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 This chapter describes how to manage protocols in caNanoLab with the Protocols function. This section includes the following topics:

Protocols Overview

The Protocols function enables you to create and search for an existing protocol. A protocol provides clear and detailed documentation about the precise actions taken in creating or annotating a sample. When you click the Protocols option on the caNanoLab menu bar, the Manage Protocol Home page appears.

On the Manage Protocol page, the Protocol Links panel lists the following options:

• Submitting a New Protocol: Displays the page to enter protocol information and submit the protocol.

• Searching Existing Protocols: Displays the page to perform a search of an existing protocol.

  There is a basic protocols search option discussed in this chapter. You can also perform a keyword search using the Search box in the upper-right of the caNanoLab window. This option searches across protocols, samples, AND publications. For more information see, Getting Started. From Sample Search Results tables, you can add a sample to the My Favorites page. This is like bookmarking a sample for quick access.

Description of a Protocol

During a caNanoLab workflow, you can identify a protocol used in creating or annotating a sample. A protocol provides clear and detailed documentation about the precise actions taken in any procedure that might be part of an experiment. For example, a protocol could describe the steps a laboratory used for characterizing samples. There are different type of protocols, such as Physical, In Vitro, and In Vivo.

With every protocol object you create in caNanoLab, you can define its visibility, in other words, its access to other users of caNanoLab. For more information about visibility options, see the tables corresponding to each characterization type.

Submitting a Protocol

To submit a new protocol

1. Click the Protocols caNanoLab menu option. On the Manage Protocols Home page, click the Submit a New Protocol link. This opens the Submit Protocol form.

2. The following table lists and describes the fields on the Submit a Protocol page. Enter and select the appropriate information as needed. Items with an asterisk are required.

   Name	Description
   Protocol Type*
   Protocol Name*	Enter or select from the drop-down list the protocol name.
   Protocol Abbreviation	Enter a shortened phrase used in place of the protocol name.
   Protocol Version	Enter or select from the drop-down list the protocol version number.
   Upload OR Enter File URL	Click the Browse button to navigate to the protocol to be associated with the protocol, or enter the URL where the protocol is located.
   File Title	Enter the title of the protocol file.
   Description	Enter any additional description information that the form does not include.
   Access to the Protocol	For more information, see Sharing and Changing Access to a Protocol.

   To clear the entries and start again, click the Reset button.

3. When you finish defining the protocol, click the Submit button.

   Once you submit a protocol, it is listed on the My Workspace page where you can manage all your submitted protocols, and view any protocols that a user has shared with you. For more information, see Using My Workspace.

Editing a Protocol

You can edit a protocol using the following techniques:

• Updating a Protocol
• Sharing and Changing Access to a Protocol
• Deleting a Protocol

Updating a Protocol

The Protocol Update page opens when you click the Edit link corresponding to a protocol listed in Protocol Search Results. The page displays all of the information for a protocol that was entered when the protocol was created in caNanoLab (Submitting a Protocol). With appropriate permissions, you can edit the title, description and visibility of a protocol in this dialog box.

The following table lists and describes the fields. An asterisk indicates a required field. Click Update when you are done editing the Protocol. To disregard the changes, click Reset.

Update Sample	Description
Protocol Type*
Protocol Name*	Enter or select from the drop-down list the protocol name.
Protocol Abbreviation	Enter a shortened phrase used in place of the protocol name.
Protocol Version	Enter or select from the drop-down list the protocol version number.
Upload OR Enter File URL	Click the Browse button to navigate to the protocol to be associated with the protocol, or enter the URL where the protocol is located.
File Title	The title of the Protocol file.
Description	Enter any additional description information that the form does not include.
Access to the Protocol	For more information, see Sharing and Changing Access to a Publication.

Sharing and Changing Access to a Protocol

Deleting a Protocol

To delete a protocol, perform a search, find the protocol that you want to delete, and click the Edit link in the first column of the the Protocol Search Results page. The Update Protocol page opens. From the Update Protocol page, click the Delete button in the lower-left corner of the window. Confirm the deletion.

Searching Existing Protocols

You can access this page after logging into caNanoLab or you can access publicly-available sample protocols from the Login page.

To launch a search for a specific protocol

1. There are three ways to access the basic protocol search: From the public home page Browse caNanoLab panel, or if you are logged in, click the Workflow menu option and Search Protocols icon, or just click the Protocols menu option.
   The Manage Protocols page displays.

2. Click Search Existing Protocols in the Sample Links panel.

   When defining search criteria, there are no required fields. You can add only those parameters that you consider essential to the search. If you do not define any search criteria, all the protocols will be found.

3. The following table lists and describes the fields. Enter text or select criteria as appropriate.

   Name	Description
   Protocol Type
   Protocol Name	Enter a partial or complete name of the protocol. Select Contains (for partial text) or Equals (for an exact search) from the dropdown list.
   Protocol Abbreviation	Enter a partial or complete name of an abbreviation assigned to the protocol.
   Protocol File Title	Enter the name of the protocol file title.

4. Click Search to launch the search.
   To clear the values and start again, click Reset to clear the search criteria.

Protocol Search Results

Once you submit a search for a protocol (Searching Existing Protocols), search results display in the caNanoLab screen. Results show pertinent protocol information defined in Submitting a Protocol.

The following table lists and describes each column.

Sample Search Results Columns	Description
Action	Click View in the first column to display the protocol on the Updating a Protocol. Edit is only available for people that have an account and are logged into the system. Click the + Add to Favorites link to add a bookmark for the protocol on your My Favorites tab. Added to Favorites appears in the column when the protocol is successfully added. If the protocol is already added as a Favorite, clicking + Add to Favorites displays the <protocol name> has already been added to your favorites message.
Protocol Type
Protocol Name	Enter or select from the drop-down list the protocol name.
Protocol Version	Enter or select from the drop-down list the protocol version number.
Protocol Abbreviation	Enter a shortened phrase used in place of the protocol name.
Protocol File	The Title and Description of the protocol are listed. Click View to download the protocol file. The column is empty when there is no protocol file associated with the Protocol.
Created Date	Indicates the date on which the protocol was added.

Adding a Protocol to My Favorites

My Favorites displays samples, protocols, and publications that you bookmark for quick access.

To add a protocol to My Favorites:

1. Perform a protocol search.
2. Find the protocol that you want to bookmark and click the + Add to Favorites link in the first column of the Protocol Search Results row.
   The Added to Favorites message appears in the results row.
3. Click the My Favorites option in the menu bar, and the bookmarked protocol is listed under My Protocols.

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