Managing Protocols in caNanoLab

Performing a caNanoLab Keyword Search | caNanoLab User's Guide| Managing Samples in caNanoLab

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

Protocols Overview

When you click the Protocols menu, the Manage Protocol page appears with the following options.

• Create a New Protocol

• Search Existing Protocols

You can also perform the following functions with a protocol.

• Share a protocol and make it public

• Edit a protocol

• Bookmark a protocol in My Favorites

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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.

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Creating a Protocol

To create a new protocol

1. Click the Protocols caNanoLab menu option. On the Manage Protocols page, click Create a New Protocol. This opens the Create Protocol page.

   To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.

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

   Name	Description
   Protocol Type*	Enter or select from the drop-down list the protocol type (required).
   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 a Protocol with a User or Group or Making the Protocol Public.

   To clear the entries and start again, click Reset

3. When you finish defining the protocol, click Save.

   My Workspace

   Once you save a protocol, it is listed on the My Workspace page where you can manage all of your submitted protocols, and view any protocols that a user has shared with you.

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Sharing a Protocol with a User or Group

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Making a Protocol Public

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Searching Existing Protocols

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

To launch a search for a specific protocol

1. Click the Protocols menu.
   The Manage Protocols page displays.

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

   Note

   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.

   The Protocol Search page displays.

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

   Name	Description
   Protocol Type	Enter or select from the drop-down list the protocol type (required).
   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.

    

   To clear the values and start again, click Reset to clear the search criteria.

4. Click Search to launch the search.

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Protocol Search Results

Once you submit a search for a protocol, search results show pertinent protocol information defined in Creating a Protocol.

The following table lists and describes each column of the search results.

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Editing a Protocol

You can edit a protocol from the protocol search results.

• Updating a Protocol
• Deleting a Protocol

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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 entered when the protocol was created in caNanoLab (Creating 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.

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Deleting a Protocol

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

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Bookmarking a Protocol to My Favorites

The caNanoLab My Favorites menu option displays samples, protocols, and publications that you bookmark for quick access.

To add a protocol to My Favorites

1. Perform a protocol search.
2. From the search results, find the protocol that you want to bookmark. Click + Add to Favorites 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 menu, and the bookmarked protocol is listed under My Protocols.

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Performing a caNanoLab Keyword Search | caNanoLab User's Guide| Managing Samples in caNanoLab