How to structure a protocol

How to structure a protocol

Protocols in SciNote format are interactive, executable and ensure traceability.

Perhaps we are thinking of protocols mostly in the scientific context, e.g. protocols that eventually get summarized in the Materials and Methods section of a research paper, graduation or PhD thesis or SOPs that you use in research or diagnostic lab. Protocols can be much more general, including cooking recipes, operational procedures, user manuals for lab or office equipment, safety or any other checklists, guidelines.

Protocols in SciNote have two main elements: Metadata (title, keywords, authors, and description), and Protocol steps.

Keywords are useful as they describe the protocol and will help you find it faster in the protocol repository.

Protocol description is a good place to summarize the protocol or describe things you need to do before executing the protocol in the lab, such as reminders to switch on instruments, unthaw frozen samples or reagents, locate all the consumables such as pipette tips, 96 well plates, test tubes, ice.

The main part of the protocol are Protocol steps. They contain instructions for execution. Protocol steps in SciNote have different elements available that help you design the steps:

  • Title: summary of the step; in case the step is really concise (e.g. Incubate at 40°C for 20 min), this is all the information you will need in this step.
Protocol creation in SciNote
  • Description: when a step is too complex to fit into a one-line-protocol-title, add the supporting information, additional explanations, notes into Step description. You can insert links, images and format text here.
SciNote
  • Checklists: the main advantage of SciNote checklists over bullet points you can insert into Step description is that checking and unchecking of individually listed items in a SciNote checklist is recorded as an individual activity. We recommend using SciNote checklists where such a level of traceability is essential e.g. to confirm you added all the components into a reagent mix or when the step is complex but it makes still sense to keep it as a whole and not break it up into more steps.
Checklist
  • Tables: can be used for simple calculations, reagent mixes, 96-well plate maps and similar.
  • Attachments (Files): use them for more elaborated plate maps (e.g. 96-well, 384-well plate maps drawn in Excel), complex reagent mixes, Excel-based templates for result calculation, pictures of instruments, instrument instructions.
Protocol creation in SciNote
  • Comments: when you have something to say about protocol execution in the lab or you are would like to propose a protocol modification, you can write it down in a Comment. Remember you can cross-reference users here as well, for example, to draw attention of your colleague or supervisor.

Check out these two projects in SciNote: Templates and [NEW] Demo project by SciNote which contain many examples of protocols on Tasks.

In addition, these guidelines will help you design individual steps in protocols:

  • Generally, it is better to have many simpler steps than fewer complex steps. It may seem more work during protocol execution (more clicking or more checking), however, in case someone disturbs you in the lab the more granulated steps you will have the less chance of you forgetting which part of the protocol you already completed and which one not.
  • Split up more complex steps like  “Add 600 μL of buffer A to the column. Close the lid, and centrifuge for 2 min at ≥8000 x g.” into two steps:
Protocol creation in SciNote
  • Write-out repeated steps: instead of “repeat steps 10-11” or “wash pellets 3 times with buffer A” spell out the individual steps:
Protocol creation in SciNote

or

Protocol creation in SciNote
  • Be concise when describing steps, less is more. Too much text makes it hard to follow. Have the gist of the step in the title and move and notes or tips to the Description of the step.
Protocol creation in SciNote
  • Use smart annotations to refer or cross-reference other Projects, Experiments, Tasks, instruments, reagents, storage when needed:
Protocol storage in SciNote