Pocket book now! Elevating Computational Notebooks


Editors’ Voice AGU’s Publications Division has a weblog.

Researchers are more and more utilizing computational notebooks to share workflows and information evaluation with others. They’re additionally utilized in classroom settings, being efficient instruments for instructing information science and different topics. Analysis computing providers usually spotlight their help of notebooks for interacting with their providers and as a collaboration and sharing facility (eg, Princeton, Caltech). Consequently, notebooks have gotten more and more ubiquitous in analysis workflows.

Jupyter and RStudio are the 2 main improvement environments within the computational pocket book house. GitHub, a preferred platform for collaborating and sharing code, together with notebooks, at the moment reveals 4 million code outcomes for “.ipynb”, the file extension used for Jupyter, whereas “.rmd” makes use of the R extension. When, for instance, RStudio, there are 2.7 million code outcomes. We’ve seen a progressive improve within the safety and quotation of software program, primarily by means of GitHub and Xenodo, a repository maintained by CERN and OpenEar, rising from about 2 thousand information in 2014 to 73 thousand in 2021.

Jupyter Notebooks began out as IPython, a command shell primarily for interactive computing in Python. Since its preliminary launch in 2001, IPython has now grown into the Venture Jupyter group whose purpose is to “develop open-source software program, open requirements, and providers for interactive computing in dozens of programming languages”. The RStudio built-in improvement setting for the R statistical programming language was initially launched in 2011. Quickly after, R Markdown, an method for embedding R code chunks in Markdown paperwork, was launched within the Knit bundle. Posit (the corporate previously often called RStudio) not too long ago developed Quarto, the subsequent era of R Markdown. Quarto is open supply with help for code written in R, Python, Julia and Observable JavaScript.

Notebooks fuse analysis fiction with information, visualization, and executable code to create an interactive expertise.

Notebooks fuse analysis narratives with information, visualizations and executable code to create an interactive expertise that enables others to stroll you thru your computational workflow and evaluation. Because of this, notebooks have additionally been an efficient studying software within the classroom (eg Data8). Advances in pocket book improvement have made it simpler to launch digital platforms, get began with coding, and use them whereas integrating them into your analysis workflows (comparable to OpenScape).

At AGU, we’ve seen a rising curiosity in publishing notebooks from teams comparable to EarthCube, the place they characteristic interactive workflows and annual calls to their group to share and publish evaluation of analysis. Notebooks from the EarthCube name are revealed in AGU’s preprint server, the Earth and Area Science Open Archive, or ESSOar. In AGU magazines, for instance, Journal of Advances in Modeling of Earth Methods (James), editors spotlight the advantages of sharing notebooks to grasp the underlying fashions offered within the papers. earth and house science The journal has additionally seen curiosity in publishing notebooks as analysis papers.

AGU will work with the Computational Pocket book group to design and implement a publishing workflow for Computational Notebooks.

AGU not too long ago revealed two transient guides on publishing notebooks, Erdmann et al. (2021a, b). Steerage was co-developed with group members and is evolving. This prompted a not too long ago funded Alfred P. Sloan Basis grant led by AGU to help the development of notebooks as a major analysis object. Guided by a steering committee of consultants, AGU will work with the computational pocket book group to design and implement a publishing workflow for Computational Notebooks over a interval of 18 months starting July 2022. The pocket book’s interactive performance is misplaced throughout publication, which remains to be primarily textual content based mostly. The venture, now referred to as Notebooks! Publishing workflows will give attention to sustaining the pocket book’s interactivity, successfully documenting reproducible workflows, increasing equitable entry to computational analysis, and increasing new types of contribution to the broader analysis group. As well as, the hassle consists of growing a pilot answer that may advance the pocket book as a format in scholarly publication. You’ll be able to study extra about notebooks now! on the venture web site.

Lately, we’ve seen an rising use of notebooks in abstracts (shows and posters) offered at AGU annual conferences and we’re taking a look at methods to extend and encourage their use in our group. In case you are excited by participating with these efforts and/or offering suggestions, please tell us by way of this manner.

—Christopher Erdmann (CErdmann@agu.org, 0000-0003-2554-180X), American Geophysical Union; Shelley Stall; Brooks Hanson; Laura Leon; Brian Sedora; Matt Giampola; Mia Ricci; And AGU’s Pocket book Now! Steering Committee

Quotation: Erdman, C., S. Stoll, B. Hanson, L. Lyon, B. Sedora, M. Giampola, & M. Ricci (2022), Notebooks Now! elevating the computational pocket book, eos, 103, https://doi.org/10.1029/2022EO225024. Revealed on 18 August 2022.
This text doesn’t signify the opinion of AGU, eos, or any of its associates. That is the opinion of the writer solely.
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