Second, prepare your capsule for reproducible publication, using the articles on this help center (starting with configuring your computational environment), or asking questions via live chat as needed. (If your code requires specialized hardware, or is intended to create a custom GUI rather than produce concrete results, Code Ocean may not be a good fit; please see this article for more details.)
Third, in most cases Code Ocean is notified of the peer review submission by the editor or the submission system (for AACR). If you're not sure whether your peer review information is in the system, please write to firstname.lastname@example.org, before you press 'Submit for Publication'. In your message, please include the journal you're submitting to, and the name and email of the corresponding editor we should send the private share link to.
Fourth, press 'Submit for publication.' This will not publish the capsule, but will instead send the capsule on for a brief verification of reproducibility by Code Ocean staff. See Code Ocean's verification process for computational reproducibility for an overview. (Note: please list the journal you are submitting to in metadata, rather than any associated preprint.)
From there, if we have any verification-related feedback, we will email you suggesting changes.
Once those changes, if any, are addressed, we will provide your editor with a private link to a copy of your capsule. Any reviewer whom the editor shares this link with will subsequently be able to view your code, data, and results and the computational environment -- with or without an account.
Please make sure that your reproducible results are as complete as possible so that reviewers can inspect them at a glance, without having to rerun your code.
The end result will look just like a published capsule -- see examples in the Explore section.
Submitting an update to the peer review copy
A peer review copy is immutable (frozen), just like a published capsule. To update the peer review copy of your capsule, please withdraw, edit, and resubmit your capsule. While doing so, please write a note to us (either via live chat or email@example.com) to let us know to update the peer review copy.
Integrating Code Ocean into a journal's peer review process
Please write to us at firstname.lastname@example.org, we will be happy to discuss further.