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Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose, Fran Lewitter
2019 PLoS Computational Biology  
Acknowledgments This paper represents a summary of the workshop "Reproducible Research and Interactive Education-Application of Jupyter Notebooks" held at UC San Diego on April 5, 2018.  ...  We thank all participants who contributed ideas to this paper, including Tiago Leao, Nathan Mih, Shweta Purawat, Michael Reich, Britton Smith, Shuai Tang, and Guorong Xu.  ...  rules for writing and sharing computational analyses in Jupyter Notebooks.  ... 
doi:10.1371/journal.pcbi.1007007 pmid:31344036 pmcid:PMC6657818 fatcat:p4jhzke7wfdr7awrvu6onkfh7m

Ten Simple Rules for Reproducible Research in Jupyter Notebooks [article]

Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
2018 arXiv   pre-print
We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications  ...  In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies?  ...  Acknowledgements This paper represents a summary of the workshop "Reproducible Research and Interactive Education -Application of Jupyter Notebooks" held at UC San Diego on April 5, 2018.  ... 
arXiv:1810.08055v1 fatcat:okjfz2syl5d7jm5fsgcijjf3sq

Reproducible Research is more than Publishing Research Artefacts: A Systematic Analysis of Jupyter Notebooks from Research Articles [article]

Max Schröder, Frank Krüger, Sascha Spors
2019 arXiv   pre-print
To empirically confirm this, we have been systematically analysing research publications that also published their investigations as Jupyter notebooks.  ...  This is true for the use of commercial software but also for the publication of research artefacts without proper sharing licence.  ...  [12] provide ten simple rules for reproducible research with Jupyter notebooks that is consistent with the problems we identified in this analysis and, thus, can help researchers in providing reproducible  ... 
arXiv:1905.00092v1 fatcat:njepcsmskbg43jlffgoh4stlne

Ten simple rules for biologists learning to program

Maureen A. Carey, Jason A. Papin, Scott Markel
2018 PLoS Computational Biology  
Acknowledgments Thank you to Ed Hall, Pat Schloss, Matthew Jenior, Angela Zeigler, Jhansi Leslie, and Gregory Medlock for their feedback.  ...  For specific advice, see "Ten Simple Rules for a Computational Biologist's Laboratory Notebook" [13] , "Ten Simple Rules for Reproducible Computational Research" [14] , and "Ten Simple Rules for Taking  ...  ] , "Ten Simple Rules for Cultivating Open Science and Collaborative R&D" [11] , and "Ten Simple Rules To Combine Teaching and Research" [12] .  ... 
doi:10.1371/journal.pcbi.1005871 pmid:29300745 pmcid:PMC5754048 fatcat:vkxwxsp5xzevdak5s3hdkql4rq

Understanding and improving the quality and reproducibility of Jupyter notebooks

João Felipe Pimentel, Leonardo Murta, Vanessa Braganholo, Juliana Freire
2021 Empirical Software Engineering  
Jupyter Notebooks have been widely adopted by many different communities, both in science and industry.  ...  Second, we sampled notebooks from the full dataset for an in-depth qualitative analysis of what constitutes the dataset and which features they have.  ...  Acknowledgments This work is partially supported by CAPES, CNPq, FAPERJ, the NYU Moore-Sloan Data Science Environment, and NSF award OAC-1640864.  ... 
doi:10.1007/s10664-021-09961-9 pmid:33994841 pmcid:PMC8106381 fatcat:2y4gu3feu5hwjdgasxop6ndjoq

Cross-facility science with the Superfacility Project at LBNL

Bjoern Enders, Debbie Bard, Cory Snavely, Lisa Gerhardt, Jason Lee, Becci Totzke, Katie Antypas, Suren Byna, Ravi Cheema, Shreyas Cholia, Mark Day, Aditi Gaur (+11 others)
2020 2020 IEEE/ACM 2nd Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing (XLOOP)  
As data sets from DOE user science facilities grow in both size and complexity there is an urgent need for new capabilities to transfer, analyze and manage the data underlying scientific discoveries.  ...  Here, we report on recent innovations in the Superfacility project, including advanced data management, API-based automation, real-time interactive user interfaces, and supported infrastructure for "edge  ...  In this mode when the user starts a notebook we spawn a compute job that runs on backend compute nodes and starts up a set of Dask workers that can accept tasks.  ... 
doi:10.1109/xloop51963.2020.00006 fatcat:od3f4jnjdzhmffo3bhc5ex3acy

Ten simple rules for writing Dockerfiles for reproducible data science

Daniel Nüst, Vanessa Sochat, Ben Marwick, Stephen J. Eglen, Tim Head, Tony Hirst, Benjamin D. Evans, Scott Markel
2020 PLoS Computational Biology  
By following the rules in this article, researchers can create containers suitable for sharing with fellow scientists, for including in scholarly communication such as education or scientific papers, and  ...  In support of this approach, we present a set of rules to help researchers write understandable Dockerfiles for typical data science workflows.  ...  ://" org.opencontainers.image.documentation = "\ ten-simple-rules-dockerfiles/ten-simple-rules-dockerfiles.pdf" org.opencontainers.image.version  ... 
doi:10.1371/journal.pcbi.1008316 pmid:33170857 fatcat:xsc3dr2oejcxhi7plh3arktzny

Introduction to Clinical Natural Language Processing with Python [chapter]

Leo Anthony Celi, Christina Chen, Daniel Gruhl, Chaitanya Shivade, Joy Tzung-Yu Wu
2020 Leveraging Data Science for Global Health  
Limitations: The field of Natural Language Processing is as broad and varied as human communication. The techniques we will discuss in this chapter are but a sampling of what the field has to offer.  ...  Although a complete understanding of this text is beyond current technology, a surprising amount of insight can be gained from relatively simple natural language processing.  ...  Setting up in Jupyter Notebook First, we import the necessary libraries for Python.  ... 
doi:10.1007/978-3-030-47994-7_14 fatcat:34ixnrjd3nboxlnfpdcb6xthuq

Towards reproducible computational drug discovery

Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
2020 Journal of Cheminformatics  
In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations  ...  Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilization for data collection, pre-processing, analysis and inference.  ...  Sirarat Sarntivijai from the European Bioinformatics Institute and Dr. Likit Preeyanon from the Department of Community Medical Technology for fruitful discussions.  ... 
doi:10.1186/s13321-020-0408-x pmid:33430992 fatcat:bvdcvjhi4jhlnifpc25t6cjthq

Publishing computational research – A review of infrastructures for reproducible and transparent scholarly communication [article]

Markus Konkol, Daniel Nüst, Laura Goulier
2020 arXiv   pre-print
This trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational results in their scientific papers.  ...  We compare the approaches across properties relevant for the involved stakeholders, e.g., provided features and deployment options, and also critically discuss trends and limitations.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
arXiv:2001.00484v1 fatcat:4nm6pmwzhvgptmcfhbkp7efvky

Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster

Jamie J. Alnasir, Francis Ouellette
2021 PLoS Computational Biology  
, if not bewildering, especially for users whose role is not predominantly computational in nature.  ...  For some users, the transition from running their analyses on a single workstation to running them on a complex, multi-tenanted cluster, usually employing some degree of parallelism, can be challenging  ...  See the Ten Simple Rules for Reproducible Computational Research article for some general best practice principles that can be applied when developing and running analysis workflows and computational pipelines  ... 
doi:10.1371/journal.pcbi.1009207 pmid:34351904 pmcid:PMC8341507 fatcat:mba2lmklvvhwdhzuhmygzhciei

BioExcel-2 Deliverable 2.1 – State of the Art and Initial Roadmap

Adam Hospital, Stian Soiland-Reyes, Josep Lluís Gelpí, Pau Andrio, Daniele Lezzi, Sarah Butcher, Ania Niewielska, Yvonne Westermaier
2019 Zenodo  
recent years, such as software containers or Jupyter notebooks.  ...  The final section of the deliverable describes the immediate future roadmap for the WP2, divided in the different tasks presented in the DoA: Application building blocks for computational biomolecular  ...  At the same time, the repository will follow the "Ten simple rules on how to create open access and reproducible molecular simulations of biological systems" [13] , storing and offering the simulation  ... 
doi:10.5281/zenodo.4604607 fatcat:u3yplgrepzfytda2zwzu37phge

Engineering Language-Parametric End-User Programming Environments for DSLs

Mauricio Verano Merino, Jurgen Vinju, Mark van den Brand, Tijs van der Storm
2022 Zenodo  
We present three different language-parametric interfaces for interacting with DSLs, namely computational notebooks, projectional editors, and block-based editors. These interfaces of [...]  ...  We mainly studied four technological spaces, namely, Grammarware, Computational Notebooks, Block-based environments, and Projectional editors.  ...  acknowledgements We would like to thank the Twitter hive mind, and Rainer Joswig in particular, for help in navigating the early history of REPLs and the anonymous reviewers for their helpful comments.  ... 
doi:10.5281/zenodo.6302885 fatcat:yr2tjs3rqvef5cftnooxjtbgcu

Ten computer codes that transformed science

Jeffrey M. Perkel
2021 Nature  
The ImageJ tool can analyse microscope images and automatically identify cell nuclei, as here.  ...  Like other computational notebooks, IPython Notebook combined code, results, graphics and text in a single document.  ...  Michael Levitt, a computational biologist at Stanford University in California who won a share of the 2013 Nobel Prize in Chemistry for his work on computational strategies for modelling chemical structure  ... 
doi:10.1038/d41586-021-00075-2 pmid:33473232 fatcat:wkoebbcjy5cwpcgrjo6tkktpwy

The "Social" Side of Big Data: Teaching BD Analytics to Political Science Students

Giampiero Giacomello, Oltion Preka
2020 Big Data and Cognitive Computing  
from human–computer interactions, thus they are social in character and nature.  ...  The authors believed that these conditions should and could be changed and thus in a few years created a specifically tailored course for students in Political Science.  ...  Jupyter Notebook can also benefit teachers in various ways, and for live coding in particular.  ... 
doi:10.3390/bdcc4020013 fatcat:wazgomf3ibguhnijrc4axo3siq
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