From f78a1221eb0b436b74e0870b09350fe4b122929f Mon Sep 17 00:00:00 2001
From: Andrea Schaffer <37759997+alschaffer@users.noreply.github.com>
Date: Fri, 10 Jan 2025 11:25:35 +0000
Subject: [PATCH] Update protocol.md

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 docs/protocol.md | 10 ++++++++--
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 !!! note
     This section is a work in progress, and will be further developed.
 
-Briefly, pre-specifying your research question and developing a study protocol which outlines your planned methodology is an important open science principle. Doing so can help reduce 'researcher degrees of freedom', and in turn minimise the risk for questionable research practices (such as ["hypothesising after the results are known" (HARKing)](https://en.wikipedia.org/wiki/HARKing) or [p-hacking](https://en.wikipedia.org/wiki/Data_dredging)).
+Briefly, pre-specifying your research question and developing a study protocol which outlines your methodology is an important open science principle. There are several benefits to developing a protocol:
+
+* It reduces "researcher degrees of freedom" and minimises the risk of questionable research practices such as ["hypothesising after the results are known" (HARKing)](https://en.wikipedia.org/wiki/HARKing) or [p-hacking](https://en.wikipedia.org/wiki/Data_dredging);
+* It increases replicability by explaining the “why” of each analytic decision (whereas study code only tells you the “what”);
+* It allows you to get feedback and identify problems early on in the process, before writing code;
+* It can help set limits on what is to be done;
+* It makes writing the manuscript easier.
 
 Taken together, this can improve both the quality and credibility of your research. Developing a detailed study plan, including figure and table shells, can be particularly helpful when using a federated analytics platform such as OpenSAFELY, as there is less scope for interactively developing these whilst working with the data.
 
-This page will eventually contain resources for how to develop an effective study protocol, as well as tips for how to pre-register these formally on [OSF](https://osf.io/) or [ENCePP](http://www.encepp.eu/), or informally by uploading "locked" protocol versions to GitHub. There is no specific template for a protocol that you should use when working with OpenSAFELY, but you can see examples of protocols we've written for OpenSAFELY studies on most of our public repositories — for example [this inhaled corticosteroid (ICS) research repository](https://github.com/opensafely/ics-research/tree/master/protocol) or [this ethnicity research repository](https://github.com/opensafely/ethnicity-covid-research/tree/master/protocol).
+When working with OpenSAFELY, we recommend using [this protocol template](https://docs.google.com/document/d/1bmk7MKSK4SiseOR2N_BsDMtx-kHN8u2WRS-gc2C-qhk/edit?tab=t.0). It includes many elements common to frequently used reporting checklists (e.g. STROBE, RECORD). You can choose to pre-register your protocol formally on [OSF](https://osf.io/) or [ENCePP](http://www.encepp.eu/), or informally by uploading "locked" protocol versions to GitHub. You can see examples of protocols we've written for OpenSAFELY studies on most of our public repositories — for example [this inhaled corticosteroid (ICS) research repository](https://github.com/opensafely/ics-research/tree/master/protocol) or [this ethnicity research repository](https://github.com/opensafely/ethnicity-covid-research/tree/master/protocol).