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This chapter describes how to manage protocols in caNanoLab with the Protocols function.  

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titleContents of This Chapter

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Topics in this chapter include:

Table of Contents
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ManageProtocols
ManageProtocols
Protocols Overview

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, refer to the tables corresponding to each characterization type in Managing Sample Characterizations.

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

You can also perform the following functions with a protocol.

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SubmitProtocol
SubmitProtocol
Creating a Protocol

To create a new protocol

  1. Click the Protocols menu.

    Manage Protocols displays.

  2. Click Create a New Protocol.

  3. From Create Protocol, fill in the following information as needed.

    NameDescription

    Anchor
    Protocol Page
    Protocol Page
    Protocol Type*

    Include Page
    Protocol type
    Protocol type

    Include Page
    Other options
    Other options

    Protocol Name*

    Enter or select from the drop-down list the protocol name (required).

    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 Browse 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 about sharing, see Sharing a Protocol with a User or Group or Making the Protocol Public.

    Include Page
    Adding access include
    Adding access include

  4. Click Submit.

    Info
    titleMy Workspace

    After saving, the protocol is listed on My Workspace where you can manage all of your saved protocols, and view any protocols that a user has shared with you.

  5. Once you submit the protocol, the Edit Protocol page opens. With the appropriate security permissions you can

    1. Edit the protocol information.

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EditProtocol
EditProtocol
Editing a Protocol

The Edit Protocol page enables you to edit protocol information and edit access to the protocol.

Info
titleUpdating data after it is Public

Once data is made Public, you can edit the data, but it will be retracted from Public, and you will need to resubmit it to the curator again for review.

  1. From the Edit Protocol page, fill in the following information as needed.

    Include Page
    Other options
    Other options

    Edit ProtocolDescription

    Anchor
    Protocol Update Page
    Protocol Update Page
    Protocol Type*

    Include Page
    Protocol type
    Protocol type

    Protocol Name*

    Enter or select from the drop-down list the protocol name (required).

    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 Browse to navigate to the protocol to be associated with the protocol, or enter the URL where the protocol is located.

    File TitleThe 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.

    Include Page
    Adding access include
    Adding access include

  2. Click Submit when you are done editing the Protocol.

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SharingProtocol
SharingProtocol
Sharing a Protocol with a User or Group

Include Page
Sharing an Item with a User or Group
Sharing an Item with a User or Group

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Anchor
MakingProtocolPublic
MakingProtocolPublic
Making a Protocol Public

Include Page
Making an Item Public
Making an Item Public

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SearchProtocols
SearchProtocols
Searching Existing Protocols

Include Page
Public Search Results include
Public Search Results include

To launch a search for a specific protocol

  1. Click the Protocols menu.
    Manage Protocols displays.

  2. Click Search Existing Protocols.

    Include Page
    Search Criteria Blank include
    Search Criteria Blank include

  3. From Protocol Search, fill in the following search criteria as needed.

    NameDescription

    Protocol Type

    Include Page
    Protocol type
    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.
    Protocol Search Results opens.

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ProtocolResults
ProtocolResults
Protocol Search Results

Once you submit a search for a protocol, search results show pertinent protocol information defined when creating a protocol.

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

Protocol Search Results ColumnsDescription
Action

Click View in the first column to display the protocol in a PDF file.

Info
titleNote:

Edit is only available for people that have an account and are logged into the system and are associated with the protocol.

Click + Add to Favorites 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.

Protocol Type

Include Page
Protocol type
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.

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 DateIndicates the date on which the protocol was added.

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Additional Protocol Tasks

The following table lists how to edit a protocol with the following techniques.

TaskHow to

Anchor
DeletingProtocol
DeletingProtocol
Deleting a Protocol

Info

Delete removes the protocol from the caNanoLab database, executed behind the scenes at a scheduled time.

To delete a protocol

  1. Perform a search.
  2. On the search results, click Edit in the Actions column.
  3. From the Edit Protocol page, click Delete in the lower-left corner of the window.
  4. Confirm the deletion.

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BookmarkProtocol
BookmarkProtocol
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 search.
  2. On the search results, click + Add to Favorites in the Actions column.
    Bookmarking a protocol from search resultsImage Added

    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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