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This chapter describes how to manage protocols in caNanoLab with the Protocols function.
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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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To create a new protocol
Click the Protocols menu.
Manage Protocols displays.
Click Create a New Protocol.
From Create Protocol, fill in the following information as needed.
Name Description
Protocol Type*Anchor Protocol Page Protocol Page 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
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Enter File URLClick 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 Click Submit.
Info title My 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.
Once you submit the protocol, the Edit Protocol page opens. With the appropriate security permissions you can
Edit the protocol information.
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The Edit Protocol page enables you to edit protocol information and edit access to the protocol.
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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. |
From the Edit Protocol page, fill in the following information as needed.
Include Page Other options Other options Edit Protocol Description
Protocol Type*Anchor Protocol Update Page Protocol Update Page 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
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Enter File URLClick Browse 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 a Protocol with a User or Group or Making the Protocol Public.
Include Page Adding access include Adding access include Click Submit when you are done editing the Protocol.
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To launch a search for a specific protocol
Click the Protocols menu.
Manage Protocols displays.Click Search Existing Protocols.
Include Page Search Criteria Blank include Search Criteria Blank include From Protocol Search, fill in the following search criteria as needed.
Name Description 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.
Click Search.
Protocol Search Results opens.
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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.
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| Action | Click View in the first column to display the protocol in a PDF file.
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 |
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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 Date | Indicates the date on which the protocol was added. |
Additional Protocol Tasks
The following table lists how to edit a protocol with the following techniques.
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To delete a protocol
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| The caNanoLab My Favorites menu option displays samples, protocols, and publications that you bookmark for quick access. To add a protocol to My Favorites
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