You’re on Arcadia’s research publications site. It contains high-level information about our research and publishing experiment, and links out to individual publications, which are hosted on The Stacks. Our main company website is arcadiascience.com.
We’re reimagining scientific publication — welcome to the first draft! This entire effort is an experiment in and of itself. At Arcadia, we share only our own research — there’s no submission process. We publish our work directly online and invite the community to engage with it through post-publication, public commenting.
In this section, we briefly run through what differences you can expect to see between our pubs and more traditional approaches. For more detailed information about our publishing policies, jump to the “Publication ethics and policies” section. And for periodic reflections about our publishing experiment, check out our “Reimagining scientific publishing” narrative.
This research site is owned, operated, and funded by Arcadia Science. It does not generate revenue and we do not publish content from external sources. We publish original research ideas, questions, perspectives, reviews, observations, positive and negative results, datasets, methods, and resources. Our publications cover computational and experimental work expanding biological research beyond traditional model organisms, including machine learning for protein engineering, novel model organism development for human diseases, and tools for protein structure analysis and phylogenomics. We write for PhD-level biologists, but aim for accessibility across fields without requiring deep expertise in each area. We release articles continuously and publish online only.
Our publications look a little different from traditional journal articles or preprints. At the top of each pub, you’ll see key info — title, subtitle, DOI, version number, and links to any external assets necessary to reproduce the work (e.g., code, data, protocols, etc.). The table of contents follows you on the right side of the page as you scroll, and you can click any section heading to jump to that point. There are buttons above the table of contents to help you share or cite the work, and another to view or download a PDF version of the publication.
As you scroll down and look through the content, you might see interactive figures, videos, downloadable files, and other content directly within the body of the publication. Comments about specific stretches of text are marked with comment bubble icons to the right of the text, which you can click to expand and join the discussion.
You’ll find additional resources at the bottom of each publication: the reference list, detailed author contributions, public comments from the community, and social media mentions of the work.
We transparently recognize everyone who contributes to our research. All contributors are listed alphabetically by last name, with roles described according to a standardized system (we’ve based ours on CRediT taxonomy). Our publishing team assigns these roles based on written descriptions and conversations with contributors to ensure uniformity across pubs.
We distinguish which names appear in the citation, or “byline,” based on the role(s) each performed in the research or pub preparation:
Byline roles: Conceptualization, Formal Analysis, Investigation, Methodology, Software, Supervision, Writing
↪ These individuals are ultimately accountable for the publication’s quality and scientific integrity and therefore must consent to its release.
Contributor roles: Critical Feedback, Data Curation, Editing, Project Administration, Resources, Validation, Visualization
↪ These individuals may not have comprehensive knowledge of the entire project, so they aren’t required to sign off on the pub’s release.
One important policy: External collaborators, including former Arcadia employees who’ve left before publication, are never listed as byline authors, though their full contributions are listed explicitly on the pub. This ensures that we can always enforce timely participation in our internal review and approval processes, and no one’s name ends up in a pub byline without their full sign-off on content.
All publications are fully open access under Creative Commons Attribution 4.0 International licensing. We make all related data, code, protocols, and research assets freely available, typically through FAIR repositories. All our figures are colorblind-friendly, high-contrast, and include alt text (as of October 2024). If you have any issues accessing our content, please leave a comment or contact publishing@arcadiascience.com.
Science is best when all feedback — positive and negative — is shared openly. Anyone can leave public comments on our publications. These modular comments allow for focused, constructive conversations about different aspects of the work.
You can leave in-line or page-level comments. You must make a free account with The Stacks and be logged in to do so.
Having technical issues? Contact publishing@arcadiascience.com for help!
All of our work is citable (click the button containing a quotation mark icon above the table of contents to view and copy the full citation in BibTeX or a few other formats). Our publications are each assigned a unique, persistent DataCite digital object identifier (DOI). If you’d like to cite a specific version of a pub, use the pub URL — these are appended with a version number (e.g., /v2). Navigating to the DOI or the base URL always takes you to the latest version.
We maintain high internal standards, and we’re committed to thoughtful and ethical publication practices.
All byline contributors sign off that the description of their contribution is accurate, they vouch for the accuracy of the content in the pub, and they agree to immediate release in its current form.
All publications receive basic copyediting and quality-control checks by members of Arcadia’s publishing team, and many receive more extensive editing or other publishing team support upon contributor request. The publishing team verifies that all pubs are legible at a basic level, performs a plagiarism check, and ensures that there are no visual accessibility issues prior to publication. The publishing team doesn’t gatekeep or select which pubs to release — we simply publish content that Arcadia Science employees choose to share.
All pub contributors complete an AI disclosure form to make clear where they’ve used any AI-based tools in the research, code, or writing. The Arcadia Science publishing team then generates standardized language summarizing these uses and makes sure they’re added to the pub, typically in the methods section.
The work we publish on this platform does not go through a formal peer review process. Once shared, it’s fully open to comments from peers. Anyone can provide constructive feedback for free. We do not delete comments unless they contain spam or harmful statements, or if they’re clear duplicates. We kindly request that readers post any feedback or criticism publicly, for the benefit of all readers, rather than communicating it privately.
Prior to release, Arcadia’s publishing team conducts a plagiarism check of the draft. If you suspect plagiarism, misconduct, or any sort of scientific fraud, please contact publishing@arcadiascience.com and we’ll investigate your claim immediately.
If you notice an error in a publication, please leave a public comment to point it out. One or more of our scientists will review your feedback. While we may not update pubs marked as “not actively updating,” where the contributors are no longer at Arcadia or we’ve moved on from the effort, we may update the pub with the correction, and the comment pointing out the error will stay visible. You can see all previous versions of a pub by clicking the “Version #” box near the top of the pub. We also include release notes summarizing the nature of changes with each new version.
We share Arcadia Science work on this site under a CC BY 4.0 International license. This license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format so long as attribution is given to Arcadia. All code, data, protocols, and other content related to our publications are shared under CC BY 4.0, MIT, or similarly open licenses, typically in FAIR repositories. It’s our intention that all content is freely and fully accessible. If you ever have trouble accessing Arcadia Science content, please comment publicly on the related pub or email publishing@arcadiascience.com for assistance.
All work conducted by Arcadia Science is the intellectual property of Arcadia Science, and we publish selected work on this site under an attribution license (see above). While Arcadia may file patent applications occasionally, we will reference any patents (pending or issued) directly in any related pub (see “Competing interests policy”). If a pub does not include a reference to patents, then we consider the science described in the post to be open to the community, and we encourage readers to build upon and improve the science that we’ve shared.
To ensure that the scientific community is comfortable providing substantive comments on our science, we will not file any patent applications for which a commenting member of the community would be considered an inventor. In other words, your comments are your own intellectual property, and we will not patent your inventions.