graph TB
branch("Create branch<br>to write protocol"):::yours
write("Protocol writing in<br>'docs/protocol/protocol.qmd'"):::yours
pr("Create pull request<br>when protocol is<br>ready"):::yours
review["Protocol review<br>and approval"]:::ours
zenodo["Protocol uploaded<br>to Zenodo"]:::ours
update["Update metadata<br>in 'dp-next.yml'"]:::ours
branch --> write --> pr --> review --> zenodo --> update
classDef ours fill:#ADD8E6;
classDef yours fill:#FFA07A;
9 Protocol
Protocol writing. It is expected that the first output from each publication will be an analysis protocol. There are two broad types of protocols: overall ones for a given work package and specific ones for a given project within (or across) a work package.
Important
Protocols are published to Zenodo. The publishing process will be handled by the Seedcase tool zen-do, which makes the process much easier and sometimes can be set up to be done automatically.
9.1 Work package protocols
These work package protocols are (generally) kept in stand-alone repositories, so that they can be directly built into a website and automatically uploaded to Zenodo whenever changes are made. Generally, it’s best to have someone from the management group create the repository for the protocol, as its better to set it up using the Template Website from Seedcase that requires some admin settings after creating the repository.
These protocols are bigger and broader in scope, as they represent the overall activity within a work package. They also will have more people working on them, so writing them will be done through pull requests, where at least one other person reviews and approves the changes. In this way, any text on the main branch (and built onto the website) will already have been approved and is “publishable” in the current state.
Sections within work package protocols may be more diverse compared to protocols for research projects, which have a template protocol file included with instructions and suggestions.
9.2 Research project protocols
Each research project is created from our template. Within the template contains a file that lists all the sections that should ideally be filled out for a protocol for the research project. When a research project is created from the template, the protocol file is kept in docs/protocol/protocol.qmd. See Figure 9.1 for an overview of the protocol writing process.
When you start working on your research project, begin by filling out the protocol file. Inside of it contains instructions and descriptions of different sections typically found in a research project’s protocol. Protocols are not a strict, “binding” set of things you will do in your project. They are meant to help you as the researcher focus your research question(s) and hypotheses, define your analysis plan, and provide you with a rough roadmap to your final research publication.
Ideally you will want to create a separate Git branch to create your protocol so that you can create a pull request where others can more easily review and approve it. After you’ve finished writing a protocol and made a pull request, notify someone (who will be coauthor on the project) to review and approve it.
Once the protocol has been reviewed and approved, someone on the management group will publish it on Zenodo for you to obtain a Digital Object Identifier (DOI). This provides a clear record connecting the hypotheses and anticipated analytic approaches with the final analysis of the data.
Any changes to the protocol as the project continues should be updated on Zenodo. If there are any changes, make sure to notify someone on the management group to update the Zenodo deposit and create a new record.
Tip
If you desire (though it is not required), you could publish a stable version of the protocol as a preprint on online preprint servers such as arXiv or medRxiv. Keep in that you would be responsible for uploading it and keeping it updated. Because publishing to Zenodo is done semi-automatically by someone in the management group, you don’t need to do the upload yourself for Zenodo.
9.3 Acknowledgement Statement
Any publication, dissemination, or communication that comes from or is related to DP-Next should mention the following acknowledgement statements.
For all publications:
The DP-Next project was funded by a Steno National Collaborative Grant from the Novo Nordisk Foundation (Grant number NNF24OC008916). Additional funding was obtained from all Steno Diabetes Centers.
Additionally for publications involving data collected through OPEN, which is used for collecting survey data from e.g. the electronic questionnaires used in Work Package 3 (questionnaire study and the clinical study):
Electronic questionnaires were distributed using the Open Patient data Explorative Network (OPEN) from Odense University Hospital, Region of Southern Denmark (open.rsyd.dk).