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| PDF (with links to downloadable code and data) | No | Research is displayed the same for all users Source code is available but not easy for users to change their experience |
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| Downloadable binary executable | No | Research is displayed the same for all users Source code is available but not easy for users to change their experience |
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| PDF (with links to downloadable code and data) | No | Research is displayed the same for all users. Source code is available but not easy for users to change their experience |
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| Downloadable binary executable | No | Research is displayed the same for all users. Source code is available but not easy for users to change their experience |
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| JATS/Metadata | No | Increases understanding, potentially drives interactivity (and accessibility) but is not interactive itself |
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| Website with research results | Usually | When user can change display of data or ideas to enhance understanding |
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| PDF research article with widgets | Yes | Static product with interactive components |
Research is often more than the text content, and can include both the software and computational environments to reproduce work. These can be shared by researchers as computational notebooks, however, scholarly communications infrastructure is currently poorly positioned to both display, interact with, and archive that content. The next-generation of executable and interactive research content in scientific publishing requires comprehensive strategies, guidelines, and frameworks to ensure long-term preservation of the scientific record.
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Research is often more than the text content, and can include both the software and computational environments needed to reproduce work. These can be shared by researchers as computational notebooks, however, scholarly communications infrastructure is currently poorly positioned to both display, interact with, and archive that content. The next-generation of executable and interactive research content in scientific publishing requires comprehensive strategies, guidelines, and frameworks to ensure long-term preservation of the scientific record.
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Modern research is increasingly computational and interactive. From data-heavy simulations to AI-driven analyses, scientists rely on code, data, and interactive tools to interrogate and produce results. Yet scholarly communication remains largely stuck in the print era – the static PDF research paper. Even online, most papers are essentially digital facsimiles of print, disconnected from the underlying code and data. This disconnect from their underlying code, data, and interactive executional environments has serious implications and “needlessly limit, inhibit and undermine effective knowledge transfer” [@10.4230/DagMan.1.1.41]—impeding discoverability, reuse, verification, and long-term access to the full scientific record. Results presented in static text and figures are hard to verify or reuse, and much of the richness of computational work is lost upon publication. The 2011 FORCE11 Manifesto noted, “online versions of ‘scholarly outputs’ have tended to replicate print forms, rather than exploit the additional functionalities afforded by the digital terrain” [@10.4230/DagMan.1.1.41]. FORCE11 itself has encouraged much progress in supporting areas such as data and software citations, FAIR principles, and transparent contributor roles, however the unit and form of the scholarly publication itself is largely the same facsimiles of print.
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Modern research is increasingly computational and interactive. From data-heavy simulations to AI-driven analyses, scientists rely on code, data, and interactive tools to interrogate and produce results. Yet scholarly communication remains largely stuck in the print era – the static PDF research paper. Even online, most papers are essentially digital facsimiles of print, disconnected from the underlying code, data and execution environments. These shortcomings have serious implications and “needlessly limit, inhibit and undermine effective knowledge transfer” [@10.4230/DagMan.1.1.41]—impeding discoverability, reuse, verification, and long-term access to the full scientific record. Results presented in static text and figures are hard to verify or reuse, and much of the richness of computational work is lost upon publication. The 2011 FORCE11 Manifesto noted, “online versions of ‘scholarly outputs’ have tended to replicate print forms, rather than exploit the additional functionalities afforded by the digital terrain” [@10.4230/DagMan.1.1.41]. FORCE11 itself has encouraged much progress in supporting areas such as data and software citations, FAIR principles, and transparent contributor roles. However the unit and form of the scholarly publication itself is largely the same facsimiles of print.
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Today, we are increasingly seeing these interactive formats where reading a scientific narrative has frictionless access to data and interactive research outputs. For example, readers might zoom into a large-scale microscopy image, adjust a simulation’s parameters and rerun results within the narrative, experiment with embedded Jupyter notebooks to test or modify code, or explore time-series visualizations to see broader patterns beyond the author’s chosen times or locations.
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Today, we increasingly see rich interactive formats, where a published scientific narrative provides frictionless access to data and interactive research outputs. For example, readers might zoom into a large-scale microscopy image, adjust a simulation’s parameters and rerun results within the narrative; experiment with embedded Jupyter notebooks to test or modify code; or explore time-series visualizations to see broader patterns beyond the author’s chosen times or locations.
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Interactive research outputs are a demonstration of reproducibility and connection to source materials of the work. Frictionless reproducibility—the ability to access, rerun, and build upon shared code, data, and results with near-zero effort [@10.1162/99608f92.b91339ef]—extends this further by transforming research into a continuously verifiable process. In our discussions with stakeholders and early adopters, we typically hear about two main barriers to adoption: (1) the need for better tools to author executable and interactive content, and (2) the challenge of preserving these formats for the long term. In recent years, many platforms—such as [Jupyter Notebooks](https://jupyter.org), [R Markdown](https://rmarkdown.rstudio.com), [Quarto](https://quarto.org), [Jupyter Book](https://jupyterbook.org), [MyST Markdown](https://mystmd.org), and [Manubot](https://manubot.org)—have significantly improved the authoring experience. Some high-profile initiatives over the past five years have also attempted aspects of interactivity ([eLife](https://elifesciences.org/labs/dc5acbde/welcome-to-a-new-era-of-reproducible-publishing), [AGU Notebooks Now](https://data.agu.org/notebooks-now), [Microscopy Society of America](https://elementalmicroscopy.com), [DistillPub](https://distill.pub/)), however, their uptake within traditional scholarly publishing remains limited.
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Interactive research outputs are a demonstration of the work's reproducibility and connection to source materials. Frictionless reproducibility—the ability to access, rerun, and build upon shared code, data, and results with near-zero effort [@10.1162/99608f92.b91339ef]—extends this further by transforming research into a continuously verifiable process. In our discussions with stakeholders and early adopters, we typically hear about two main barriers to adoption: (1) the need for better tools to author executable and interactive content, and (2) the challenge of preserving these formats for the long term. In recent years, many platforms—such as [Jupyter Notebooks](https://jupyter.org), [R Markdown](https://rmarkdown.rstudio.com), [Quarto](https://quarto.org), [Jupyter Book](https://jupyterbook.org), [MyST Markdown](https://mystmd.org), and [Manubot](https://manubot.org)—have significantly improved the authoring experience. Some high-profile initiatives over the past five years have also attempted aspects of interactivity ([eLife](https://elifesciences.org/labs/dc5acbde/welcome-to-a-new-era-of-reproducible-publishing), [AGU Notebooks Now](https://data.agu.org/notebooks-now), [Microscopy Society of America](https://elementalmicroscopy.com), [DistillPub](https://distill.pub/)). However their uptake within traditional scholarly publishing remains limited.
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We believe that better infrastructure for the long-term preservation of interactive research content would significantly accelerate adoption of interactive research communication tools. Today, many researchers hesitate to commit to formats such as executable notebooks or interactive visualizations because they worry that the content may not be runnable in just a few years. This uncertainty discourages experimentation, even when the tools themselves hold great promise for improving transparency and reproducibility. If publishers and tool developers had more robust preservation strategies—ensuring that interactive research objects could be reliably archived, cited, and re-executed—researchers would feel more confident that their work would endure. This reassurance would encourage researchers to learn and adopt these technologies, ultimately enriching scholarly communication with more transparent and engaging research outputs.
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@@ -19,7 +19,7 @@ Fortunately, many technologies already exist to support the preservation of inte
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:::{card} ↔️ Graceful Degradation
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:url: graceful-degradation.md
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Complex systems can fail or simplify_incrementally_ rather than catastrophically, we promote designing systems that provide the richest experience possible _when everything works_, while still offering meaningful, functional fallback options _when conditions change_.
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Complex systems can fail or downgrade_incrementally_ rather than catastrophically. We promote designing systems that provide the richest experience possible _when everything works_, while still offering meaningful, functional fallback options _when conditions change_.
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:::
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:::{card} 📖 Expanding the Idea: Perspectives from the Ecosystem
@@ -29,9 +29,9 @@ As we move forward with advancing the PIRC Working Group’s framework for grace
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:::{card} 📗 Definitions
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:url: definitions.md
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Terms and definitions, in this context, including our definition of preservation and interactive research content.
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Terms and definitions, including our definition of preservation and interactive research content.
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:::
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## Working Group Contribution
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Preserving interactive research content—not just code or data in isolation—means capturing the integrated environments and narratives that underpin computational science. This is essential for reproducibility, transparency, and educational value. To achieve this, we must support a spectrum of preservation strategies, from fully interactive environments, to readable and static export formats, to archived artifacts with embedded provenance. PIRC takes a higher-level mindset on how to adopt better practices gradually through progressive enhancement, adding computation, data and interactivity in, and then proposing how we “fall back” to today.
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Preserving interactive research content—not just code or data in isolation—means capturing the integrated environments and narratives that underpin computational science. This is essential for reproducibility, transparency, and educational value. To achieve this, we must support a spectrum of preservation strategies, from fully interactive environments, to readable and static export formats, to archived artifacts with embedded provenance. PIRC takes a higher-level mindset on how to adopt better practices gradually through progressive enhancement, adding computation, data and interactivity in, and then proposing how we “fall back” to today's baseline.
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