Lesson 4 of 8

37,5%

Learn

In this lesson, we will tackle something you’re very familiar with – protocols.

SciNote offers you a protocol management tool, a protocol repository, where you can create your own custom protocols or import external protocols from the public online database protocols.io.

You will learn how to create and manage personal and shared protocols, and how to follow their steps right at the bench.

Let’s jump right in!

Protocol repository

In SciNote there is a protocol repository that serves as a library of your protocols – shared or personal. The protocols you choose to store under the TEAM PROTOCOLS tab are visible and can be used by everyone on the team. On the other hand, the protocols stored under MY PROTOCOLS tab are personal and visible to you only.

When it comes to transferring lab protocols into SciNote’s protocol repository, you have two options: you can either create a protocol from scratch by copy-pasting the content from your existing protocol file (Word or PDF) or you can import a public protocol from protocols.io – an open access online repository of research protocols.

At this point, you are probably wondering ‘Why not simply upload a Word or PDF file?’ but this option has its own disadvantages. If you upload an existing Word or PDF protocol, you cannot print out the protocol as part of your experiment report. Besides, you lose the advanced audit trail capability for tracking all the changes made to the document – meaning, you will be able to see who changed the document and when but not which changes were made.

To create a protocol from scratch, go to the protocol repository by clicking the Protocols tab in the menu bar on the left. When you are in, click the blue +New button, name the protocol and click the blue Create button.

After that, you will have a blank page with some basic protocol information above, such as the time when the protocol was created, whom it was created by, etc. You can also write a short description of a protocol, but this is completely optional.

A protocol can consist of multiple protocol steps where each of them represents an actual step of an experimental protocol or an individual instruction of a standard operating procedure.

To create your first protocol step, click the blue +New step button, write the step name, and the description in the field with a rich text formatting toolbar. Here, you can also insert an image, hyperlink, or code. When you are finished with creating a protocol step, click the blue Add button in the bottom right corner.

Furthermore, you can create checklists, tables, or upload files under separated tabs of the protocol step above the Step name field. If you want to create a checklist e.g. for different buffers, open the Checklists tab and click the +Add checklist action. It’s similar to creating tables, except that you need to open the Tables tab instead. As for the Files tab, here you can upload any types of files, including images and MS Office files.

Managing protocols

The creator of the protocol has all the managing privileges. This means, only the protocol creator can edit the protocol, archive it, or move it between shared and personal protocol repositories.

If you want to enable other users to create protocols, their role has to be Team Administrator or Normal user. This has to be settled at the team level, so go to Settings in the menu bar on the left and open the Teams tab. Open the team, so you can see all the team members and change their role under the Actions column by clicking the cogwheel icon.

To move the protocol from TEAM PROTOCOLS to MY PROTOCOLS tab check the box of a selected protocol and click the Move to My protocols button. If you want to share your personal protocol with your team members, select the protocol stored in MY PROTOCOLS tab and click the Move to Team protocols button

To edit the protocol, select it by checking the box and click the Edit button. In case you want to edit someone else’s protocol or use it as a template, you need to make a copied version first and then make changes to it.

To make a copy of a parent protocol, select the protocol, and click the Copy button.

To locate the copied protocol in the repository, click the Published at table column, so the copied protocol displays at the top. Continue with checking the box of a copied protocol and clicking the Edit button. After that, you can add a new step to the protocol or simply make changes to the steps of the existing protocol. Don’t forget to click the blue Add button when you are creating new steps or the blue Save button when you are editing the existing ones.

As mentioned before, you can also import public protocols from protocols.io platform. You can do so by simply clicking the EXTERNAL PROTOCOLS tab. When entering a query in the search field, the list of query matched protocols from protocols.io is displayed.

You can preview a protocol by clicking on it and then import it either to TEAM PROTOCOLS by clicking the Import to Team Protocols button or to MY PROTOCOLS by clicking the Import to Private Protocols button.

Besides importing, there is also the Export button that enables you to download a protocol as a .eln file and share it via email with other SciNote users or external collaborators. These .eln protocol files can be opened and read-only within SciNote.

It is possible to print out your protocol as well, and it is explained in the next chapter: Task protocol.

Task protocol

So far, we’ve learned how to create a protocol in the repository. We will continue by explaining how to create a protocol directly within a task.

Each task can contain a step-by-step protocol i.e. detailed instructions or guidelines on how to perform the task (e.g. SOP).

It is true that you can upload your existing protocols as attachments into SciNote, however, taking some time to create your protocols in SciNote will result in multiple benefits of connecting your data and keeping track of all activities. In SciNote, a protocol can include text, checklists, tables, images, and other attached files.

The principle of creating a protocol is the same in both cases, and the main advantage of creating a protocol in the repository is that it can be available to other team members if stored under the TEAM PROTOCOLS tab.

If you created your protocol in the repository, you can easily upload it to the task from the repository. Then, if needed, you can also add notes to each task either in the Notes section or as Comments under each protocol step in the task (e.g. number of counted cells). This suggests that the task protocol is actually the protocol you need to execute at the bench.

To load a protocol to the task, first, open a task and click the Protocol options button. Select Load from repository option from the drop-down list and then search for the preferred protocol in the Filter field on the right. After that, select the protocol and click the blue Load button.

Please note that this action will overwrite the current protocol in the task with a new one if the task already contains a protocol.

Furthermore, you can edit the protocol steps, delete them, or rearrange their order. After editing, you can save the modified task protocol with a new name to the protocol repository and maintain the protocol versioning.

To do this, click the Protocol options button, and select Save to repository option from the drop-down list, type in a new protocol name or use the same name but add the version number. Then choose if you want to share the protocol with other team members (click the Team protocols button) or simply store it for personal use (click the My protocols button).

After that, you can check the box below if you wish to link the task to the protocol repository. This is recommended, so you and your team members can easily keep track of the changes that are made to the protocol.

To finish the action, click the blue Copy button in the right lower corner.

So, the task protocol is basically the lab protocol you complete at the bench. If you want to track your progress, you can mark individual steps as completed by clicking the Complete Step button at the top right corner of each step. Once you complete all the steps in a task protocol, a message pops up asking you if you want to complete the entire task and mark it as completed or leave it in progress.

We also promised to teach you how to download and print your protocols and for now, this is possible by using the reporting function.

First, open the Reports tab in the main menu bar on the left and click the blue +New report button. Then select a project that includes the task(s) that has/have your desired protocol(s). You can create a report for one individual project at once but this report can include multiple protocols from different tasks that are within the same project.

In the next step choose the task(s) under the Choose tasks tab by checking the boxes. You can choose the entire project (including all the experiments and tasks), individual experiments, or individual tasks. Under the second tab Choose content, check the box Steps to include the steps of the protocol in your final PDF or DOCX report. You can choose to include the completed or uncompleted steps, but leave all the other boxes empty.

Furthermore, if you scroll down a bit, you can decide which specific information from protocol steps you want to include in the report. You can select between ChecklistsFilesTables, and Comments.

When you finish adding the content, confirm the action with the blue Add button.

When a report document is created you can download it as a PDF or DOCX file on your computer or print it out directly.


Practice

  1. Log into your SciNote Free account or shared SciNote Premium site that has a unique URL link (i.e. companyname.scinote.net).
  2. Create a protocol in the protocols repository (e.g. qPCR protocol).
  3. Load the protocol to a task.
  4. Write comments under the steps of a task protocol.
  5. Save the modified task protocol to the repository.
  6. Download the protocol as a PDF.
  7. Bonus: Complete one or more steps of a task protocol.

Feeling stuck?

Read the following articles:

Watch the following video tutorials:


Quiz

Previous lesson