A comment on “The big idea: should we get rid of the scientific paper?” | SciELO in Perspective

“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”! ”

Part 1: Interaction in Context · Promoting and Nurturing Interactions with Open Access Books: Strategies for Publishers and Authors

“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….”

eLife authors relay their experiences with Executable Research Articles | Labs | eLife

“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….”

A web-native approach to open source scientific publishing | Opensource.com

“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….”

A web-native approach to open source scientific publishing | Opensource.com

“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….”

Welcome to a new ERA of reproducible publishing | Labs | eLife

“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….”

The H5P OER HUB | H5P

“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….”

Incredible 19th-Century Botanical Catalog Put Online and Made Interactive

“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….”

Publishing at the speed of research | EurekAlert! Science News

“Today, the open-access, open-data journal GigaScience and the technology and publishing services company River Valley Technologies announce a new partnership to deliver a research publishing process that is extremely rapid, low-cost, and modular. As a pioneer of open data and open science publishing, GigaScience brings editorial expertise in publishing research that includes all components of the research process: data, source code, workflows, and more. River Valley Technologies, with 30 years of expertise in publishing production, delivers an end-to-end publishing solution, including manuscript submission, content management and hosting, using its collaborative online platforms. The collaboration is developing a publishing process that, in addition to providing on-the-fly article production, will create more interactive articles that can be versioned and forked….”

The Scientific Paper Is Obsolete. Here’s What’s Next. – The Atlantic

“Perhaps the paper itself is to blame. Scientific methods evolve now at the speed of software; the skill most in demand among physicists, biologists, chemists, geologists, even anthropologists and research psychologists, is facility with programming languages and “data science” packages. And yet the basic means of communicating scientific results hasn’t changed for 400 years. Papers may be posted online, but they’re still text and pictures on a page.

What would you get if you designed the scientific paper from scratch today? …

Software is a dynamic medium; paper isn’t. When you think in those terms it does seem strange that research like Strogatz’s, the study of dynamical systems, is so often being shared on paper …

I spoke to Theodore Gray, who has since left Wolfram Research to become a full-time writer. He said that his work on the notebook was in part motivated by the feeling, well formed already by the early 1990s, “that obviously all scientific communication, all technical papers that involve any sort of data or mathematics or modeling or graphs or plots or anything like that, obviously don’t belong on paper. That was just completely obvious in, let’s say, 1990,” he said. …”

 

 

Pathfinders: Documenting the Experience of Early Digital Literature

“Pathfinders begins the necessary process of documenting early digital literature, specifically pre-web hypertext fiction and poetry, from 1986-1995. These literary works were produced with programming languages like BASIC or authoring systems like Storyspace and HyperCard and require a degree of interactivity between the reader and the work. They were also among the first computer-based works of literature to be sold commercially in the U.S. and, because of their availability through commercial distribution, were influential in shaping literary theory and criticism that, today, are used to discuss born digital writing. They are also literary works in danger of becoming inaccessible to the public because they were produced on and for computer platforms that today are obsolete….”