---

SciLifeLab protocols.io User Guidelines

This guide will help you get started with SciLifeLab protocols.io. Here you will learn about the platform’s main components, how to access a premium licence, and how to create, collaborate on, and share protocols seamlessly. The instructions are tailored for users with premium access, so you can make the most of the platform’s advanced features. We hope this resource helps you streamline your protocol work and boost collaboration.

For more in-depth documentation and tutorials, visit the protocols.io Help Center or check out their webinars.

NOTE: The protocols.io interface may change over time. If you notice any changes, please let the SciLifeLab Data Centre know at datacentre@scilifelab.se, thank you!

1. Getting started with protocols.io

How to create an account and log in

1. Go to the protocols.io home page and click Sign up free (or go directly to the account creation page).
   Enter your email and password to register.
2. Check your inbox for an authentication code and enter it on the email verification page.
3. Follow the prompts to create a new workspace, then click Continue to complete the setup.

To sign in, go to the protocols.io home page and click Log in to access the Sign in page.

For details on how to customise and manage your profile, visit the Profile section of protocols.io’s Help Center.

How to access a SciLifeLab premium licence

Contact SciLifeLab Data Centre via email at datacentre@scilifelab.se. Please create a free account first and review the SciLifeLab premium licence terms of use.

Include the following in your email:

• Your affiliation with SciLifeLab (e.g., fellow, infrastructure facility staff, or member of a SciLifeLab-affiliated research group)
• How you plan to use protocols.io (e.g., to publish protocols and obtain a DOI, run protocols in the lab, or co-develop protocols as part of a collaborative team)
• Your institutional email address

You will be notified once your account has been upgraded to premium. After that, simply log in with your email and password.

NOTE: SciLifeLab reviews premium licence usage annually. Users that do not meet the minimum usage criteria (more than 0 Mb of storage used, personal or public protocols created, at least one protocol published within a two-year period) may be downgraded to the free tier, but can request reactivation.

If you are a student, postdoc, or research engineer, we encourage you to ask your PI to request a SciLifeLab protocols.io premium licence, so they can create a premium workspace and give your group access to all premium features for the content within that workspace

Main platform features

The platform consists of three key features: workspaces, file manager, and editor.

• Workspaces – Collaborative group environments where researchers can organise, manage, and share protocols.
• File manager – An interface for storing, organising, and attaching files relevant to a workspace.
• Editor – A structured, interactive interface for creating and modifying protocols, featuring components that enhance protocol functionality.

A quick walk-through of the user interface
 
Create new content: Click the + New button in the upper-right corner. Use the drop-down menu to create a new folder, protocol, collection, or document, or to import a protocol, upload files, and more.
Manage your storage: In the top-left panel of the file manager, take a look at the STORAGE panel. Click the three-dot menu on the right to view your current storage usage and add more storage if needed.
Access workspace files: Click View all files in the upper-right corner to see all workspace files, including those shared with you.
Create new workspaces: Click the Create new workspaces icon (two people with a + sign) in the left sidebar to create new workspaces and better organise your projects.
Manage workspace settings: Your workspaces appear on the left-side menu. Click a workspace to manage its settings, such as adding members or adjusting access levels. 

2. Create or join a workspace

Workspaces are the basic units for organising, sharing and collaborating on protocols and associated files. Indeed, creating a workspace is the first step in setting up a new user account.

Create a workspace

To create a workspace:

1. Click the New workspace icon (two people and + sign) in the file manager’s left sidebar.
2. Follow the on-screen instructions to set up your workspace. 

NOTE: A workspace created by a premium user is automatically designated as premium, granting all members access to premium features for its content. 

When you create a workspace, you will automatically become the owner and administrator (“workspace admin”).

As a workspace admin, you can:

• Manage workspace settings and members.
• Add file manager instructions that appear as a pop-up message that members must to acknowledge when joining the workspace.
• Transfer the admin role to another workspace member.
• Enable the signing flow for review and approval of protocols before publication.
• Configure file access or sharing settings.
• Perform other administrative tasks to maintain workspace organisation and accessibility.

For more information, see the protocols.io Help Center page on workspace management, or the SciLifeLab protocols.io Workspace Admin Guidelines.

Join a workspace

To join a workspace:

1. Navigate to the workspace profile page
   Search for the name of the workspace using the search bar in the top-right corner of the page. Make sure to select the appropriate search category
   (e.g., active workspace, my workspaces, organization, or entire protocols.io). 
2. Select the workspace
   Browse the search results and click on the workspace you wish to join.
3. Request access
   On the right side of the workspace profile, click the Join button to request access. This option is only available if the workspace is open for others to join.

NOTE: It is possible to join the workspace that is closed for join requests.
This can be done via personal invitation from the workspace admin.

By joining a workspace as a member, you gain the ability to:

• Create new content within the workspace.
• Add or update protocols within it to keep research methods current.
• Start discussions and collaborate with team members.

For more details, see the collaboration with other scientists page in the protocols.io Help Center.

3. Create a private protocol

As a premium workspace member, you can create a protocol using one of the following options:

• Built-in editor – Create a protocol from scratch.
• AI-powered import protocol tool – Convert a file into the protocols.io format.
• Protocol Entry service – Request assistance from protocols.io staff to import your protocol.

Details for each option are provided in the sub-sections below.

Using the built-in editor

Start a new protocol

In the workspace file manager, you can create a protocol in two ways: 

• Click the + New button in the top-right corner and select Protocol, or
• Click the New Protocol icon (file with a + sign) in the toolbar on the left.

In the pop-up window, choose the workspace and folder where the new protocol will be saved. The editor window will then open. Assign a title to your protocol by replacing the default text untitled protocol in the top-left corner.

Steps and Sections

Protocols are organised into Steps, which represent action points, and steps are grouped into Sections. Sections help structure related steps, for example, by time (e.g., Day 1, Day 2), stage (e.g., initial, main, final), or another logical criteria, and are visually distinguished by different colours on the left side.

In the built-in Editor, add Steps and Sections manually via the left sidebar (Insert section, Insert step, Insert sub-step, etc.) or the + New button. Use the six-dots menu (visible on hover over the left side of a step) to convert Steps to Sub-steps, mark them as Critical, or delete them.

Components

Components are predefined interactive elements that enhance reproducibility, structure, precision, and dynamic functionality in protocol steps.

To view available components, click the Components icon (a box symbol) in the top of the right-hand toolbar. Components are grouped by category, such as Generic, Biology, Computational, or Chemistry, or select All to view the full list.

See the complete list of components with descriptions here.  

Add information about your protocol (metadata)

The Steps tab (first on the left) contains the protocol’s procedural steps, while the other tabs (Description, Guidelines & Warnings, References, Materials, Acknowledgements, etc.) are intended to hold additional essential information: the protocol metadata. 

To add protocol metadata, navigate to the appropriate tab in the editor corresponding to each sub-section described below.

Description tab

This tab includes various sections, such as (but not limited to) Abstract, Authors, Keywords, External Link, Manuscript citation, and Attachments:

• Protocol image
• Abstract: A brief summary of your protocol that provides context and helps others understand its purpose. Provide all necessary details to enhance its reusability.
• Authors: List of all protocol authors. Ensure you have their permission to publish the protocol. Include affiliations if possible (e.g., lab or institute name). 
• Keywords: Terms that categorise your protocol and enhance discoverability.
• External Link(URL): Link to your lab website, research group, publication, or other relevant resources. 
• Manuscript citation: If the protocol is part of a published manuscript, include the citation in this section. 
• Image Attribution: Credit the authors of any images used in your protocol.
• Disclaimer: Add a relevant statement, if applicable.
• Attachments: Upload supporting materials (e.g., original protocol file in PDF, Microsoft Word, or other text format, or other relevant documents).

Guidelines and Warnings tab

• Guidelines: General recommendations and useful tips for using the protocol. 
• Before start: Important information to review before beginning the experiment; shown before step one in View and Run protocol modes.
• Warnings(if applies).
• Ethics statement(if applies).
• Safety Warnings: Additional safety notices for sensitive content or confidentiality.

References tab

A comprehensive list of references to give credit to the authors of your sources.

Materials tab

This section can be populated in two ways:

• Manually enter a complete list of all materials required for your protocol.
• Generate a ready-made list of reagents and materials used in each step of the protocol.

NOTE: The second option requires creating a reagent library for your workspace, which can become accessible via the Components functionality. This allows all workspace members to use the reagents library in their protocols. For more details, refer to the protocols.io Help Center documentation on creating a library of reagents for your workspace.

Acknowledgements tab

Providing acknowledgements ensures integrity, credibility, and openness in scientific research.

Using the AI-powered import protocol tool

To import an existing protocol in a digital file format such as PDF, Word, or plain text (e.g., .docx, .pdf, .txt), follow these steps:

1. Open the file manager of your workspace.

Method A:

2. Drag and drop the document file from your local computer into the file manager.
3. Select the uploaded document with one click. A right-side panel will appear.
4. Click the box Create a new protocol from this file (assisted by OpenAI).

Method B:

2. Once the protocol has been imported, click the View protocol button.
3. The imported protocol will open in a new window.
4. If edits are needed, click the Edit button in the top-right corner of the screen.

NOTE: The imported document may not perfectly retain its original formatting. Review and edit the converted protocol as needed to ensure accuracy.

Using the Protocol Entry service

You can request protocols.io staff to format and import your protocol using the online submission form. This service is free for premium licence holders; otherwise, a fee applies.

NOTE: This service is not a peer review. However, protocols.io staff may suggest improvements for clarity and presentation, and may contact you for additional information

To access this service: 

1. Contact SciLifeLab Data Centre via email at datacentre@scilifelab.se to request the Promo code for the Protocol Entry service.
   Please indicate if you are a premium user and your affiliation with SciLifeLab.
2. Upload your protocol as a file or share it as a link. Multiple PDFs or documents can be submitted at once, along with any relevant notes for the import staff.
3. Enter the Promo code in the box on the right and click Apply.
4. Click CONTINUE to begin the import process.
5. A protocol.io editor will format and import your protocol.
6. A second editor will review it to ensure accuracy relative to your original documents.
7. You will receive a private link for review. Use the comments section to request any changes. 
8. When satisfied, click APPROVE to transfer the protocol to your account.

After accepting the transfer, your protocol will remain private and editable. You can choose to keep it private, share it with others, or make it public at any time.

4. The signing flow (protocol approval process)

NOTE: This feature is available only in premium workspaces and must be enabled by a workspace admin. Instructions are provided in the SciLifeLab protocols.io Workspace Admin Guidelines.

The signing flow allows you to digitally sign your own protocol and request signatures from designated workspace members (“approval signers” or witnesses). When approval signers are involved, the process serves as a quality-control step, ensuring the protocol is reviewed and approved by members who confirm that the content is complete, accurate, and ready for public release. 

Sign and get your protocol signed

If your workspace uses the signing flow with additional signers, your protocol must be signed by you (the owner) and by the designated approval signer(s).

To start the signing process when the protocol is open in the editor:

1. Leave the protocol editor by clicking View on the top-right corner.
2. Click the Sign button in the top-left.
3. In the Additional Signers section, select the workspace designated signer(s) from the drop-down list.
4. Request a one-time password (OTP) to be sent to your email, then enter the OTP to proceed.
5. Click Sign and route for signatures button to submit the protocol for review.

A confirmation banner will appear at the top of the protocol, showing that it is under signing review, along with the submission date and the names of pending reviewer(s).

Additional signers will receive signing requests via email and through a notification in their accounts. Protocols awaiting signatures appear with a red icon in the file manager.

The approval signer(s) can either accept or reject the signing request:

• If accepted: You will receive an email notification, and the confirmation banner will update to show that the protocol has been signed.
• If rejected: You will receive the reason for rejection. After making the necessary updates, you may resubmit the signing request.

Once a protocol is signed, it becomes locked and cannot be edited. In order to re-open it for edits the “approval signer” should reject a protocol. Then it becomes editable again so corrections can be made before resubmitting it for approval.

NOTE: Workspace admins are able to publish unsigned protocols if they choose so.

After all required signatures are collected, the protocol is ready for publication. See section 5. Publish a Protocol, for an overview of the available publication options. However, keep in mind that by default nothing prevents publication from proceeding without signatures.

Sign a protocol as a designated approval signer

If you are a designated signer, you will receive signing requests from workspace members via email and through notifications accessible via the bell icon in the top navigation bar of your account.

To respond to a signing request, click the Accept or Reject button:

• If you accept, request for a one-time password (OTP) to be sent to your email. Enter the OTP to proceed.
• If you reject, provide a reason and optionally suggest modifications.

5. Publish a protocol

To publish a private protocol, you have the following options:

• Publish: Assigns a DOI, makes the protocol public and permanent, and prevents further edits.
• Reserve DOI: Reserves a DOI while keeping the protocol private. It can still be edited and shared via a private link. The DOI may be cited in a manuscript submitted to peer review, and the protocol must be published at a later date or will be automatically published if the DOI is identified in a published research article.
• Post draft: The draft protocol does not receive a DOI but is visible to everyone. It can be unlisted or deleted at any time. The draft itself cannot be edited, but new versions can be created.

You can access these three options in various ways:

• In the editor (Edit mode): Click the three dots icon on the top-right corner to open a drop-down menu.
• In the editor (View mode): The three options appear as buttons in the top-left corner.
• In the file manager: Click once the protocol of interest, and a menu will appear on the right-hand side. Alternatively, click the three dots icon on the right side of the protocol to open a drop-down menu.

Besides protocols, you can also publish documents or collections of files. The same navigation options described above apply.

Publish a protocol without prior DOI reservation

You can publish a protocol directly without first reserving a DOI. Once published, the protocol immediately receives a DOI, becomes publicly accessible, and can no longer be edited. Ensure all details are finalised before publishing, as changes will require creating a new version.

When you are ready to make your protocol, document, or collection public, click the Publish button. This will initiate the publishing flow, which includes the following steps:

1. Review the title and abstract, and add a disclaimer notice if needed.
2. Complete the authors and funders information.
3. Manage comments (you may wish to remove any comments added on the protocol before publication), and specify the status and type of the protocol.
4. Associate your protocol(s) with any relevant workspaces.
5. Preview the final version (check formatting, blank steps, etc.).
6. Carefully read the confirmations and publish your protocol(s).

NOTE: Once a protocol is published, it receives a DOI and can no longer be edited. Protocols with a DOI must remain unchanged to preserve the permanence of the scholarly record, comply with DOI issuance rules, and ensure reproducibility. This guarantees a snapshot of the version that was shared and cited.
If your protocol requires changes or optimisations, you can create a new version at any time.

Publish a protocol after DOI reservation

If you reserved a DOI for your protocol and now wish to publish it, please return to the protocol and click Publish to finalise the process. This involves reconfirming co-author consent and ensuring you are ready to make the protocol publicly available.

Publish a collection of protocols

When you have several protocols belonging to the same project or to the same manuscript submission, you can organise them in a collection. Learn more in the protocols.io Help Center section on collection of protocols.

When protocol publishing is restricted to admins

For quality control purposes, some workspaces may restrict protocol publication to admins. This feature must to be enabled by a workspace admin. In such cases, only workspace admins can publish protocols, and members will not see the publication button.

Therefore, you must notify an admin when the protocol is ready for publication. There is no feature at the moment that automates this notification, but a possible workaround is to ask a workspace admin to enable the signing flow and assign themselves as an approval signer. The admin will then be responsible for completing the publication once all required signatures have been collected.

6. Run protocols as checklists

In the lab, you can run any private (View mode) or public protocol as a step-by-step checklist.

To start a run:

• Open the protocol and click Run in the top-right corner.
• As you go, mark each step as complete by clicking Done on the right.

To modify a step during a run:

• Click the Edit or scale icon to adjust the step.
• Click the Add comment icon to leave a note.

NOTE: The edits and notes added while running a protocol apply only to the current run and do not change the original protocol. They will, however, be saved within the run for future reference.

To finish and save your run:

• Click Finish Run on the top-right corner. Once saved, the run record, including any edits, will be saved in your file manager.

You can add comments and attach files to the saved run. Each step is time-stamped, so you can review exactly what was done at any point. Runs can be kept private or shared with others.

7. Reuse and adapt existing protocols

Version, fork, or copy protocols

Protocols.io offers several ways to reuse and adapt existing protocols, allowing you to refine methods, create customised versions, or build new procedures based on established work.

The three main options are: versions, forks, and copies. They serve different purposes depending on whether you want to update an existing protocol, create a modified variant, or generate an independent duplicate.

The table below summarises the key characteristics of each option:

	VERSION	FORK	COPY
Permanent linking	Linked to previous versions.	Linked to original protocol.	No link.
Who can create	Anyone.	Anyone.	Protocol owner / co-admins.
Who can publish	Owner of the original protocol ONLY.	Anyone.	Protocol owner / co-admins.
When to use	Correct an error in a step. Add optimisation details to improve protocol efficiency.	Adapt a single-sample protocol for multiplexing. Use alternative kits or equipment. Create variants for different species, strains, or sample types.   Take a look at this example.	Use a protocol as a template e.g. Create a collection of related protocols that share metadata (e.g., abstract, authors, affiliations, acknowledgements) but contain different steps.   Take a look at this example.