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Bringing documentation, live code and data together using Jupyter Notebooks

Harsha Ummerpillia, Thomas Murphy
2020 Zenodo  
in the notebooks.  ...  ICPSR also plans to provide options to download Jupyter notebooks in R Python along with our data bundles, allowing users to easily dive into analysis and data re-use with the help of documentation included  ...  The Hub can offer notebook servers to a class of students, a corporate data science workgroup, a ➢ Website : ➢ IPython created in 2001 as an interactive computing in multiple languages  ... 
doi:10.5281/zenodo.3775638 fatcat:ow4uo3oqufchdivhynuumqwswy

CoolBox: a interactive genomic data explorer for Jupyter Notebook [article]

Weize Xu, Da Lin, Ping Hong, Liang Yi, Rohit Tyagi, Guoliang Li, Gang Cao
2019 bioRxiv   pre-print
Summary: CoolBox is a Python package for interactive genomic data exploration based on Jupyter notebook.  ...  It provides a ggplot2-like Application Programming Interface (API) for genomic data visualization, and a Jupyter/ipywidgets based Graphical User Interface (GUI) for interactive data exploration.  ...  Conclusion CoolBox is a versatile toolkit for the visualization of most types of genomic data and exploring multi-omics data in Jupyter notebook.  ... 
doi:10.1101/614222 fatcat:4mgsb73turcbjdmkqiyxebvrua

An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks

N Braun, T Hauth, C Pulvermacher, M Ritter
2017 Journal of Physics, Conference Series  
This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain.  ...  During recent years interactive programming environments, such as Jupyter, became popular.  ...  Probably the biggest advantages of Jupyter notebooks is the fast turn-around time and the direct feedback between data and visualization.  ... 
doi:10.1088/1742-6596/898/7/072020 fatcat:ucscd6cxmjex5pqmeaqlcw6uty

Interactive Supercomputing With Jupyter

Rollin Thomas, Shreyas Cholia, Kathryn Mohror, John M. Shalf
2021 Computing in science & engineering (Print)  
advanced supercomputing capabilities that can extend the interactive notebook environment.  ...  Rich user interfaces like Jupyter have the potential to make interacting with a supercomputer easier and more productive, consequently attracting new kinds of users and helping to expand the application  ...  Jupyter was used to combine simulations, data analysis, and machine learning with interactive visualization.  ... 
doi:10.1109/mcse.2021.3059037 fatcat:txtv4sjbwvhkpktrjma7j6cy6e

Jupyter: Thinking and Storytelling With Code and Data

Brian E. Granger, Fernando Perez
2021 Computing in science & engineering (Print)  
Project Jupyter is an open-source project for interactive computing widely used in data science, machine learning, and scientific computing.  ...  Namely, Jupyter helps humans to think and tell stories with code and data.  ...  The work of Brian Granger and Fernando P erez on Project Jupyter was supported in part by the Alfred P.  ... 
doi:10.1109/mcse.2021.3059263 fatcat:3wsufp5z6ndgjkbdgdb7ajip2i

Towards Interactive, Reproducible Analytics at Scale on HPC Systems

Shreyas Cholia, Lindsey Heagy, Matthew Henderson, Drew Paine, Jon Hays, Ludovico Bianchi, Devarshi Ghoshal, Fernando Perez, Lavanya Ramakrishnan
2020 2020 IEEE/ACM HPC for Urgent Decision Making (UrgentHPC)  
We demonstrate the use of this software to run our use case and interactively visualize real-time streams of HDF5 data.  ...  In this paper, we outline our efforts that bring together core technologies based on the Jupyter Platform to create interactive, reproducible analytics at scale on HPC systems.  ...  We thank Rollin Thomas for helping us with the Jupyter support at NERSC. This work and the resources at NERSC are supported by the U.S.  ... 
doi:10.1109/urgenthpc51945.2020.00011 fatcat:3riyidbo4nghdmtymzn5x5avum

Bacatá: a language parametric notebook generator (tool demo)

Mauricio Verano Merino, Jurgen Vinju, Tijs van der Storm
2018 Proceedings of the 11th ACM SIGPLAN International Conference on Software Language Engineering - SLE 2018  
Notebooks are currently being used extensively in domains such as data science, data journalism, and machine learning.  ...  In this tool paper, we present Bacatá, a language parametric notebook generator for domain-speci c languages (DSL) based on the Jupyter framework.  ...  Interactive Visualizations Jupyter notebooks run in the browser, so this allows output cells to contain almost arbitrary interactive visualizations, beyond plain text output.  ... 
doi:10.1145/3276604.3276981 dblp:conf/sle/MerinoVS18 fatcat:6nz7ihboqjesdh2bp5um3lgbzu

Teaching Semantic Web Technologies through Interactive Jupyter Notebooks

Lars Pieschel, Sascha Welten, Lars Christoph Gleim, Stefan Decker
2021 International Conference on Semantic Systems  
Inspired by the success of structured digital learning materials in other domains of computer science, we present SemWebNotebooks, a portfolio of interactive Jupyter Notebook tutorials for teaching Semantic  ...  Web technologies interactively.  ...  Conclusion In this work, we have presented Jupyter-RDFify, which is an IPython kernel extension for Jupyter Notebooks.  ... 
dblp:conf/i-semantics/PieschelWGD21 fatcat:ogjglwmxyffvndife5ypbhtcmq

Reproducible Bioconductor workflows using browser-based interactive notebooks and containers

Reem Almugbel, Ling-Hong Hung, Jiaming Hu, Abeer Almutairy, Nicole Ortogero, Yashaswi Tamta, Ka Yee Yeung
2017 JAMIA Journal of the American Medical Informatics Association  
Materials and methods: We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq  ...  These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified.  ...  Our interactive notebooks enable clinicians and biomedical scientists to visually interact with the analyses while exploring the results through different types of interactive visualizations (eg, Plotly  ... 
doi:10.1093/jamia/ocx120 pmid:29092073 fatcat:tyzs65gzbzb3dm4aaxovkwupn4

BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud [article]

Denis Torre, Alexander Lachmann, Avi Ma'ayan
2018 bioRxiv   pre-print
Generated notebooks have executable code of the entire pipeline, rich narrative text, interactive data visualizations, and differential expression and enrichment analyses.  ...  Here we introduce BioJupies, a web server that enables automated creation, storage, and deployment of Jupyter Notebooks containing RNA-seq data analyses.  ...  Acknowledgements This work is supported by NIH grants U54-HL127624 (LINCS-DCIC), U24-CA224260 (IDG-KMC), and OT3-OD025467 (NIH Data Commons).  ... 
doi:10.1101/352476 fatcat:ybcjvpf5ujdhvgf5z5i6ulkncq

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

Nicolas F. Fernandez, Gregory W. Gundersen, Adeeb Rahman, Mark L. Grimes, Klarisa Rikova, Peter Hornbeck, Avi Ma'ayan
2017 Scientific Data  
Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks.  ...  Clustergrammer generates shareable interactive visualizations via a web application, or as a Jupyter Notebook widget (Fig. 1) .  ...  We would like to thank Dr Kathleen Jagodnik for copyediting the Help documentation, and Michael McDermott for assisting in software development tasks.  ... 
doi:10.1038/sdata.2017.151 pmid:28994825 pmcid:PMC5634325 fatcat:jbcdmot2jfhgdjtxrhvclzjexe

Appyters: turning Jupyter Notebooks into data-driven web apps

Daniel J.B. Clarke, Minji Jeon, Daniel J. Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles Dai, Zhuorui Xie, Megan L. Wojciechowicz, Skylar Litz, Jason Hom, John Erol Evangelista, Lucas Goldman (+12 others)
2021 Patterns  
Jupyter Notebooks have transformed the communication of data analysis pipelines by facilitating a modular structure that brings together code, markdown text, and interactive visualizations.  ...  Once the form is filled, the Appyter executes the corresponding notebook in the cloud, producing the output without requiring the user to interact directly with the code.  ...  Some prior efforts have been made to present Jupyter Notebooks as web-based applications for the purpose of interactive dashboards constructed directly from Jupyter Notebooks.  ... 
doi:10.1016/j.patter.2021.100213 pmid:33748796 pmcid:PMC7961182 fatcat:n2xqpmun45dddfqn756hagj72m

Viv Visualization Library Use Cases [article]

Trevor Manz, Ilan Gold, Nathan Heath Patterson, Chuck McCallum, Mark S Keller, Bruce W Herr II, Katy Börner, Jeffery M Spraggins, Nils Gehlenborg
We have embedded Viv into several visualization tools designed for specific tasks, demonstrating its modularity and reuse.  ...  Widgets for Python and R are available for creating and interacting with Vitessce visualizations in computational notebook environments.  ...  a Jupyter Notebook.  ... 
doi:10.6084/m9.figshare.19416401.v1 fatcat:ah53xitn6rfaraksuz7ww6yn4q

Jupyter-enabled astrophysical analysis using data-proximate computing platforms

Stephanie Juneau, Knut Olsen, Robert Nikutta, Alice Jacques, Stephen Bailey
2021 Computing in science & engineering (Print)  
Future advances may involve science platform networks, and tools for simultaneously developing Jupyter notebooks to facilitate collaborations.  ...  The need to work closely to the data has motivated the creation of online science platforms, which include a suite of software tools and services, therefore going beyond data storage and data access.  ...  ACKNOWLEDGMENT We thank the remainder of the Astro Data Lab team members, including A. Bolton, M. Fitzpatrick, D. Herrera, L. Huang, D. Nidever, R. Pucha, and A. Scott. In particular, we thank B.  ... 
doi:10.1109/mcse.2021.3057097 fatcat:ffwv4nfdsjhu5hc3jdk4gggane

Reproducible Bioconductor Workflows Using Browser-Based Interactive Notebooks And Containers [article]

Reem Almugbel, Ling-Hong Hung, Jiaming Hu, Abeer M. Almutairy, Nicole E. Ortogero, Yashaswi Tamta, Ka Yee Yeung
2017 bioRxiv   pre-print
data.  ...  These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified.  ...  Our interactive notebooks enable clinicians and biomedical scientists to visually interact with the analyses while exploring the results through different types of interactive visualizations (e.g.  ... 
doi:10.1101/144816 fatcat:dohinknpmvadpkp4ovzph57oiu
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