by Simon Bowie
As part of COPIM’s pilot project looking at computational book publishing, we’ve worked on a new technical model and workflow for publishing computational books using a combination of Jupyter Notebook, Quarto, and GitHub Pages. This blogpost outlines the details of this model and further blogposts in this series will examine how we have applied it practically to produce some computational publications.
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“Project MUSE is pleased to host a new interactive, open-access, born-digital chapter, “The Web of History” from A New Vision for Islamic Pasts and Futures by Shahzad Bashir published by the MIT Press. The chapter of the publication hosted on MUSE mirrors the content from the born-digital product’s primary site, and is intended to provide an additional pathway to discovery, as well as spotlight the MUSE platform’s suitability for hosting robust and innovative digital humanities works.
A New Vision for Islamic Pasts and Futures brings together the MIT Press’s global publishing experience and the Brown University Library’s digital publication expertise. The groundbreaking scholarship decenters Islam from a geographical identification with the Middle East, an articulation through men’s authority alone, and the assumption that premodern expressions are more authentically Islamic than modern ones. Aimed at a wide international audience, the publication consists of engaging stories and audiovisual materials that will enable readers at all levels to appreciate Islam as an aspect of global history for centuries. The book URL is islamic-pasts-futures.org.”
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“Quarto® is an open-source scientific and technical publishing system built on Pandoc
Create dynamic content with Python, R, Julia, and Observable.
Author documents as plain text markdown or Jupyter notebooks.
Publish high-quality articles, reports, presentations, websites, blogs, and books in HTML, PDF, MS Word, ePub, and more.
Author with scientific markdown, including equations, citations, crossrefs, figure panels, callouts, advanced layout, and more….”
“Is A New Vision for Islamic Pasts and Futures—an interactive, open-access, born-digital monograph developed by Brown University Digital Publications and published in August by MIT Press—the monograph of the future? Asking readers to imagine Islam anew, as a vast web of interconnected traces seen through the prism of time, the book opens with a networked table of contents. Portals lead to different time periods across different parts of the world, inviting readers to explore Islam via a path of their choosing. In designing a one-of-a-kind trajectory that follows their own interests and queries, the reader, effectively, creates their own journey while traversing the world of ideas and evidence that has been curated by the author.
This groundbreaking interface, says author Shahzad Bashir, Aga Khan Professor of Islamic Humanities at Brown, “performs, rather than simply states, the book’s argument—namely, that we see pasts and futures as fields of unlimited possibility that come alive through a combination of close observation and ethical positioning.” …
In working together to produce and disseminate essential knowledge for broad audiences, Brown University Library and the MIT Press are also addressing issues of scalability and sustainability. A critical goal of the series is to mobilize knowledge creation and sharing. To this end, On Seeing will comprise a publication suite that includes a multiplicity of forms. The print book, providing a revenue stream to help offset costs, will be offered at a reasonable price and distributed globally in order to reach the widest possible readership. The enhanced, open-access digital publication will be developed using the open-source publishing platform PubPub, which introduces a less bespoke approach to interactive design and development….
We are seeing the payoff from these investments through the expansive reach and impact that this approach to digital publication, together with presses gravitating to open access….”
Abstract: Increasingly code and algorithms are techniques also applied in textual scholarship, giving rise to new interactions between software engineers and textual scholars. This book argues that much of that process and its effects on textual scholarship are still poorly understood and go unchecked by otherwise normal processes of quality control in scholarship such as peer review. The text provides case studies in which some of these interactions become more apparent, as well as the academic challenges and problems that they introduce. The book demonstrates that the space between code creation and conventional scholarship is one that offers many affordances to textual scholarship that until now remain unexplored. The author argues that it is an intellectual obligation of programmers and textual scholars to examine the properties of digital text and how its existence changes and challenges textual scholarship.
“For more than 20 years, the scientific journal Atmospheric Chemistry and Physics (ACP) has been a pioneer in open access publishing and public peer review with interactive discussion. All articles published in it are accessible free of charge via the internet. By recording and opening up the peer review process, the interactive open access journals lead to an internet of knowledge or epistemic web that does not only reflect what we know but also how we know it, i.e., how well it has been validated.
The achievements of ACP and further interactive open access sister journals of the European Geosciences Union (EGU) will be celebrated, reflected, and further developed at a special meeting of the ACP editorial board and the EGU publications committee on 19 September 2022 at the Max Planck Institute for Chemistry (MPIC) in Mainz. The meeting is supported by the open access publisher Copernicus, which operates the journal on behalf of EGU in a not-for-profit manner.
Ensure free speech, critical discussion, and transparency in scientific communication and quality assurance
Since the journal launch in 2001, ACP has grown to become one of the major international journals in atmospheric science, now handling around a thousand submissions per year. ACP’s success was not assured when it launched. Open peer review, in which the reviewer comments, author replies, and additional public comments from the scientific community are published immediately, was radical in 2001. “Our guiding principle was to achieve highest levels of scientific integrity through free speech and transparency in scientific exchange and quality assurance”, says Max Planck Director Ulrich Pöschl, who had initiated ACP.
The interactive open access publishing concept was developed more than 20 years ago by researchers connected through the MPI for Chemistry. “It has been a lot of joy and work to initiate, design, and establish interactive open-access publishing with an equally pleasant and strong team of friends and colleagues, including Paul Crutzen and Arne Richter, who are unfortunately not with us anymore but deserve special thanks for the swift initial gain of momentum”, says Uli Pöschl, who led ACP until recently, chaired the EGU publications committee for many years, and continues to promote open access also through the global initiative OA2020 and related activities.”
Abstract: This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing–linking articles to a code repository–was also the most useful method of accessing code from the reader’s perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools.
“In The big idea: should we get rid of the scientific paper?, published by the Guardian newspaper, Stuart Ritchie argues for a radical action: scientists should abandon the current format of the scientific paper, which is static and not interactive. Despite being currently published in electronic medium, they are still very similar to the printed version that dominated the scientific publishing landscape for more three centuries. In fact, the current scientific article is only an electronic version of “the physical black and white printed paper” in PDF (portable document format). This format is not friendly for reading on the screen of computers, tablets and mobile phones, which are dynamic and offer countless alternatives to interact with information. Reading a scientific article nowadays should be more than getting passive information about a subject matter, rather it should be an opportunity to think, check, review and reproduce the data and analysis presented in the article.
However, the standards of scientific publishing industry, and the rules of academic establishment as well, oppose any change in this static, passive and mostly non-transparent system of science dissemination. The Guardian newspaper article points out some alternatives to the PDF packaging of scientific articles, e.g., interactive “notebooks” that combine images, data, code, methods, and analysis into a single interactive and dynamic “article” that might be read, reviewed, reproduced, edited, and shared at any time. This format is known as “living article”.
But the problem does not lay solely on the “static scientific article”. There are the journals and the rules dictated (mostly) by the financial interests of the major commercial publishers. The predominant system for the communication of scientific results has not been developed by scientists, and they cannot freely decide what is the best “vehicle” or format to disseminate their research work. Actually, the publishers of scientific journals decide and control which format is accepted or not. A scientist today must follow the rules determined by journal editors, who are also dependent on the consensus and standards defined by the entire publishing industry.
By this reasoning, the problem is not the article itself, rather it is the vehicle that widespread the scientist’s message: the scientific journal and its rules! It is not possible to “get rid of the scientific article” without reforming the concept and practice of the “scientific journal”! ”
“Web-based annotations of digital books enrich a scholarly text through overlays and filters that sit on top of the text in order to show additional commentary and feedback. Annotations—in short, a form of readerly or writerly interaction that consists of notes (in any medium) added to texts (of any medium)undefined—already have a long history in a print and manuscript context (e.g., marginalia, errata, rubrics), but the immediacy of two-way discussion between users is a notable feature of digital open annotations, both of comments at the bottom of a text and in-line text annotations. Bertino and Staines therefore liken annotation to a “conversation” between authors and audiences that was previously much less interactive [undefined]. In addition to this, for Tara McPherson annotations (of e.g., digital visual archives) may also facilitate a more “seamless integration of research materials and scholarly analysis” through a closer presentation between commentary and the object studied [undefined]. This is particularly useful in a scholarly communication environment where annotations enable discussions to take place in direct proximity to the material that is under consideration, for example with linguistic markup of text corpora….”
“We are grateful to these authors for taking their time to share their feedback with us, and for helping us showcase how Executable Research Articles can help improve the transparency, reproducibility and discoverability of research content across a variety of research subjects. Executable Research Articles are an open-source technology available to all, and we encourage any authors or publishers interested in the format to [get in touch] for more information….”
“This summer, eLife was pleased to launch Executable Research Articles (ERAs) in partnership with Stencila, allowing authors to post computationally reproducible versions of their published papers in the open-access journal.
The open source ERA technology stack delivers a truly web-native format that treats live, interactive code as a first-class asset. It was developed to address current challenges around reproducing and reusing published results—challenges mostly caused by the lack of infrastructure for publishers to showcase the richness and sophistication of the computational methods used by researchers in their work.
As part of its mission to transform research communication, eLife invests in open source technology innovation to modernize the infrastructure for science publishing and improve online tools for sharing, using, and interacting with new results. The organization began work on the concept of computationally reproducible papers in 2017, first in partnership with Substance and later, with Stencila, and announced a number of milestones along the road to delivering ERA….”
“This summer, eLife was pleased to launch Executable Research Articles (ERAs) in partnership with Stencila, allowing authors to post computationally reproducible versions of their published papers in the open-access journal.
The open source ERA technology stack delivers a truly web-native format that treats live, interactive code as a first-class asset. It was developed to address current challenges around reproducing and reusing published results—challenges mostly caused by the lack of infrastructure for publishers to showcase the richness and sophistication of the computational methods used by researchers in their work.
As part of its mission to transform research communication, eLife invests in open source technology innovation to modernize the infrastructure for science publishing and improve online tools for sharing, using, and interacting with new results. The organization began work on the concept of computationally reproducible papers in 2017, first in partnership with Substance and later, with Stencila, and announced a number of milestones along the road to delivering ERA….”
“Since 2017, we have been working on the concept of computationally reproducible papers. The open-source suite of tools that started life as the Reproducible Document Stack is now live on eLife as ERA, the Executable Research Article, delivering a truly web-native format for taking published research to a new level of transparency, reproducibility and interactivity.
From today, authors with a published eLife paper can register their interest to enrich their published work with the addition of live code blocks, programmatically-generated interactive figures, and dynamically generated in-line values, using familiar tools like R Markdown and Jupyter in combination with Stencila Hub’s intuitive asset management and format conversion interface. The resulting new ERA publication will be presented as a complement to the original published paper. Very soon, a Google Docs plugin will also be made available to let authors insert executable code and data blocks into their documents using the cloud service.
Readers of ERA publications will be able to inspect the code, modify it, and re-execute it directly in the browser, enabling them to better understand how a figure is generated. They will be able to change a plot from one format to another, alter the data range of a specific analysis, and much more. All changes are limited to an individual’s browsing session and do not affect the published article, so anyone can experiment safely. Readers can also download the ERA publication – with all embedded code and data preserved – and use it as a basis for further study or derivative works….”
“H5P usage has doubled up many times over the last few weeks. It is good to see indications of us in the H5P community providing value in times like these, and we can still do much more. Our goal right now must be to provide students with amazing content as fast as possible. Having millions of H5P users around the world producing the same content will be a duplication of efforts and far too slow. We need to work together.
The most important part of our roadmap has long been to finish up and integrate an OER Hub in the H5P authoring tool to facilitate global collaboration. It was also the most requested roadmap item by far on the last H5P Conference. The H5P Core Team has now tasked all developers with finishing up the H5P Hub as fast as possible. It will be an integral part of the H5P authoring tool and allow users to easily share their content with every H5P user in the world! Content shared by others will of course be searchable and repurposable.
The H5P Content Hub is the heart of H5P and the soul of our vision of empowering everyone to create, share and reuse interactive content….”
“Designer Nicholas Rougeux has spent the last year combining his love for data visualization with his tech skills to lovingly restore and place 19th-century texts online. After the success of Werner’s Nomenclature of Colours and the geometry tome Byrne’s Euclid, Rougeux is tackling a new topic—botanical illustration.
After scouring the internet for different 19th-century botanical catalogs, Rougeux set his sights on Illustrations of the Natural Orders of Plants by Elizabeth Twining. This 1868 two-volume catalog is the second edition of a work first published in 1849 (volume 1) and 1855 (volume 2). The rare first edition can go for upward of £40,000 (about $49,000), but luckily for Rougeux, the second edition is available for consultation online at the Internet Archive (volume 1, volume 2) and the Biodiversity Heritage Library….”