TITLE: Creating a protocol with protocols.io for BD2
AUTHORS: Kelsey Barcomb

[DESCRIPTION]
This protocol describes how to create and post a protocol on the BD2 workspace.

[STEPS]
SECTION: Create a new protocol file on the BD2 workspace
1. Login and open your team's folder. In the upper right corner click 'NEW +' and then 'New protocol'.
 

SECTION: Create a new protocol file on the BD2 workspace
2. Confirm the destination folder for the new protocol. Click continue.

 

SECTION: Add steps to the protocol
4. This step describes adding steps manually using 'Insert step' and related functions. See the next step for instructions on adding steps from text.

 

SECTION: Create a new protocol file on the BD2 workspace
3. In the title bar where it says 'untitled protocol', give your protocol a descriptive name.

 

 

SECTION: Create a new protocol file on the BD2 workspace
3.1. Your protocol should now be visible in the main BD2 workspace landing page. You may need to refresh the page to see it.
SECTION: Add steps to the protocol
4.1. Add steps and sections using either the menu on the left or by clicking '+ New' on the body of the page.

SECTION: Add steps to the protocol
5. This step describes adding steps from text. See the previous step for instructions on adding steps manually.

SECTION: Add steps to the protocol
5.2. Indicate the manner in which steps are split in the protocol and paste the text into the text box.
 

SECTION: Add steps to the protocol
5.1. Click 'Insert steps from text' on the left menu bar.
SECTION: Add steps to the protocol
5.3. Click preview and edit the resulting text as needed. You may need to adjust how the steps are split.
SECTION: Add steps to the protocol
6. Adjust and annotate steps as needed. You may need to convert steps to sub-steps or add annotations using the 'Components' menu on the right side of the screen.

Some common changes are added in sub-steps below.



SECTION: Add steps to the protocol
6.1. Sub-steps. 
To convert a step to a sub-step, click the 6 dots to the left of the step and select 'Convert to sub-step'.
SECTION: Add steps to the protocol
6.2. Critical steps
To mark a step as critical, click the 6 dots to the left of the step and select 'Mark a critical step' and select the appropriate icon(s) to label the step.
SECTION: Add steps to the protocol
6.3. Notes.
Under the components menu select 'Note' to add in a note. Notes are useful for adding troubleshooting details or tips to your protocol.
SECTION: Add steps to the protocol
6.4. Reagent or Equipment.
To add a link to a specific reagent or piece of equipment, use these relevant functions under the Components menu. These options allow you to link the protocol to the specific company and product and provide annotations on product identification. 
Any materials added will automatically populate the 'Materials' tab on the top of the page.
SECTION: Add protocol description
7. Navigate to the 'Description' section of the protocol at the top of the screen

 

SECTION: Add protocol description
8. Add an abstract. As per protocols.io recommendations, "The recommended abstract format is to include 1-2 sentences that summarize the protocol, followed by 1-2 sentences that describe the expected results. If this is an updated version or a fork, you should also briefly summarize the major changes and optimizations."
SECTION: Add protocol description
9. Add the protocol authors. 
 

SECTION: Add protocol description
10. As is applicable, add any other details within the Description section. These are all optional, though you are encouraged to add citations to any publications that reference this protocol.
SECTION: Converting a private protocol to another status
11. After you create a protocol, it is saved as a draft. This protocol can be converted to multiple status types, as described below.
SECTION: Converting a private protocol to another status
11.1. Post draft.
This option allows you to post a draft of a protocol to make it public. The protocol can no longer be changed, but it can be deleted. This is useful for sharing within a network a protocol that is not yet ready for publication.
SECTION: Converting a private protocol to another status
11.2. Reserve DOI.
This option allows you to obtain a DOI for a protocol that is not yet public. This status is useful for adding DOIs into a manuscript submission that has not yet been published. It requires updating the status once the manuscript is fully published.
SECTION: Converting a private protocol to another status
11.3. Publish.
This option allows you to obtain a DOI and makes your protocol public. It can be searched for within the protocols.io public index. This status is required for final publication.
SECTION: Converting a private protocol to another status
11.4. Versioning and forking a protocol.
An existing protocol that needs to be updated for a new publication or usage can be versioned or forked. Versioning should be used for updating the same protocol and forking should be used for creating a new workflow based on an existing protocol.