---
title: "Methods and Protocols"
source: The Turing Way
source_url: https://github.com/the-turing-way/the-turing-way
licence: CC-BY-4.0
domain: data-and-analysis
subdomain: turing-way
date_added: 2026-04-25
---

(rr-rdm-methods)=
# Methods and Protocols

This chapter will provide an overview of how to manage your methods or protocols and possibilities for sharing this work with others.

## Why

In order to ensure that others can reproduce your research, it is key that you document all the steps you took during the research process. 
In a wetlab, this is often done in a lab notebook that can be kept on paper or digitally. 
(See the sections on [](#rr-rdm-elns) and [](#rr-open-notebooks) for more on the latter.)
In both cases the lab notes should record what you did or observed in the laboratory. 
It should be recording why steps were taken, including mistakes and thoughts or difficulties experienced during data collection and processing. 
You should take notes in a manner that someone else, with a similar research background or yourself in six months, could use your notebook and repeat the work with the same results. 
It is very important to clearly describe every step taken and to be specific, otherwise reusers might misinterpret your documentation which will lead to challenges (as can be seen in this [exact instruction challenge video](https://www.youtube.com/watch?v=cDA3_5982h8)). 
See also the [](#rr-rdm-metadata-documentation) for more information on how to properly document your workflow. 

(rr-rdm-methods-open)=
## Open Methods/Protocols

[protocols.io](https://www.protocols.io/) and [Bio-protocol Exchange](https://bio-protocol.org/exchange) are repositories for protocols. 
For protocols.io, you can watch two short introduction videos by [Emma Ganley](https://www.youtube.com/watch?v=hva-oTapSWU&list=PL1CvC6Ez54KCcs99wV3eex1v5GUry6Yb7&index=12) and [Lenny Teytelman](https://www.youtube.com/watch?v=1wN6RqCmpqM&list=PL1CvC6Ez54KDvJbbdLn5rPvf1kInifEh9&index=13) to learn more. 

See this video on [methods & protocols](https://youtu.be/CzpY4A5G70s?si=YPX9L_LAC5FAv7G3) from the [ReproducibiliTeach](https://www.bihealth.org/en/translation/innovation-enabler/quest-center/events/course/reproducibiliteach-strategies-to-make-your-research-more-transparent-robust-reproducible-2) team for the differences between protocol journals and protocol repositories (at 23:33).

You can also choose to [share your electronic lab notes openly](https://www.lornecampbell.org/?p=179).

(rr-rdm-methods-resources)=
## Additional Resources

* [Course Syllabi for Open and Reproducible Methods](https://osf.io/vkhbt/)
* [Developing a modern data workflow for evolving data](https://doi.org/10.1101/344804) by {cite:ps}`Yenni2018workflow`
* [Webinar:  How To Perform A Workflow Analysis ](https://www.youtube.com/watch?v=9H9xnVRlc_M)
