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ProvenanceWeek 2020: ReproduceMeGit: A Visualization Tool for Analyzing Reproducibility of Jupyter Notebooks [article]

Sheeba Samuel, Birgitta König-Ries
2020 Figshare  
This will help repository users and owners to reproduce and directly analyze and assess the reproducibility of any GitHub repository containing Jupyter Notebooks.  ...  This presentation is given in ProvenanceWeek2020.This slide presents ReproduceMeGit, a visualization tool for analyzing the reproducibility of Jupyter Notebooks.  ...  Computational Notebooks ➢ Large-scale studies on notebooks ➢ usage and structure [Adam Rule et al.  ... 
doi:10.6084/m9.figshare.12529604.v1 fatcat:4r6ejhyyfvcirlga45gynf7bfe

Bugarium: 3d interaction for supporting large-scale bug repositories analysis

Papon Yongpisanpop, Hideaki Hata, Kenichi Matsumoto
2014 Companion Proceedings of the 36th International Conference on Software Engineering - ICSE Companion 2014  
We present Bugarium that integrate 3D Motion Controller and datadriven documents to ease both interaction and visualization on a large-scale bug repository.  ...  An user study shows that Bugarium made users satisfied while using it to interact and visualize a large-scale bug tracking system.  ...  on a large-scale bug repositories.  ... 
doi:10.1145/2591062.2591125 dblp:conf/icse/YongpisanpopHM14 fatcat:ke3u7h2mvfdilagx5x5yrhvytu

VR-Based Sensor Management System for USN-Based Air Quality Monitoring

Hansoo Kim, HyungSeok Kim, Hanku Lee, Sung-Ryul Kim
2009 2009 Fourth International Conference on Computer Sciences and Convergence Information Technology  
We introduce a visualization system of micro-scale air quality monitoring system in the virtual reality environment.  ...  For the adaptive visualization, the visualization and interaction data are separated from air quality data.  ...  Finally, we constructed a large display system for easy access to the air quality information in public place.  ... 
doi:10.1109/iccit.2009.69 fatcat:gn4yfj3um5dztbhxdfixnsew6i

SemMedDB: a PubMed-scale repository of biomedical semantic predications

H. Kilicoglu, D. Shin, M. Fiszman, G. Rosemblat, T. C. Rindflesch
2012 Bioinformatics  
We propose the repository as a knowledge resource that can assist in hypothesis generation and literature-based discovery in biomedicine as well as in clinical decision-making support.  ...  Availability and implementation: The SemMedDB repository is available as a MySQL database for non-commercial use at http://skr3. nlm.nih.gov/SemMedDB. An UMLS Metathesaurus license is required.  ...  Large-scale information extraction in the form of semantic relations is increasingly proposed for advanced knowledge management and discovery systems (Bjo¨rne et al., 2010 (Bjo¨rne et al., , 2012 Cohen  ... 
doi:10.1093/bioinformatics/bts591 pmid:23044550 pmcid:PMC3509487 fatcat:zkwx45vttfgllnprk5q2e76me4

Metabolic pathway databases and model repositories

Abraham A. Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua, Feng-Biao Guo
2017 Quantitative Biology  
at large.  ...  The review aims to help researchers choose a suitable database or model repository according to the information and data required, by providing an insight look of each pathway resource.  ...  Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua and Feng-Biao Guo declare that they have no conflict of interest.  ... 
doi:10.1007/s40484-017-0108-3 fatcat:j6osebecqjehzj6lkchtldkwke

Methods for visual mining of genomic and proteomic data atlases

John Boyle, Richard Kreisberg, Ryan Bressler, Sarah Killcoyne
2012 BMC Bioinformatics  
Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make sense at scales from single samples to entire populations.  ...  Ultimately these visual tools enable new inferences, new analyses and further refinement of the large scale data being provided in atlases such as PeptideAtlas and The Cancer Genome Atlas.  ...  Acknowledgements This work was supported by grants U24CA143835 and R01CA137442 from the National Cancer Institute, P50GM076547 and R01GM087221 from the National Institute of General Medical Sciences, and  ... 
doi:10.1186/1471-2105-13-58 pmid:22524279 pmcid:PMC3352268 fatcat:ac4khd4tmbedjiu7yuja3lypmq

Large-scale neuroanatomical visualization using a manifold embedding approach

Shantanu H. Joshi, Ian Bowman, John Darrell Van Horn
2010 2010 IEEE Symposium on Visual Analytics Science and Technology  
Our workflow implements predefined metrics for clustering and classification, and data projection schemes to aid in visualization.  ...  We present a unified framework for data processing, mining and interactive visualization of largescale neuroanatomical databases.  ...  Our goal is to enable large-scale informatics, mining, and visualization of the existing neuroimaging data repositories by developing streamlined data processing work-flows and visualizing the results  ... 
doi:10.1109/vast.2010.5652532 pmid:21318096 pmcid:PMC3037590 dblp:conf/ieeevast/JoshiBH10 fatcat:4m2fc7lfrnbdnbwkezjwilyviu

Browsing large-scale cheminformatics data with dimension reduction

Jong Youl Choi, Seung-Hee Bae, Judy Qiu, Bin Chen, David Wild
2011 Concurrency and Computation  
Visualization of large-scale high dimensional data tool is highly valuable for scientific discovery in many fields.  ...  PubChemBrowse is built around in-house high performance parallel MDS (Multi-Dimensional Scaling) and GTM (Generative Topographic Mapping) services and supports fast interaction with an external property  ...  DATA VISUALIZATION AND REMOTE DATA ACCESS Large scale data visualization is an active research area in many fields of science: The Sloan Digital Sky Survey (SDSS) project [2] for astronomy, UCSC [3]  ... 
doi:10.1002/cpe.1781 fatcat:ffby3z6ptzgkvbeqc6sfh3wts4

Webzeitgeist

Ranjitha Kumar, Arvind Satyanarayan, Cesar Torres, Maxine Lim, Salman Ahmad, Scott R. Klemmer, Jerry O. Talton
2013 Proceedings of the SIGCHI Conference on Human Factors in Computing Systems - CHI '13  
This idea is manifest in Webzeitgeist, a platform for large-scale design mining comprising a repository of over 100,000 Web pages and 100 million design elements.  ...  However, while visual presentation is an intrinsic part of the Web, traditional data mining techniques ignore render-time page structures and their attributes.  ...  For more information, please visit http://hci.stanford.edu/research/webzeitgeist.  ... 
doi:10.1145/2470654.2466420 dblp:conf/chi/KumarSTLAKT13 fatcat:7uv72ozh3jbmde3xg2mcrautby

Browsing large scale cheminformatics data with dimension reduction

Jong Youl Choi, Seung-Hee Bae, Judy Qiu, Geoffrey Fox, Bin Chen, David Wild
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
Visualization of large-scale high dimensional data tool is highly valuable for scientific discovery in many fields.  ...  PubChemBrowse is built around in-house high performance parallel MDS (Multi-Dimensional Scaling) and GTM (Generative Topographic Mapping) services and supports fast interaction with an external property  ...  DATA VISUALIZATION AND REMOTE DATA ACCESS Large scale data visualization is an active research area in many fields of science: The Sloan Digital Sky Survey (SDSS) project [2] for astronomy, UCSC [3]  ... 
doi:10.1145/1851476.1851549 dblp:conf/hpdc/ChoiBQFCW10 fatcat:jwjbvabe3rgp5botbvcggcwtlm

VizNet: Towards A Large-Scale Visualization Learning and Benchmarking Repository [article]

Kevin Hu and Neil Gaikwad and Michiel Bakker and Madelon Hulsebos and Emanuel Zgraggen and César Hidalgo and Tim Kraska and Guoliang Li and Arvind Satyanarayan and Çağatay Demiralp
2019 arXiv   pre-print
In this paper, we present VizNet: a large-scale corpus of over 31 million datasets compiled from open data repositories and online visualization galleries.  ...  To demonstrate VizNet's utility as a platform for conducting online crowdsourced experiments at scale, we replicate a prior study assessing the influence of user task and data distribution on visual encoding  ...  VizNet is informed and inspired by the digital experimentation capabilities of large-scale data repositories in machine learning research.  ... 
arXiv:1905.04616v1 fatcat:d46eqdu55fbv7ely5u7h3jhmnu

NetworkRepository: An Interactive Data Repository with Multi-scale Visual Analytics [article]

Ryan A. Rossi, Nesreen K. Ahmed
2015 arXiv   pre-print
Unlike other data repositories (e.g., UCI ML Data Repository, and SNAP), the network data repository (networkrepository.com) allows users to not only download, but to interactively analyze and visualize  ...  Network Repository (NR) is the first interactive data repository with a web-based platform for visual interactive analytics.  ...  Acknowledgments We thank all of the donors who contributed data to the repository and all others who have supported and continue to support this effort.  ... 
arXiv:1410.3560v2 fatcat:lm7ejqowdrbm3huj6ycd562rxq

Content-Based Medical Image Retrieval and Intelligent Interactive Visual Browser for Medical Education, Research and Care

Camilo G. Sotomayor, Marcelo Mendoza, Víctor Castañeda, Humberto Farías, Gabriel Molina, Gonzalo Pereira, Steffen Härtel, Mauricio Solar, Mauricio Araya
2021 Diagnostics  
search for and efficiently navigate through a large-scale medical imaging repository, even if it has been set with incomplete and curated metadata.  ...  Yet, to date, browsing of large-scale medical image repositories has been troublesome, time-consuming, and generally limited by text search engines.  ...  Acknowledgments: We thank Miguel Angel Jordan and Mariela Yañez for their management support of the current project.  ... 
doi:10.3390/diagnostics11081470 fatcat:3z4qgfeh5za65inmcmhk5qunuu

Informatics Resources for Electron Tomography

Maryann E. Martone, Shenglan Zhang, Steven Peltier, Abel W. Lin, David Lee, Tomas Molina, Amarnath Gupta, Mark H. Ellisman
2003 Microscopy and Microanalysis  
At the National Center for Microscopy and Imaging Research, we are developing several informatics-based approaches both to increase the throughput of large scale light and electron microscopic studies  ...  In the molecular realm, large shared data repositories like the Protein Data Bank have been well established and are proving to be indispensable research tools.  ...  In the molecular realm, large shared data repositories like the Protein Data Bank have been well established and are proving to be indispensable research tools.  ... 
doi:10.1017/s1431927603445820 fatcat:cwdfobtmnzhljla5xlttrhzf34

Evaluating Visual Data Analysis Systems

Leilani Battle, Marco Angelini, Carsten Binnig, Tiziana Catarci, Philipp Eichmann, Jean-Daniel Fekete, Giuseppe Santucci, Michael Sedlmair, Wesley Willett
2018 Proceedings of the Workshop on Human-In-the-Loop Data Analytics - HILDA'18  
In their discussions, the group brainstormed initial steps towards new joint evaluation methods and developed a first concrete initiative -a trace repository of various real-world workloads and visual  ...  In November 2017, members of both the Database and Visualization communities came together in a Dagstuhl seminar to discuss the grand challenges in the intersection of data analysis and interactive visualization  ...  However, there is generally a lack of quantitative and comparative methods for evaluating the performance of large-scale visual exploration systems.  ... 
doi:10.1145/3209900.3209901 dblp:conf/sigmod/BattleABCEFSSW18 fatcat:k57wsmv2pbh53b7ronweskm7ga
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