Off Türkiye, May 7. Image – Getty: Serkan Ezer
By Porter Anderson, Editor-in-Chief | @Porter_Anderson
‘Streamlines Code-Sharing as Part of Article Submission’
In an announcement from its London and Cambridge offices, Springer Nature is announcing an expansion of its transatlantic partnership with the “computational science platform for researchers” called Code Ocean.
A first extension of the project was announced in November 2022. It seems to be working: What this newly announced extension will do is make it possible for writers submitting primary papers to the Nature-branded journals—including Nature and all the Nature Research journals—can share their code and data through the Code Ocean platform as part of the manuscript submission process.
According to Springer Nature, the Code Ocean approach supports researchers “with a fast and efficient way to start, scale, collaborate, and reproduce computational research central to their work.
“As part of the integration, Nature journals also allow authors who have other means of sharing code—for example, via GitHub or Zenodo—to provide those details directly through the journal submission platform. Using this integration, editors will be able to track the sharing of code directly on the submission platform, and where appropriate, will automatically see the relevant information and instructions to reviewers to peer-review the code.”
Simon Adar
In a comment on the news of the partnership’s extension, Code Ocean founding CEO Simon Adar says, “This partnership demonstrates our commitment to computational reproducibility and accessibility in scientific research.”
“The integration of Code Ocean with Nature Portfolio’s submission platform,” Adar says, “streamlines code-sharing as part of the article submission process and ensures that code submitted to these journals meets rigorous standards for reproducibility.”
Erika Pastrana
And speaking for Springer Nature, Erika Pastrana, editorial director of Nature Journals, says, “This collaboration represents a significant step forward in our commitment to computational reproducibility in published research.
“We want to support all authors in being able to share openly and publish key research objects.
“Enabling this integrated workflow across the Nature branded journals means more authors will benefit from a streamlined experience—increasing transparency in research, reducing duplication of effort and facilitating the faster advancement of science.”
In 2022, as the first extension of its relationship with Code Ocean was announced—following an initial trial—Pastrana told the news media, “Code is a key component of research and increasingly computational approaches are utilized or developed as part of a research project.
“At Springer Nature, we want to support authors openly sharing and publishing the key research objects that support [a] manuscript, such as code, data, and protocols.
“The sharing of code and data improves reproducibility, reduces duplication of effort, supports better transparency and enables faster advancement of research.”
Her comments then included an interesting point: “We believe that the code (and other key research objects) should be peer-reviewed alongside the manuscript.”
That logical aspect of peer-review, she said then,was why “we have looked to deploy suitable technological capabilities to support authors and reviewers to comply with our open-science policies.
“By extending this partnership, we are building on the success we have seen in previous pilots, by now enabling a streamlined process for authors, editors and reviewers to easily share and review code – something which is fundamental to open science.”
Each Piece of Code Has an Associated License
Code Ocean is a company that reports it was incubated as a start-up in 2014 at the Jacobs Technion-Cornell Institute, prior to opening its platform to address a challenging topic in scientific research—the crisis of reproducibility and transparency.
Its own promotional material refers to the company as “a cloud-based platform that makes the computational code used in research both accessible and usable. Researchers and software engineers can now share and run code.” As a key principle, the company’s information about itself asserts that “When code is not accessible, research cannot be easily replicated.”
According to Adar, the goal of Code Ocean is to share code and algorithms more easily using an embedded link, just like a YouTube video, he has said. Researchers upload code to the platform, then link it to the associated article in journal.
Each piece of code also has an associated license, according to company information, allowing researchers to define how it’s used, with a model that’s said to be not unlike Creative Commons’ assignment of various permissions levels. This is part of a company principle of giving credit where it’s due. “Traditionally,” the company’s material says, “previously published papers are credited in new research, but the code underlying the work is not. Code Ocean rectifies this by allocating digital object identifiers (DOIs) to code.”
Code Ocean is based in New York City.
More from Publishing Perspectives on open artificial intelligence is here, more on scholarly and academic publishing is here, and more on Springer Nature is here.