dee, D., Thépaut, J-N. (2018): ERA5 hourly data on single levels from 1959 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS). 10.24381/cds.adbb2d47</li> </ul>
Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication: insertion data and derivative models
<p>This data repository provides access to the LINE-1 (L1) insertion site data from Flasch, et al., 2019:<br><a href="https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub">https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub</a></p> <p>Please see file <strong>L1_actual_and_random_insertions_help.docx</strong> for more detailed information.</p> <p>Files <strong>weighted_model_142_102917_corrected.txt</strong> and <strong>weighted_model_142_102917_uncorrected.txt</strong> carry a list of all possible 7-mer insertion sites, one per row, with site weights calculated based on observed L1 insertion sites. The files are either corrected or uncorrected for the frequency of those sites as found in the human genome, respectively. A header line defines the columns.</p> <p>The weight files described above were used to construct the simulated <strong>hg19 </strong>insertions sets described below.</p> <p>Archive <strong>all_insertion_sets.tar</strong> contains a series of insertion files, each with the complete data set used to analyze insertions from the named cell line.</p> <p>Column 5 is the iteration number, where:</p> <ul> <li>iteration == 0 identifies the actual, observed insertions</li> <li>each iteration > 0 identifies one round of simulation, up to 10K total simulations</li> <li>each iteration has the same number of insertions</li> </ul> <p>Column 4 is the insertion number within each actual or simulated insertion set.</p> <p>Please see the companion Zenodo data set:<br>10.5281/zenodo.12538130<br>for more information about creating insertion site models from your own insertion data.</p>
Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication: creating new models
<p>This data repository provides code and general instructions for creating new LINE-1 (L1) insertion site models as described in Flasch, et al., 2019:<br><a href="https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub">https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub</a></p> <p>Please see file <strong>L1_Simulation_Files_help.docx</strong> for more detailed information.</p> <p>File <strong>L1Simulation_filelist.xlsx</strong> lists the files described in the Word file and found in <strong>L1Simulations.tar.gz</strong>.</p> <p>Required large file <strong>ChrmsALL_table_sortEN.bed.gz</strong> is found individually. Importantly, like the paper analysis, this file is specific to the <strong>hg19 </strong>version of the human genome.</p> <p>Please see the companion Zenodo data set<br>10.5281/zenodo.8233858<br>if you only want to access our insertion data and the resulting models we created.</p> <p> </p>
Replication Package for the Paper Titled "How Well Do Software Practitioners Fix Code Vulnerabilities with Different Types of Explanations?"
<p>This is a replication package for the article 'How Well Do Software Practitioners Fix Code Vulnerabilities with Different Types of Explanations?'. The survey questions can be found here, and we encourage the survey to be re-used.</p> <p>We also include survey data (with demographic data and qualitative responses removed for anonymity reasons).</p> <p>The project team consists of Tracy Hall, Emily Winter, Fahad Al Debeyan (Lancaster University) and Lech Madeyski (Wroclaw University of Science and Technology). If you have any questions about the re-use of this survey, feel free to contact Fahad at <a href="mailto:e.winter@lancaster.ac.uk">f.aldebeyan@lancaster.ac.uk</a>.</p>
Replication data for: "How does Docker affect energy consumption? Evaluating workloads in and out of Docker containers"
<p>Database of raw power measurements and energy summaries for our Docker energy tests.</p> <p>Please cite us if you use this dataset.</p> <p>Schema</p> <pre><code>CREATE TABLE configuration( name TEXT PRIMARY KEY, description TEXT ); CREATE TABLE experiment( name TEXT PRIMARY KEY, description TEXT ); CREATE TABLE run( id PRIMARY KEY, configuration TEXT REFERENCES configuration(name) ON DELETE CASCADE ON UPDATE CASCADE, experiment TEXT REFERENCES experiment(name) ON DELETE CASCADE ON UPDATE CASCADE ); CREATE TABLE measurement( run REFERENCES run(id) ON DELETE CASCADE ON UPDATE CASCADE, timestamp REAL NOT NULL, -- Unix timestamp in milliseoncds power REAL NOT NULL ); CREATE TABLE energy( id PRIMARY KEY REFERENCES run(id), configuration TEXT REFERENCES configuration(name) ON DELETE CASCADE ON UPDATE CASCADE, experiment TEXT REFERENCES experiment(name) ON DELETE CASCADE ON UPDATE CASCADE, energy REAL NOT NULL, started REAL NOT NULL, ended REAL NOT NULL, elapsed_time REAL NOT NULL -- in milliseconds );</code></pre>
Replication Data for: Probing magnetism in 2D materials at the nanoscale with single spin microscopy
<p>Data repository for: <strong>Probing magnetism in 2D materials at the nanoscale with single spin microscopy</strong></p> <p><em>Data description.pdf </em>describes the uploaded data.<br> <em>Data.xlsx</em> is the data represented in the paper.<br> <em>MzFromBNV.m</em>, <em>kvalues.m</em>, <em>NVZeemanShiftFromMagnetizedSampleEdge.m</em> are Matlab code files used to transform and fit the data.</p> <p> </p>
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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)
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DANDI Archive for NWB datasets
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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.