diff --git a/_quarto.yml b/_quarto.yml index a60e587..7432cab 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -30,6 +30,7 @@ book: - docs/getting-started/index.qmd - docs/getting-started/new-project.qmd - docs/getting-started/dst.qmd + - docs/protocol/index.qmd - docs/publishing/authorship.qmd appendices: - CHANGELOG.md diff --git a/docs/protocol/index.qmd b/docs/protocol/index.qmd new file mode 100644 index 0000000..9b4b6d0 --- /dev/null +++ b/docs/protocol/index.qmd @@ -0,0 +1,93 @@ +# Protocol {#sec-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. + +::: callout-important +Protocols are published to Zenodo. The publishing process will be handled by the +Seedcase tool [zen-do](https://zen-do.seedcase-project.org), which makes the +process much easier and sometimes can be set up to be done automatically. +::: + +## 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. + +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 to follow. + +## Research project protocols + +Each research project is created from our +[template](https://dp-next.github.io/template-project). 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 +@fig-research-project-protocol 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. + +```{mermaid} +%%| label: fig-research-project-protocol +%%| fig-cap: >- +%%| Protocol development steps to follow for a research project. The rounded +%%| boxes in orange are tasks you are responsible for doing. The rectangular +%%| ones in light blue are for coauthors or the management to do. +%%| fig-alt: >- +%%| Boxes and arrows indicating the flow of tasks from preparation to +%%| publication. The boxes are colored according to whether they are the +%%| responsibility of the authors or the committee members. These tasks are +%%| visual representations of the text below. + +graph TB + branch("Create branch
to write protocol"):::yours + write("Protocol writing in
'docs/protocol/protocol.qmd'"):::yours + pr("Create pull request
when protocol is
ready"):::yours + review["Protocol review
and approval"]:::ours + zenodo["Protocol uploaded
to Zenodo"]:::ours + branch --> write --> pr --> review --> zenodo + + classDef ours fill:#ADD8E6; + classDef yours fill:#FFA07A; +``` + +::: callout-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. +::: + +{{< include /includes/_acknowledgement-statement.qmd >}} diff --git a/includes/_acknowledgement-statement.qmd b/includes/_acknowledgement-statement.qmd new file mode 100644 index 0000000..fd318dd --- /dev/null +++ b/includes/_acknowledgement-statement.qmd @@ -0,0 +1,19 @@ +## 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](https://open.rsyd.dk), 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).