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Example Microscopy Metadata JSON files produced using Micro-Meta App to document example microscopy experiments performed at individual core facilities
<p>Example <strong>Microscopy Metadata </strong>(Microscope.JSON and Settings.JSON)<strong> files </strong>produced using<strong> <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">Micro-Meta App</a> </strong>to document the <strong>Hardware Specifications</strong> of example Microscopes and the <strong>Image Acquisition Settings</strong> utilized to acquire example images as listed in the table below.</p> <blockquote> <p>For each facility, the dataset contains two JSON files:</p> <ol> <li><strong>Microscope.JSON file</strong> (e.g., 01_marcello_uliverpool_cci_zeiss_axioobserz1_lsm710.json)</li> <li><strong>Settings.JSON file</strong> (indicated with the name of the image and with the _AS suffix)</li> </ol> </blockquote> <p><strong>Micro-Meta App was</strong> developed as part of a <strong>global community initiative</strong> including the <a href="http://www.4dnucleome.org/"><strong>4D Nucleome (4DN)</strong> </a>Imaging Working Group, <strong>BioImaging North America (BINA)</strong> <a href="https://www.bioimagingna.org/qc-dm-wg">Quality Control and Data Management Working Group</a>, and <strong>QUAlity and REProducibility for Instrument and Images in Light Microscopy</strong> (<a href="https://quarep.org/"><strong>QUAREP-LiMi</strong></a>), to extend the <strong>Open Microscopy Environment (OME)</strong> <a href="https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome.html">data model</a>.</p> <blockquote> <p>The works of this <strong>global community effort</strong> resulted in multiple publications featured on a recent <strong>Nature Methods FOCUS ISSUE </strong>dedicated to <a href="https://www.nature.com/collections/djiciihhjh">Reporting and reproducibility in microscopy</a>.</p> </blockquote> <blockquote> <p><strong>Learn More!</strong> For a thorough description of <strong>Micro-Meta App</strong> consult our recent <a href="https://doi.org/10.1038/s41592-021-01315-z">Nature Methods</a> and <a href="https://doi.org/10.1101/2021.05.31.446382">BioRxiv.org</a> publications!</p> </blockquote> <p> </p> <table> <tbody> <tr> <td><strong>Nr.</strong></td> <td><strong>Manufacturer</strong></td> <td><strong>Model</strong></td> <td><strong>Tier</strong></td> <td><strong>Εxperiment Type</strong></td> <td><strong>Facility Name</strong></td> <td><strong>Department and Institution</strong></td> <td><strong>URL</strong></td> <td><strong>References</strong></td> </tr> <tr> <td>1</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1 (with LSM 710 scan head)</strong></td> <td>1</td> <td>3D visualization of superhydrophobic polymer-nanoparticles</td> <td>Centre for Cell Imaging (CCI)</td> <td>University of Liverpool</td> <td>https://cci.liv.ac.uk/equipment_710.html</td> <td>Upton et al., 2020</td> </tr> <tr> <td>2</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer (Axiovert 200M)</strong></td> <td>2</td> <td>Μeasurement of illumination stability on Chinese Hamster Ovary cells expressing Paxillin-EGFP</td> <td>Advanced BioImaging Facility (ABIF).</td> <td>McGill University</td> <td>https://www.mcgill.ca/abif/equipment/axiovert-1</td> <td>Kiepas et al., 2020</td> </tr> <tr> <td>3</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1 (with Spinning Disk)</strong></td> <td>2</td> <td>Immunofluorescence imaging of cryosection of Mouse kidney</td> <td>Imagerie Cellulaire; Quality Control managed by Miacellavie (https://miacellavie.com/)</td> <td>Centre de recherche du Centre Hospitalier Université de Montréal (CR CHUM), University of Montreal</td> <td>https://www.chumontreal.qc.ca/crchum/plateformes-et-services (the web site is for all core facilities, not specifically for the core facility hosting this microscope)</td> <td>Pilliod et al., 2020</td> </tr> <tr> <td>4</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Imager Z2 (with Apotome)</strong></td> <td>2</td> <td>Immunofluorescence imaging of mitotic division in Hela cells using </td> <td>Bioimaging Unit</td> <td>Newcastle University</td> <td>https://www.ncl.ac.uk/bioimaging/</td> <td>Watson et al., 2020</td> </tr> <tr> <td>5</td> <td><strong>Carl Zeiss Microscopy</strong></td> <td><strong>Axio Observer Z1</strong></td> <td>2</td> <td>Fluorescence microscopy of human skin fibroblasts from Glycogen Storage Disease patients.</td> <td>Life Imaging Center (LIC)</td> <td>Centre for Integrative Signalling Analysis (CISA), University of Freiburg</td> <td>https://miap.eu/equipments/sd-i-abl/</td> <td>Hannibal et al., 2020</td> </tr> <tr> <td>6</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DMI6000B</strong></td> <td>2</td> <td>3D immunofluorescence imaging rhinovirus infected macrophages </td> <td>IMAG'IC Confocal Microscopy Facility</td> <td>Institut Cochin, CNRS, INSERM, Université de Paris</td> <td>https://www.institutcochin.fr/core_facilities/confocal-microscopy/cochin-imaging-photonic-microscopy/organigram_team/10054/view</td> <td>Jubrail et al., 2020</td> </tr> <tr> <td>7</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DM5500B</strong></td> <td>2</td> <td>Immunofluorescence analysis of the colocalization of PML bodies with DNA double-strand breaks</td> <td>Bioimaging Unit</td> <td>Edwardson Building on the Campus for Ageing and Vitality, Newcastle University</td> <td>https://www.ncl.ac.uk/bioimaging/equipment/leica-dm5500/#overview</td> <td>da Silva et al., 2019; Nelson et al., 2012<br> </td> </tr> <tr> <td>8</td> <td><strong>Leica Microsystems</strong></td> <td><strong>DMI8-CS (with TCS SP8 STED 3X)</strong></td> <td>2</td> <td>Live-cell imaging of N. benthamiana leaves cells-derived protoplasts</td> <td>Center for Advanced Imaging (CAi)</td> <td>School of Mathematics/Natural Sciences, Heinrich-Heine-Universität Düsseldorf</td> <td>https://www.cai.hhu.de/en/equipment/super-resolution-microscopy/leica-tcs-sp8-sted-3x</td> <td>Singer et al., 2017; Hänsch et al., 2020</td> </tr> <tr> <td>9</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti</strong></td> <td>2</td> <td>Immunofluorescence analysis of the cytoskeleton structure in COS cells</td> <td>Advanced Imaging Center (AIC)</td> <td>Janelia Research Campus, Howard Hughes Medical Institute</td> <td>https://www.janelia.org/support-team/light-microscopy/equipment</td> <td>Abdelfattah et al., 2019; Qian et al., 2019; Grimm et al., 2020</td> </tr> <tr> <td>10</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti-E (HCA)</strong></td> <td>2</td> <td>Τime-lapse analysis of the bursting behavior of amine-functionalized vesicular assemblies</td> <td>Light Microscopy Facility (IALS-LIF)</td> <td>Institute for Applied Life Sciences, University of Massachusetts at Amherst</td> <td>https://www.umass.edu/ials/light-microscopy</td> <td>Fernandez et al., 2020</td> </tr> <tr> <td>11</td> <td><strong>Nikon Instruments/Coleman laboratory (customized)</strong></td> <td><strong>TIRF HILO Epifluorescence light Microscope (THEM)/ Eclipse Ti</strong></td> <td>2</td> <td>Single-particle tracking of Halo-tagged PCNA in Lox cells</td> <td>Coleman laboratory</td> <td>Anatomy and Structural Biology Department, The Albert Einstein College of Medicine</td> <td>https://einsteinmed.org/faculty/12252/robert-coleman/</td> <td>Drosopoulos et al., 2020</td> </tr> <tr> <td>12</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti (with Andor Dragon Fly Spinning Disk)</strong></td> <td>2</td> <td>Investigation of the 3D structure of cerebral organoids</td> <td>Montpellier Resources Imagerie</td> <td>Centre de Recherche de Biologie cellulaire de Montpellier (MRI-CRBM), CNRS, Univerity of Montpellier</td> <td>https://www.mri.cnrs.fr/en/optical-imaging/our-facilities/mri-crbm.html</td> <td>Ayala-Nunez et al., 2019</td> </tr> <tr> <td>13</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti2</strong></td> <td>2</td> <td>Ιmmunofluorescence imaging of cryosections of mouse hearth myocardium </td> <td>Neuroscience Center Microscopy Core</td> <td>Neuroscience Center, University of North Carolina</td> <td>https://www.med.unc.edu/neuroscience/core-facilities/neuro-microscopy/</td> <td>Aghajanian et al., 2021</td> </tr> <tr> <td>14</td> <td><strong>Nikon Instruments</strong></td> <td><strong>Eclipse Ti2</strong></td> <td>2</td> <td>Live-cell imaging of bacterial cells expressing GFP-PopZ</td> <td>Microscopy Resources on the North Quad (MicRoN)</td> <td>Harvard Medical School </td> <td>https://micron.hms.harvard.edu/</td> <td>Lim and Bernhardt 2019; Lim et al., 2019</td> </tr> <tr> <td>15</td> <td><strong>Olympus/Biomedical Imaging Group (customized)</strong></td> <td><strong>TIRF Epifluorescence Structured light Microscope (TESM)/IX71</strong></td> <td>3</td> <td>3D distribution of HIV-1 in the nucleus of human cells</td> <td>Biomedical Imaging Group</td> <td>Program in Molecular Medicine, University of Massachusetts Medical School</td> <td>https://trello.com/b/BQ8zCcQC/tirf-epi-fluorescence-structured-light-microscope</td> <td>Navaroli et al., 2012</td> </tr> <tr> <td>16</td> <td><strong>Olympus/Computer Vision Laboratory (customized)</strong></td> <td><strong>3D BrightField Scanner/IX71</strong></td> <td>3</td> <td>Transmitted light brightfield visualization of swimming spermatocytes</td> <td>Laboratorio Nacional de Microscopia Avanzada (LNMA) and Computer Vision Laboratory of the Institute of Biotechnology</td> <td>Universidad Nacional Autonoma de Mexico (UNAM)</td> <td>https://lnma.unam.mx/wp/</td> <td>Pimentel et al., 2012; Silva-Villalobos et al., 2014</td> </tr> </tbody> </table> <p><strong>Getting started</strong></p> <p>Use these videos to get started with using Micro-Meta App after installation into OMERO and downloading the example data files:</p> <ol> <li><a href="https://vimeo.com/562022222">Video 1</a></li> <li><a href="https://vimeo.com/562022281">Video 2</a></li> </ol> <p><strong>More information</strong></p> <blockquote> <p>For full information on how to use Micro-Meta App please utilize the following resources:</p> <ol> <li>Micro-Meta App <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">website</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/index.html">Full documentation</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/intro/installation.html">Installation</a> instructions</li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/tutorials/index.html#step-by-step-instructions">Step-by-Step Instructions</a></li> <li><a href="https://micrometaapp-docs.readthedocs.io/en/latest/docs/tutorials/VideoTutorials.html#micro-meta-app-video-tutorials">Tutorial Videos</a></li> </ol> </blockquote> <p><strong>Background</strong></p> <p>If you want to learn more about the importance of <strong>metadata and quality contro</strong>l to ensure full <strong>reproducibility, quality and scientific value</strong> in light microscopy, please take a look at our recent publications describing the development of community-driven light <strong>4DN-BINA-OME Microscopy Metadata</strong> specifications <a href="https://doi.org/10.1038/s41592-021-01327-9">Nature Methods</a> and <a href="https://doi.org/10.1101/2021.04.25.441198">BioRxiv.org</a> and our <a href="https://arxiv.org/abs/1910.11370">overview manuscript</a> entitled <strong>A perspective on Microscopy Metadata: data provenance and quality control</strong>.</p> <p> </p> <p> </p>
Example Microscopy Metadata JSON files produced using Micro-Meta App to document the acquisition of example images using a custom-built TIRF Epifluorescence Structured Illumination Microscope
<p><strong>Example Microscopy Metadata JSON files produced using the <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">Micro-Meta App</a> documenting an example raw-image file acquired using the custom-built TIRF Epifluorescence Structured Illumination Microscope.</strong></p> <p>For this use case, which is presented in Figure 5 of <a href="http://doi: https://doi.org/10.1101/2021.05.31.446382">Rigano et al., 2021</a>, Micro-Meta App was utilized to document:</p> <p>1) The <strong>Hardware Specifications</strong> of the custom build TIRF Epifluorescence Structured light Microscope (TESM; <a href="https://www.pnas.org/content/109/8/E471.long">Navaroli et al., 2010</a>) developed, built on the basis of the based on Olympus IX71 microscope stand, and owned by the Biomedical Imaging Group (http://big.umassmed.edu/) at the Program in Molecular Medicine of the University of Massachusetts Medical School. Because TESM was custom-built the most appropriate documentation level is <strong>Tier 3</strong> (<em>Manufacturing/Technical Development/Full Documentation</em>) as specified by the <a href="https://doi.org/10.5281/zenodo.4710731">4DN-BINA-OME</a> Microscopy Metadata model (<a href="https://doi.org/10.1101/2021.04.25.441198">Hammer et al., 2021</a>).</p> <p>The TESM Hardware Specifications are stored in: <strong>Rigano et al._Figure 5_UseCase_Biomedical Imaging Group_TESM.JSON</strong></p> <p>2) The <strong>Image Acquisition Settings</strong> that were applied to the TESM microscope for the acquisition of an example image (FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif) obtained by Nicholas Vecchietti and Caterina Strambio-De-Castillia. For this image, TZM-bl human cells were infected with HIV-1 retroviral three-part vector (FSWT+PAX2+pMD2.G). Six hours post-infection cells were fixed for 10 min with 1% formaldehyde in PBS, and permeabilized. Cells were stained with mouse anti-p24 primary antibody followed by DyLight488-anti-Mouse secondary antibody, to detect HIV-1 viral Capsid. In addition, cells were counterstained using rabbit anti-Lamin B1 primary antibody followed by DyLight649-anti-Rabbit secondary antibody, to visualize the nuclear envelope and with DAPI to visualize the nuclear chromosomal DNA.</p> <p>The Image Acquisition Settings used to acquire the FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif image are stored in: <strong>Rigano et al._Figure 5_UseCase_AS_fswt-6hvirus-10minfix-stk_4-epi.tif.JSON</strong></p> <p><em><strong>Instructional video tutorials on how to use these example data files:</strong></em><br> Use these videos to get started with using Micro-Meta App after downloading the example data files available here.</p> <ul> <li><a href="https://vimeo.com/562022222">Part 1/2</a></li> <li><a href="https://vimeo.com/562022281">Part 2/2</a></li> </ul>
WKU experimental epidemic game using research version of Operation Outbreak app
<p>This dataset contains the full list of participants and events in the experimental epidemic game at Wenzhou-Kean University (WKU) in China, run between November 20 and December 4 of 2023 using a customized version of the Operation Outbreak mobile app and cloud backend for research uses. The following blog post provides some more information about this simulation:</p> <p>https://colabobio.medium.com/667295c43907</p> <p> </p>
Replication package and appendixes for Causal inference of server- and client-side code smells in web apps evolution
<p>-Analysis <br>--R scripts used to make the analisys, divided by folders<br>--Data folders used in the questions</p> <p>-Appendixes - used in the article to shwo extra tables and plots</p> <p>-data folders - Aggregation of data, each app has two files, CSV and xls</p> <p>-separated data folders - 5 files for each app, with lines corresponding to the each released official version<br>--serversmells<br>--clientsmells<br>--javascriptsmells<br>--Cloc(metrics)<br>--version (all oficial releases)</p> <p>-issues_bugs<br>--data -issues by app by release <br>--data_bugs_more - the same but only bugs, by app by release<br>--scripts - scrips used to aggregate issues (from daily issues to by release) anf the same for bugs</p> <p> </p>
Odour observations from Odourcollect app (D-NOSES)
<p>This is the anonymized dump (28 November 2021) of the OdourCollect tool from the D-NOSES project ( Grant Agreement No 789315. ). There are 10332 Odour Observations from volunteers, including type and subtype of odour.</p> <p>The OdourCollect tool is provide as web-page: <a href="https://odourcollect.eu/">https://odourcollect.eu/ </a>and as <a href="https://play.google.com/store/apps/details?id=es.nobone.manchesterwebapp&hl=en_US">android</a> and <a href="https://apps.apple.com/mx/app/odourcollect/id1457119732">iphone</a> apps.</p> <p>Find out more about the project in the main webpage: <a href="http://dnoses.eu">http://dnoses.eu</a></p>
Data Set on Accuracy of Symptom Checker Apps in 2020
<p>These two data sets present the accuracy of triage (disposition) and diagnostic advice of symptom checker apps sampled in 2020. The sample consists of 22 commonly used symptom checker apps, of which 14 also provide diagnostic advice. The apps were tested on 45 case vignettes, i.e. fictitious descriptions of patients. As not every app was able to appraise every vignette our study yielded a total of 796 unique triage evaluations and 520 unique diagnostic evaluations. The data sets are a supplement to the paper "Triage Accuracy of Symptom Checker Apps: A Five-year Follow-up Evaluation" (doi: <a href="https://doi.org/10.2196/31810">10.2196/31810</a>).</p> <p>The was collected by Anna Dames as partial requirement for her MSc degree in Human Factors in the Department of Psychology and Ergonomics (IPA) at Technische Universität Berlin.</p> <p>The clinical vignettes were originally compiled and modified by Semigran et al. in 2015 (https://doi.org/10.1136/bmj.h3480), and further adapted by Hill et al. (2020) (doi: 10.5694/mja2.50600) and in the study these data sets are supplement to (doi: <a href="https://doi.org/10.2196/31810">10.2196/31810</a>).</p>
INFO-CSO (PSR Emilia-Romagna) - Indagine sull'intenzione d'uso dell'App
<p>Dati del questionario agli ortofrutticoltori per valutare l'intenzione d'uso dell'App</p> <p>Dati Progetto: </p> <p>INFO-CSO Informazione fruibile per lo sviluppo del sistema ortofrutticolo Regionale dell'Emilia Romagna</p> <p><a href="http://agricoltura.regione.emilia-romagna.it/psr-2014-2020/temi/tipi-di-operazioni/16-1-01-gruppi-operativi-del-partenariato-europeo-per-la-produttivita-e-la-sostenibilita-dellagricoltura/bandi-e-documenti-utili/Bando-2018/bando-goi-2018">Deliberazione di Giunta regionale nr. 2144 del 10 dicembre 2018 </a></p> <p><strong>Focus Area: </strong>3.A - Migliorare la competitività dei produttori primari integrandoli meglio nella filiera agroalimentare attraverso i regimi di qualità, la creazione di un valore aggiunto per i prodotti agricoli, la promozione dei prodotti nei mercati locali, le filiere corte, le associazioni e organizzazioni di produttori e le organizzazioni interprofessionali</p> <p><strong>Tipo di Operazione: 16.1.01 </strong> - Gruppi Operativi del PEI per la produttività e la sostenibilità dell'Agricoltura</p> <p><br> <strong>Id domanda: 5116697</strong><br> <strong>Finanziamento ricevuto</strong><strong>: </strong><strong>€ 31.522,22</strong></p> <p><br> <strong>Obiettivi e Finalità: </strong></p> <p>Supportare le imprese della regione Emilia-Romagna ad intraprendere un vero e proprio percorso di ammodernamento e crescita, mettendo a disposizione con modalità di accesso rapido ed in formato facilmente fruibile, dati ed informazioni sulla produzione e sul mercato dei principali prodotti ortofrutticoli al fine di rendere più competitive le aziende, consentendo loro di fare programmazione, e di mettere a punto strategie produttive, organizzative e commerciali più efficaci ed in linea con le esigenze del mercato e dei consumatori. Il servizio online proposto intende mette in contatto i produttori, gli operatori della filiera e gli acquirenti nella catena del valore dei prodotti ortofrutticoli freschi, offrendo loro visibilità e trasparenza. L'accesso ai dati in tempo reale potrà supportare tutti gli attori della filiera, consentendo loro di risparmiare tempo, rafforzare le relazioni, essere meglio informati e migliorare i processi decisionali.</p> <p><strong>Risultati attesi</strong>:</p> <p>I risultati attesi sono relativi all’applicazione delle informazioni identificate alle scelte imprenditoriali dei produttori ortofrutticoli dell’Emilia Romagna. CSO, tramite i suoi soci, copre circa il 50%% della produzione ortofrutticola regionale. Una corretta gestione imprenditoriale, tramite l’utilizzo di informazioni strutturate, può portare ad un aumento delle marginalità sufficiente a garantire la redditività di tutti gli attori della filiera. Inoltre, il presente piano avrà tra le applicazioni, la realizzazione di uno studio LCA che consentirà di dare agli agricoltori indicazioni sulle migliori tecnologie per la gestione ambientale, le quali se applicate, statisticamente consentono di ridurre il peso ambientale delle scelte agronomiche. Lo studio relativo alle certificazioni sociali ed etiche, consentirà di fornire un altro strumento per le scelte imprenditoriali, in quanto fornirà informazioni circa la percezione dei consumatori di tali certificazioni (GLOBALGAP-GASP, SA 8000).</p> <p> <strong>Referente scientifico: </strong>Canavari Maurizio</p>
Taxonomy of Security Weaknesses in Java and Kotlin Android Apps
<p>This is the replication package for the paper "Taxonomy of security weaknesses in Java and Kotlin Android apps" accepted for inclusion in The Journal of Systems & Software</p>
Investigating Types and Survivability of Performance Bugs in Mobile Apps
<p>Replication package of the paper entitled "Investigating Types and Survivability of Performance Bugs in Mobile Apps" published in The Empirical Software Engineering Journal</p>
Context-Aware Dataset: STS - South Tyrol Suggests IoT Mobile App Data
<p><strong>STS dataset </strong>was collected by a context-aware recommender system mobile app named as<strong> <a href="https://play.google.com/store/apps/details?id=it.unibz.sts.android&hl=en">"South Tyrol Suggests"</a></strong>. The app provides <strong>context-aware recommendations</strong> for attractions, events, public services, restaurants, and much more based on the rating preferences and personality factors of users.</p> <p><strong>Contextual</strong> <strong>variables</strong> includes </p> <ul> <li><strong>distance:</strong> far away, near by</li> <li><strong>time available:</strong> half day, one day, more than one day</li> <li><strong>temperature:</strong> burning, hot, warm, cool, cold, freezing</li> <li><strong>crowdedness:</strong> crowded, not crowded, empty</li> <li><strong>knowledge of surroundings:</strong> new to area, returning visitor, citizen of the area</li> <li><strong>season:</strong> spring, summer, autumn, winter</li> <li><strong>budget:</strong> budget traveler, price for quality, high spender</li> <li><strong>daytime:</strong> morning, noon, afternoon, evening, night</li> <li><strong>weather:</strong> clear sky, sunny, cloudy, rainy, thunderstorm, snowing</li> <li><strong>companion:</strong> alone, with friends/colleagues, with family, with girlfriend/boyfriend, with children</li> <li><strong>mood:</strong> happy, sad, active, lazy weekday: weekday, weekend</li> <li><strong>travel goal:</strong> visiting friends, business, religion, health care, social event, education, scenic/landscape, hedonistic/fun, activity/sport</li> <li><strong>means of transport:</strong> no transportation means, a bicycle, a car, public transport</li> </ul> <p>More details can be found here:</p> <p><em>Braunhofer, Matthias, Mehdi Elahi, and Francesco Ricci. <a href="https://www.researchgate.net/profile/Mehdi_Elahi2/publication/283502363_Techniques_for_cold-starting_context-aware_mobile_recommender_systems_for_tourism/links/56ccaa7608ae059e37507cc0.pdf">"<strong>Techniques for cold-starting context-aware mobile recommender systems for tourism</strong>."</a> Intelligenza Artificiale 8, no. 2 (2014): 129-143.</em></p>
SAST database of repository Luca App Android
<p>SAST database as sqlite database containing the<a href="https://gitlab.com/lucaapp/android"> LucaApp Android Gitlab repository</a>.</p> <p>Retrieved on June 21<sup>nd</sup>, 2021 using our SAST analysis pipeline.</p>
AWARE: Dataset for Aspect-Based Sentiment Analysis of Apps Reviews
<p> </p> <p><em><strong>The peer-reviewed paper of AWARE dataset is published in ASEW 2021, and can be accessed through: <a href="http://doi.org/10.1109/ASEW52652.2021.00049">http://doi.org/10.1109/ASEW52652.2021.00049</a>. Kindly cite this paper when using AWARE dataset.</strong></em></p> <p> </p> <p>Aspect-Based Sentiment Analysis (ABSA) aims to identify the opinion (sentiment) with respect to a specific aspect. Since there is a lack of <em>smartphone apps reviews</em> dataset that is annotated to support the ABSA task, we present AWARE: <strong>A</strong>BSA <strong>W</strong>arehouse of <strong>A</strong>pps <strong>RE</strong>views.</p> <p>AWARE contains apps reviews from three different domains (Productivity, Social Networking, and Games), as each domain has its distinct functionalities and audience. Each sentence is annotated with three labels, as follows: </p> <ul> <li><strong>Aspect Term: </strong>a term that exists in the sentence and describes an aspect of the app that is expressed by the sentiment. A term value of “N/A” means that the term is not explicitly mentioned in the sentence.</li> <li><strong>Aspect Category:</strong> one of the pre-defined set of domain-specific categories that represent an aspect of the app (e.g., security, usability, etc.).</li> <li><strong>Sentiment:</strong> positive or negative.</li> </ul> <p><em>Note: games domain does not contain aspect terms.</em></p> <p>We provide a comprehensive dataset of 11323 sentences from the three domains, where each sentence is additionally annotated with a Boolean value indicating whether the sentence expresses a positive/negative opinion. In addition, we provide three separate datasets, one for each domain, containing only sentences that express opinions. The file named “AWARE_metadata.csv” contains a description of the dataset’s columns.</p> <p><strong>How AWARE can be used?</strong></p> <p>We designed AWARE such that it can be used to serve various tasks. The tasks can be, but are not limited to:</p> <ul> <li>Sentiment Analysis.</li> <li>Aspect Term Extraction.</li> <li>Aspect Category Classification.</li> <li>Aspect Sentiment Analysis.</li> <li>Explicit/Implicit Aspect Term Classification.</li> <li>Opinion/Not-Opinion Classification.</li> </ul> <p>Furthermore, researchers can experiment with and investigate the effects of different domains on users' feedback.</p>
CSI-COP Citizen Scientists App Investigations
<p>This open-access dataset presents project results from CSI-COP project work package 4 task T4.2 in which citizen scientists conducted investigations on apps in their smart devices. The App investigations dataset was created using Excel spreadsheet. Users can explore the information recorded by the citizen scientists by using the filters on the column headings, for example, on type of app (games; news, etc.), or language of app (including English, Greek, Hebrew).</p>
Energy-Saving Strategies for Mobile Web Apps and their Measurement: Results from a Decade of Research - Dataset
<p>In 2022, over half of the web traffic was accessed through mobile devices. By reducing the energy consumption of mobile web apps, we can not only extend the battery life of our devices, but also make a significant contribution to energy conservation efforts. For example, if we could save only 5% of the energy used by web apps, we estimate that it would be enough to shut down one of the nuclear reactors in Fukushima. This paper presents a comprehensive overview of energy-saving experiments and related approaches for mobile web apps, relevant for researchers and practitioners. To achieve this objective, we conducted a systematic literature review and identified 44 primary studies for inclusion. Through the mapping and analysis of scientific papers, this work contributes: (1) an overview of the energy-draining aspects of mobile web apps, (2) a comprehensive description of the methodology used for the energy-saving experiments, and (3) a categorization and synthesis of various energy-saving approaches.</p>
NHS England COVID-19 Exposure Notification App and Test Availability Data
<p>This dataset was scraped from the API serving the NHS COVID-19 App for England and Wales, and the NHS COVID-19 test availability service.</p> <p>It contains the following files:</p> <p><strong>exposure_keys.csv</strong><br> Metadata associated with the published exposure keys for the Bluetooth Google/Apple Exposure Notification (GAEN) system. The actual broadcast keys were not collected, only the metadata attached to them. The columns in the table match those in the <a href="https://developers.google.com/android/exposure-notifications/exposure-key-file-format">exposure key export format</a>, with the exception of the "export_date" field which is the "end_timestamp" of the key export in which that key was first seen. This file is believed to be complete between 2020-09-13 and 2023-04-29 when the NHS COVID-19 app was retired.</p> <p><strong>exposure_configuration.csv</strong><br> This table contains the NHS COVID-19 App's exposure configuration JSON file fetched from the API, with a new record inserted whenever this changed. History of this file is also available in the <a href="https://github.com/ukhsa-collaboration/covid19-app-system-public">app's git repository</a>, and entries in this file from before 2021-07-11 were imported from there. The timestamps for entries dated since that point will match the time that the configuration was published to the API, which may not be the case for the git repository as this was normally updated after a delay.</p> <p><strong>risky_venues.csv</strong><br> "Risky venue" notification data for the COVID-19 App. This was an NHS App-specific feature, not part of the GAEN specification, which allowed users to "check in" to a venue and receive a notification if they were present at the same time as someone who subsequently tested positive for COVID-19. This file is believed to be complete between 2020-09-24 and 2022-02-22 (when it appears the "risky venue" feature was retired), with a known data collection gap between 2021-08-03 and 2021-08-06.</p> <p><strong>walk_in_pcr_availability.csv</strong><br> Walk-in PCR test availability for the entire UK, used by the NHS PCR test booking service. This contains JSON objects provided by the API, which are broken down by region. A new row was inserted whenever this JSON object changed. This file is believed to be complete between 2021-12-27 and 2022-03-30 (after which it appears the online test booking service was retired).</p> <p><strong>home_test_availability.csv</strong><br> Home test (PCR or Lateral Flow Device) availability, for the public and for "key workers" who had priority ordering PCR tests. A new row was inserted whenever the availability changed. This file is believed to be complete between 2021-12-27 and 2022-08-22 when the data ended.</p> <p> </p> <p>The final version of the source code used to fetch this data is <a href="https://doi.org/10.5281/zenodo.7883754">available here</a>.</p>
Takeout Recommendation Dataset (TRD) from Meituan Takeout app
<p>This is a takeout recommendation dataset (TRD) which contains a vast amount of meta information from Meituan Takeout app. We collect orders from 11 commercial districts in Beijing between March 1st and March 28th, 2021. The first three weeks of orders are as training, while the last week is used for testing to avoid data leakage. We briefly summarize each file as follows and for more details, please refer to README.md.</p> <p>1. users.txt (attributes of all users)<br> 2. pois.txt (attributes of all takeout restaurants)<br> 3. spus.txt (attributes of all food)<br> 4. orders_poi_session.txt (a sequence of restaurants clicked by user before ordering)<br> 5. orders_spu_train.txt (order-food in training set)<br> 6. orders_train.txt (order-restaurant in training set)<br> 7. orders_test.txt (order-restaurant in training set)<br> 8. orders_poi_test_label.txt (test labels of order-restaurant)<br> 9. orders_spu_test_label.txt (test labels of order-food)</p> <p>10 graph.bin (graph in DGL format)</p> <p>graph.bin is build by above *.txt files, there is a vast amount of meta informarion on nodes and edges. just several codes can load this graph with 18,931,400 edges and 408,849 nodes:</p> <pre><code class="language-python">from dgl import load_graphs #should install dgl ds,_ = load_graphs("./graph.bin") g = ds[0] print(g)</code></pre> <p> </p>
PLAE web app enables powerful searching and multiple visualizations across one million unified single-cell ocular transcriptomes
<p>Supplementary Data for "PLAE web app enables powerful searching and multiple visualizations across one million unified single-cell ocular transcriptomes"</p> <p> </p>
A Replication Package of Learning Features that Predict Developer Responses for iOS App Store Reviews
<p>This replication package contains the dataset and script used in our paper "<em>Learning Features that Predict Developer Responses for iOS App Store Reviews.</em>" The paper has been accepted at the ACM/IEEE International Symposium on Empirical Software Engineering and Measurement (ESEM), 2020. For further modification and versioning of the dataset (as well as the preprint) please go to <a href="https://github.com/Kamonphop/ESEM20-Replication">https://github.com/Kamonphop/ESEM20-Replication</a></p>
Datasets from the RecSys 2020 article "Carousel Personalization in Music Streaming Apps with Contextual Bandits"
<p>We publicly release the anonymized <em>user_features.csv</em> and <em>playlist_features.csv</em> datasets, from the music streaming platform Deezer, as described in the article "<em>Carousel Personalization in Music Streaming Apps with Contextual Bandits"</em> published in the proceedings of the 14th ACM Conference on Recommender Systems (<em>RecSys 2020</em>). The paper is available <a href="https://arxiv.org/abs/2009.06546">here</a>.</p> <p>These datasets are used in the GitHub repository <a href="https://github.com/deezer/carousel_bandits">deezer/carousel_bandits</a> to reproduce experiments from the article.</p> <p>Please cite our paper if you use our code or data in your work.</p>
Artefacts for ICSE 2021 technical paper: "RAICC: Revealing Atypical Inter-Component Communication in Android Apps"
<p>This repository represents our artefacts to replicate our paper which is in the proceedings of ICSE 2021: "RAICC: Revealing Atypical Inter-Component Communication in Android Apps"</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.