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. 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). See also the Documentation section for more information on how to properly document your workflow.

Electronic Lab Notebooks#

An Electronic Laboratory Notebook (commonly known as an ELN or a digital lab notebook) is a software system designed to help you document and maintain reproducibility of your research and share information more easily.

Electronic lab notebooks provide the following functionalities:

  • A text editor with similar functions as a paper notebook

  • A search function

  • Secure storage and back up (especially in comparison to paper notebooks)

  • Tools for working with tabular data (calculations and formatting of tables and graphs)

  • Templates for documenting standard procedures

  • Laboratory inventories for managing and documenting samples, reagents and apparatus

  • Collaboration tools for sharing experimental information

  • Some ELNs will allow you to comply with standards and regulations because of their certification processes

ELNs also have their limitations:

  • Costs: Most ELN solutions can only be used through paid plans, or the free plans have reduced functionalities in the number of users, storage space or file sizes. Your lab may also not have access to tables or pens that would make the use of ELNs easier. Check if your institution is offering a solution that you can use without additional costs.

  • File format: Always check if files can be exported in your preferred file formats to avoid format lock-in. Some ELNs also have API’s that allow integration with other software and workflows.

  • Vendor-lock-in: Once you’re using a certain solution you may become dependent on it. Always have an exit strategy in case the solution is no longer offered or if you’re moving institutions and you no longer have access.

  • Sustainability: Choose a solution that has a larger chance of being around for a long time.

  • Drawing: Not all solutions have the tools or capabilities to include drawings or integration with drawing software.

  • Security: Before using an ELN solution you should check any backup plans and data security measures, especially if you’re working with sensitive data.

  • Laboratory situation: Your lab may not have an internet collection or electronic tools could affect samples, reagents or magnets in the lab.

  • Learning curve: ELNs have a longer learning curve than paper notebooks and it takes time to learn how to use them. User-friendliness and flexibility are important to accommodate the widely varying workflows of each lab member.

ELNs can be software that is specifically build as an ELN, such as RSpace or you can combine workflows such as Atom and the Open Science Framework to take notes digitally. There are many solutions to choose from: How to pick an electronic laboratory notebook by [Kwo18] or 2019 Review of the Best Electronic Laboratory Notebooks may help you to find your solution!

Additional ELN resources#

Open Methods/Protocols#

protocols.io is a repository for methods. You can watch two short introduction videos by Emma Ganley and Lenny Teytelman to learn more.

See methods & protocols - ReproducibiliTeach for the differences between protocol journals and protocol repositories (at 23:33).

You can also choose to share your electronic lab notes openly.

Additional Resources#