Hands-on: Protocol creation and creating an experiment from a protocol

• 15 min
• Easy

Overview

The goal of this hands-on is to understand how the protocol module integrates with experiments.

• Creating a protocol and exploring functionalities (PDF export)
• Cloning a protocol and the parent-child relationship
• Deriving an experiment from an existing protocol

Walkthrough

In Hands-on - Explore Lab Notes, we learned how to create an experiment from scratch in our ELN. In most situations, experiments are not created from scratch, as they follow precise protocols. Here, we learn more about the this protocol-experiment relationship.

Material

Download

Download the material archive to your computer and unzip it

Archive content

- Tea-Coffee_consumables.xlsx
- Tea-Coffee_equipment.xlsx
- pexels-chevanon-photography-324028.jpg
- pexels-jessica-lewis-creative-593328.jpg
- pexels-lisa-7393900.jpg
- pexels-pratik-gupta-2748535.jpg
- water_boiler.jpg

Step 1. Create a new protocol

Protocols are classified into different types that match the ones found in public data repositories (growth, extraction, labeling, NGS library preparation, sequencing ...) or broad categories (biochemistry, molecular biology, buffer...).

• Open the Protocols menu

  • This displays the different protocol types available. Click on the Other sub-category to display the list of protocols available in this category.
  • The actual content may vary depending on the ownership selector position.

• Click on the New other button available on the top left of the list page

  • On the name prompt, type e.g. Preparing the coffee with a french press and click create.

Protocols are organised by types

Creating a protocol is very similar to creating an experiment.

• The protocol new page (see above) is very similar to the experiment detail page, and the text editor provides the same functionalities including attachments, image embedding and item linking.

Differences between experiment and protocols

• Mandatory Summary: Sums up the entire protocol in a few sentences without any formatting (i.e. no images, tables, links, lists ...). The protocol summary is used when we need to submit protocols to public data archives (e.g. ENA, BioStudies...).
• Mandatory Type: every protocol is classified into a type as mentioned earlier.
• Optional Parent protocol which we will talk about later in this tutorial. Here we'll leave it empty.

• Type in a summary e.g. Put the ground coffee in the french press, pour boiling water and press the filter down after few minutes.

• Copy/paste the protocol content below into the description field, adjust formatting if needed

  Protocol description

  • Step 1: Measure your coffee. The standard ratio is approximately 2 tablespoons of coffee per 6 ounces of water. Don’t be afraid to add a few extra beans to be on the safe side – you can more approximately measure out your coffee using a scale after it’s ground.

  • Step 2: Prepare the water. You’ll want to prepare the water last, to ensure the water is the temperature you’re aiming for. Pour from the filter, and let the water sit off from the boil for about 30 seconds before immersing your coffee grounds in the French Press.

  • Step 3: Pour. Saturate the grounds evenly with a smooth, steady pour that will agitate the coffee grounds. Do not put the lid on top of the brewer just yet.

  • Step 4: Soak and stir. Let the grounds absorb the water for approximately 30 seconds before stirring – a few gentle motions using the back of a spoon around the top layer of the mixture and along the sides, to immerse any grounds that are stuck.

  • Step 5: Brew. Let the water extract from the grounds for 2 minutes and 30 seconds. Less than that, and you’ll find your coffee may be too sweet or even sour. Any longer, and your coffee will be over-extracted and unappetizingly bitter – so, set a timer.

  • Step 6: Plunge. There really is no wrong way to push here – just a simple, even push-through of the filter down to the bottom. However, it’s not a clogged toilet – don’t exert too much force or, of course, your coffee will splash. Or you may break the machine, if it’s glass.

  • Step 7: Pour. Word to the wise: The flavor notes of your coffee will change as the cup cools. If at first you’re not tasting what was intended, let it continue to setup. What you taste when it’s piping hot is not what you’ll taste when it’s cooled to a lukewarm temperature.

  • Step 8: Flavor to taste. Add milk or sugar, or not.

  Copied from timothy.propst 2022. World's Best Cup of Coffee. protocols.io

• Scroll down to the Permissions section and uncheck the Edit permission of your group (Tea Lovers on the picture, red circle on below picture) to make sure no one else can modify it. We indeed strongly advise against sharing protocols in edit mode to prevent others to modify instructions while the protocol is already used and referred to.

  The Permission/Sharing Section

  

  Protocols are shared in edit mode with your primary group by default.

• Save your work: click the & exit button.

• We now have a nice protocol to prepare coffee with a French press. You may click on PDF to export your protocol into a (printable) PDF.

Step 2. Cloning a protocol

Let's jump few months ahead in time, many people used your protocol and linked it from their experiments (e.g. "Coffe was prepared according to this link-to-protocol"). Meanwhile, you realised that step 5 should be changed from 2min30s to 5 min for a much better result. You could Edit your protocol and change the value but we advise against this approach as your protocol was shared and is referenced by others.

Instead, we'll make a new version of our protocol so information is preserved.

• Navigate to your protocol "Preparing the coffee with a french press" if you are not there yet.

• Click the Clone button available on the top. Note that you must be in view mode i.e. & exit if needed.

• Your "Preparing the coffee with a french press" protocol has now been duplicated (including embedded pictures and attachments when applicable); also :

  1. The protocol name was modified by adding a timestamp, here "- 2022-07-19 16:05:33" (boxed in orange on the picture). Here, we suggest removing this timestamp and adapting the nam e.g. "Preparing the coffee with a french press - version 2"

  2. The initial protocol is linked as the parent of this new protocol version (boxed in green)

Making a new version of a protocol using the clone option

• Finally, edit the text to reflect the new brew time (visible in red in step 5) and & exit

Step 3. Deriving an experiment from a protocol

In the previous exercise, we explained that protocols in production (i.e. that may have been used to perform experiments) should not be changed in case users linked to them. Still this is a risky approach as it relies on good practices and you have no guarantee that everyone will follow the rule.

In LabID, we wanted a safer approach and we thought that every experiment should contain a full copy of the protocol it followed, instead of linking to a protocol. Let's see how this works.

• Navigate to your protocol "Preparing the coffee with a french press - version 2" if you are not there yet.

• Click the Derive Lab Note button available on the top. Note that you must be in view mode

• A new experiment has been created using the protocol as a template. This means that the full text including embedded images, links and attached documents have been duplicated and used to create the new experiment. Like when cloning a protocol, the name is modified by adding a timestamp (boxed in orange on the picture)

  • Change the name as you see fi e.g. "Preparing a much better coffee with a french press"
  • Set the mandatory project. Here select the Tea Project or the Coffee Project according to your group.

'Derive Lab Note' creates an experiment using a protocol as a template

• Finally, edit the text to enrich the experiment i.e. modify times, add pictures ... and & exit

With this approach, protocols are used as templates to initialise your experiments. This is a much safer approach as each experiment is now self contained and you can easily modify the text to reflect exactly what you did. You can of course still link to the original protocol but your experiment won't be impacted in case the original protocol is modified.

Congrats! You now have completed this hands-on!