07-11, 10:45–11:15 (US/Pacific), Room 315
The SciPy Proceedings (https://proceedings.scipy.org) have long served as a cornerstone for publishing research in the scientific python community; with over 330 peer-reviewed articles being published over the last 17 years. In 2024, the SciPy Proceedings underwent a significant transformation, adopting MyST Markdown (https://mystmd.org) and Curvenote (https://curvenote.com) to enhance accessibility, interactivity, and reproducibility — including publishing of Jupyter Notebooks. The new proceedings articles are web-first, providing features such as deep-dive links for cross-references and previews of GItHub content, interactive 3D visualizations, and rich-rendering of Jupyter Notebooks. In this talk, we will (1) present the new authoring & reading capabilities introduced in 2024; (2) highlight connections to prominent open-science initiatives and their impact on advancing computational research publishing; and (3) demonstrate the underlying technologies and how they enhance integrations with SciPy packages and how to use these tools in your own communication workflows.
Our presentation will give an overview of the revised authoring process for SciPy Proceedings; how we improve metadata standards in a similar way to code-linting and continuous integration; and the integration of live previews of the articles, including auto-generated PDFs and JATS XML (a standard used in scientific publishing). The peer-review process for the proceedings currently happens using GitHub’s peer-review commenting in a similar fashion to the Journal of Open Source Software; we will demonstrate this process as well as showcase opportunities for working with distributed review services such as PREreview (https://prereview.org). The open publishing pipeline has streamlined the submission, review, and revision processes while maintaining high scientific quality and improving the completeness of scholarly metadata. Finally, we will present how this work connects into other high-profile scientific publishing initiatives that have incorporated Jupyter Notebooks and live computational figures as well as interactive displays of large-scale data. These initiatives include Notebooks Now! by the American Geophysical Union, which is focusing on ensuring that Jupyter Notebooks can be properly integrated into the scholarly record; and the Microscopy Society of America’s work on interactive publishing and publishing of large-scale microscopy data with interactive visualizations. These initiatives and the SciPy Proceedings are enabled by recent improvements in open-source tools including MyST Markdown, JupyterLab, BinderHub, and Curvenote, which enable new ways to share executable research content. These initiatives collectively aim to improve both the reproducibility, interactivity, and the accessibility of research by providing improved connections between data, software and narrative research articles.
By embracing open science principles and modern technologies, the SciPy Proceedings exemplify how computational research can be more transparent, reproducible, and accessible. The shift to computational publishing, especially in the context of the scientific python community, opens new opportunities for researchers to publish not only their final results but also the computational workflows, datasets, and interactive visualizations that underpin them. This transformation aligns with broader efforts in open science infrastructure, such as integrating persistent identifiers (DOIs, ORCID, ROR), and adopting FAIR (Findable, Accessible, Interoperable, Reusable) principles for computational content. Building on these foundations, as well as open tools like MyST Markdown and Curvenote, provides a scalable model for open scientific publishing that bridges the gap between computational research and scholarly communication, fostering a more collaborative, iterative, and continuous approach to scientific knowledge dissemination.
Presentation Outcomes
By highlighting the new capabilities in the SciPy Proceedings and putting them in context of other ongoing open-science initiatives, we aim to:
- Strengthen and celebrate the SciPy Proceedings as a leading example of modern computational publishing;
- Showcase the possibilities of interactive and executable research articles with live examples;
- Demonstrate open workflows, tools and publishing environments that make computational research publishing more accessible and reproducible.
Target Audience
This talk is ideal for:
- People who are interested in scientific publishing and reproducibility
- Researchers interested in sharing computational narratives and reproducible workflows.
- Attendees who have published in the SciPy Proceedings and are interested in the underlying workflows.
Rowan is the CEO and founder of Curvenote (https://curvenote.com), where we build tools to free science from static PDF documents such that the scientific community can share more interactive, reproducible, and richly-linked scientific content. Curvenote provides an all-in-one publishing platform for researchers, societies and institutes, with a focus on computational research.
Rowan is also on the steering-council for JupyterBook and MyST Markdown, which is part of Project Jupyter and provides widely used open-source tools for authoring and sharing scientific content. Rowan has a Ph.D. in computational geophysics from the University of British Columbia (UBC). While at UBC, Rowan helped start SimPEG (https://simpeg.xyz), a large-scale simulation and parameter estimation package for geophysical processes (electromagnetics, fluid-flow, gravity, etc.), which is used in industry, national labs, and universities globally.
Rowan has won multiple awards for innovative dissemination of research and open-educational resources, including a geoscience modeling application, Visible Geology, that has been used by more than a million geoscience students to interactively explore conceptual geologic models. In his previous role as the VP of Cloud Architecture at Seequent, Rowan ran a large software team working on computational software platforms, visualization tools, and version control systems for geoscientists.