Code Ocean is part of the peer review process at a few different journals, with more soon to be announced. While you may be contacted by an editor about using the platform during peer review, we are also happy to provide the same functionality to all who ask. It works as follows.
Second, prepare your capsule for reproducible publication, using answers prepared on https://help.codeocean.com, such as those on configuring your computational environment or collaboration, 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, if your managing editor (or Editor-in-Chief) has not already contacted us, please write to firstname.lastname@example.org, before you press 'submit for publication', to let us know:
- that your forthcoming capsule is for peer review rather than publication;
- the name and email of the corresponding editor we should send the private share link to;
- If peer review will be double-blind (the default settings are for single-blind).
Fourth, press 'Submit for publication.' This will not publish the capsule, but will instead send the capsule on for a brief verification process 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, so we know to make a peer review copy rather than publish.)
From there, if we have any verification-related feedback, we will email you suggesting changes.
Once those changes, if any, are addressed, we will email your editor (or you, to send on to your editor, if the editor is not known yet) a 'private share link' to a PEER REVIEW COPY: [your capsule's title]. Anyone whom the editor shares this link with will subsequently be able to view and download a copy of your code, data, and results (and the computational environment via export capsule) -- with or without an account.
Reviewers won't be able to run your code until they sign up for the platform, duplicate the capsule to their own dashboards, and press 'Run'. In light of this, we recommend that you make your reproducible results as complete as possible, to let all reviewers inspect your results at a glance.
The link will look like: https://codeocean.com/capsule/c61a9bda-0216-40e0-86b2-2ccfe67ae948/?ID=9ff63b350fbb4f94b48508899835d7d1 (this is a test capsule, though it's forked from a real one).
Submitting an updated peer review copy:
A peer review copy, by default, will be held fixed across time. The intent is that all reviewers will evaluate the same work, regardless of when they log on or modifications that they or other reviewers make (to duplicate capsules).
To provide updates to 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 make a new peer review copy. We will then create a new peer review copy of your work and send it on to your corresponding editor.
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.
Please write to us at email@example.com, we will be happy to help.