Lesson 4 of 8

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Now that we are familiar with the pre-set structure in SciNote, we can focus on the data entry at the task level.

Each task starts with the task description, a text field into which you can add your notes.

Each task can also 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.

Below, you will learn what these benefits are.

Protocol repository

In SciNote there is a protocol repository that serves as a library of your protocols – shared or personal. This means you can store your protocols under TEAM PROTOCOLS or MY PROTOCOLS tab. Shared protocols are visible and can be used by everyone from the team, while protocols stored under MY PROTOCOLS are visible to you only.

Team Protocols

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 uploading 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 green +New button, name the protocol and click the green 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, by whom it was created, 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 presents an actual step of an experimental protocol or an individual instruction of a standard operating procedure.

To create the first protocol step, click the green +New step button, write the step name and the description in the field with 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 green 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 with 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 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 Admin 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. Then you need to find the copied protocol in the repository by clicking 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 existing protocols steps. Don’t forget to click the green Add button when you are creating new steps or the green 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 this by simply clicking the EXTERNAL PROTOCOLS tab. When entering a query in the search field, the list of query matched protocols from protocols.io gets displayed.

Import private protocls

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 an .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 learned how to create a protocol in the repository. To continue, we will explain how to create a protocol directly within a task.

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 protocols in the repository, you can easily upload a protocol from the repository to the task. If needed, you can also add notes (e.g. number of counted cells) as Comments under each protocol step in the task. This suggests that the task protocol is actually the protocol you need to execute at the bench.

To add a protocol to the task, first open a task and click the Load Protocol button. Select the from repository option from the drop-down menu and search for the protocol in the Filter field on the right. After that, select the protocol and click the green Load button.

Please note that this action will overwrite the current protocol in the task with a new one, if the task already has 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 Copy To Protocol Repository button, 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 green 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 actually mark individual steps as competed by clicking the blue Complete Step button on the right. 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 out your protocols and you need to know that, 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 green +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 only but a 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 protocols steps 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 to include in the report. You can select between Checklists, Files, Tables and Comments.

When you finish adding the content, confirm the action with the green 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.

Report

Practice

  1. Log into your SciNote account or shared SciNote Premium site that has a unique URL link (i.e. companyname.scinote.net).
  2. Create a protocol in the 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:


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