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Jupyter in Computational Science

Hans Fangohr, Thomas Kluyver, Massimo DiPierro
2021 Computing in science & engineering (Print)  
He authored more than 150 scientific articles in computational science and materials modeling, several open-source software projects, and a text book Python for Computational Science and Engineering.  ...  He has authored more than 70 articles in physics, computer science, and finance and has authored or coauthored three books.  ... 
doi:10.1109/mcse.2021.3059494 fatcat:5oxlvj2nvvdvzkyy5icaikimwq

Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing

Kevin M. Mendez, Leighton Pritchard, Stacey N. Reinke, David I. Broadhurst
2019 Metabolomics  
To enable FAIR data science in metabolomics, methods and results need to be transparently disseminated in a manner that is rapid, reusable, and fully integrated with the published work.  ...  To ensure broad use within the community such a framework also needs to be inclusive and intuitive for both computational novices and experts alike.  ...  KMM & DIB developed the tutorial Jupyter notebook code. LP and SNR edited the learning tutorials to align to current pedagogical best practices. KMM wrote the initial draft of the review section.  ... 
doi:10.1007/s11306-019-1588-0 pmid:31522294 pmcid:PMC6745024 fatcat:riwra7xbxzav7cb7nz44kanpgi

ProB and Jupyter for Logic, Set Theory, Theoretical Computer Science and Formal Methods [chapter]

David Geleßus, Michael Leuschel
2020 Lecture Notes in Computer Science  
We present a tool for using the B language in computational notebooks, based on the Jupyter Notebook interface and the ProB tool.  ...  Applications of B notebooks include executable documentation of formal models, interactive manuals, validation reports but also teaching of formal methods, logic, set theory and theoretical computer science  ...  for teaching mathematical foundations in general or theoretical computer science in particular.  ... 
doi:10.1007/978-3-030-48077-6_19 fatcat:ylwiumjy7zddreuqrhtxdude2u

The Python/Jupyter Ecosystem: Today's Problem-Solving Environment for Computational Science

Lorena A. Barba
2021 Computing in science & engineering (Print)  
IN THE MARCH/APRIL 2021 ISSUE, CISE IS PROUD TO FEATURE SEVERAL ARTICLES SHOWCASING JUPYTER IN COMPUTATIONAL SCIENCE.  ...  In the March/April 2021 issue, CiSE is proud to feature several articles showcasing Jupyter in computational science.  ... 
doi:10.1109/mcse.2021.3074693 fatcat:mo7bqy2wpvggxnmsso7r7fp7ae

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)  
We describe the main uses of Jupyter and the interfaces that needed to be created to embed it within science platform ecosystems.  ...  We present two example applications of Jupyter as a part of astrophysical science platforms for professional researchers and students.  ...  Snyder (STSci) for sharing information about astronomical science platforms in which they are directly involved, R. Thomas (NERSC) and G. Jacoby for comments on the manuscript.  ... 
doi:10.1109/mcse.2021.3057097 fatcat:ffwv4nfdsjhu5hc3jdk4gggane

Prototyping Controlled Mathematical Languages in Jupyter Notebooks [chapter]

Jan Frederik Schaefer, Kai Amann, Michael Kohlhase
2020 Lecture Notes in Computer Science  
In this paper, we will explore how GLF can be used to prototype such languages and present a new Jupyter kernel that4 adds visual support for the development of GLF-based syntax/semantics interfaces.  ...  In particular, software for formal mathematics (such as proof checkers) require formal input languages.  ...  Introduction The work of mathematicians is increasingly supported by computer software ranging from computer algebra systems to proof checkers and automated theorem provers.  ... 
doi:10.1007/978-3-030-52200-1_40 fatcat:qgdfqgve4zacpa4re4yi2tv6yi

Reproducible research in computational sciences: A use case for uncertainty quantification using Jupyter Notebooks

Mojtaba Barzegari, Liesbet Geris
2021 KU Leuven Open Science Day  
KU Leuven Open Science DayReproducible research in computational sciences: A use case for uncertainty quanti cation using Jupyter Notebooks 2 Abstract Reproducible research is gaining attention as a crucial  ...  aspect of open science in recent years, emphasizing the core idea that the results of research should be reproducible and replicable by everyone given the original dataset, code, and software.  ...  One of the best approaches in this regard for scientific computing and data science research projects is taking advantage of Jupyter environments, in which researchers can provide a full representation  ... 
doi:10.21428/1192f2f8.7b6d2ad0 fatcat:rr6wmq7tpzabbjzxfzk62gwehm

Interactive Supercomputing With Jupyter

Rollin Thomas, Shreyas Cholia, Kathryn Mohror, John M. Shalf
2021 Computing in science & engineering (Print)  
of supercomputing to new science domains.  ...  Jupyter checks most if not all of these boxes.  ...  k https://github.com/jupyterhub/batchspawner Computing in Science & Engineering Computing in Science & EngineeringMarch/April 2021  ... 
doi:10.1109/mcse.2021.3059037 fatcat:txtv4sjbwvhkpktrjma7j6cy6e

Open, Transparent and Reproducible Data Science in Clinical Metabolomics using Jupyter Notebooks and Cloud Computing

David Broadhurst
2020 Figshare  
Metabonews Vol 9 Issue 10 Dec 2019 feature article contributed by David Broadhurst, Centre for Integrative Metabolomics & Computational Biology, Edith Cowan University, Perth, Western Australia.  ...  In our recent review for Metabolomics "Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing" Mendez et al. (2019), we provide a brief overview of current data  ...  in the form of Jupyter Notebooks.  ... 
doi:10.6084/m9.figshare.11497023 fatcat:uvgvxwklynaiziaegvegdsiy5i

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.  ...  We illustrate the impact of these dimensions on a community of practice in earth and climate science.  ...  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

Using Jupyter for reproducible scientific workflows

Marijan Beg, Juliette Belin, Thomas Kluyver, Alexander Konovalov, Min Ragan-Kelley, Nicolas Thiery, Hans Fangohr
2021 Computing in science & engineering (Print)  
In this work, we report two case studies - one in computational magnetism and another in computational mathematics - where domain-specific software was exposed to the Jupyter environment.  ...  Literate computing has emerged as an important tool for computational studies and open science, with growing folklore of best practices.  ...  towards more efficient computational workflows, reproducibility and re-usability in science.  ... 
doi:10.1109/mcse.2021.3052101 fatcat:qdac3unk75fzdophnssiv7lyha

Jupyter notebooks as discovery mechanisms for open science: Citation practices in the astronomy community

Morgan Wofford, Bernadette Marie Boscoe, Christine Borgman, Irene Pasquetto, Milena Golshan
2019 Computing in science & engineering (Print)  
We report on a study of references to Jupyter notebooks in astronomy over a 5-year period (2014-2018).  ...  Citation principles encourage authors to provide full descriptions of objects, with stable links, in their papers.  ...  From a computational science perspective, each software layer depends upon the robustness of the all the layers below it.  ... 
doi:10.1109/mcse.2019.2932067 fatcat:q2vemqobhfgajnqqfu7hdsar4u

Deploying Jupyter Notebooks at scale on XSEDE resources for Science Gateways and workshops

Andrea Zonca, Robert S. Sinkovits
2018 Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18  
Jupyter Notebooks have become a mainstream tool for interactive computing in every field of science.  ...  Jupyter Notebooks are suitable as companion applications for Science Gateways, providing more flexibility and post-processing capability to the users.  ...  The work is supported by the National Science Foundationnder Grant No.: 1548562 (https://www.nsf.gov/awardsearch/showAward?  ... 
doi:10.1145/3219104.3219122 dblp:conf/xsede/ZoncaS18 fatcat:asgxzxmfqreknknzcqixsdzyjm

Modernizing computing by structural biologists with Jupyter and Colab

Blaine Mooers
2021 Proceedings of the 20th Python in Science Conference   unpublished
We have made libraries of code templates to ease running the crystallography packages in Jupyter notebooks when editing them with JupyterLab or Colab.  ...  Our combined use of GitHub, snippet libraries, Jupyter notebooks, JupyterLab, and Colab will help modernize the computing done by structural biologists.  ...  Acknowledgements This work is support in part by these National Institutes of Health grants: R01 CA242845, P20 GM103640, P30 CA225520.  ... 
doi:10.25080/majora-1b6fd038-002 fatcat:6ojwdoz43nemhdi2j5iabufliu

Using the Jupyter Notebook as a Tool for Open Science: An Empirical Study [article]

Bernadette M. Boscoe, Irene V. Pasquetto, Milena S. Golshan, Christine L. Borgman
2018 arXiv   pre-print
In this poster, we show how the Jupyter notebook, a tool originally designed as a free version of Mathematica notebooks, has evolved to become a robust tool for scientists to share code, associated computation  ...  As scientific work becomes more computational and data intensive, research processes and results become more difficult to interpret and reproduce.  ...  We are grateful to Fernando Perez for discussions about the origins and goals of Jupyter Notebooks. We also thank Peter T. Darch for commenting on earlier drafts of this paper.  ... 
arXiv:1804.05492v1 fatcat:gpjrueuqcbc2jpbcnwewnhvlh4
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