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This chapter describes how to manage protocols in caNanoLab with the Protocols function. This section includes the following topics:
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Protocols Overview
The Protocols function enables you to create or search for a 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. The Protocol links on the Manage Protocol Home page provide the following options:
- Submitting a New Protocol: This takes you to a form for entering information for a new protocol you want to submit.
- 2 - Managing Protocols in caNanoLab 2.1 DRAFT: This takes you to a form for launching a search for an existing protocol.
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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If you do not select an option for visibility, by default, Private is selected, meaning only the owner can view and/or modify it. |
Submitting a Protocol
To submit a new protocol:
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.
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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 fields.
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Protocol Type*
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Protocol Name*
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Enter or select from the drop-down list the protocol name.
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Protocol Abbreviation
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Shortened phrase used in place of the protocol name
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Protocol Version
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Enter or select from the drop-down list the protocol version number.
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Click the Browse button to navigate to the protocol to be associated with the protocol, or enter the URL where the protocol is located.
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File Title
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Enter the title of the protocol file.
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Description
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Enter any additional description information that the form does not include.
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To clear the entries and start again, click the Reset button.
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Editing a Protocol
You can edit a sample using the following techniques:
- 2 - Managing Protocols in caNanoLab 2.1 DRAFT
- 2 - Managing Protocols in caNanoLab 2.1 DRAFT
- 2 - Managing Protocols in caNanoLab 2.1 DRAFT
Updating a Protocol
The Protocol Update page opens when you click the Edit link corresponding to a protocol listed in 2 - Managing Protocols in caNanoLab 2.1 DRAFT. The page displays all of the information for a protocol that was entered when the protocol was created in caNanoLab (2 - Managing Protocols in caNanoLab 2.1 DRAFT). 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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Protocol Type*
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Protocol Name*
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Enter or select from the drop-down list the protocol name.
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Protocol Abbreviation
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Shortened phrase used in place of the protocol name.
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Protocol Version
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Enter or select from the drop-down list the protocol version number.
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Click the Browse button to navigate to the protocol to be associated with the protocol, or enter the URL where the protocol is located.
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Protocol Abbreviation
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Shortened phrase used in place of the protocol name.
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Enter any additional description information that the form does not include.
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Changing Group Access to the Protocol
To change the group access to the protocol:
- From the Access to the Protocol field, click Add.
The Access Information dialog box opens. - For Access By, you will specify the group or user to which you are specifying access:
- Collaboration Group: If you click this option, Collaboration Group appears below the selection. You can type in a group name and click Search or select a group from the drop down to the right.
- User: If you click this option, User Login Name appears below the selection. You can type in a login name and click Search or select a login from the drop down to the right.
- Public: If you click this option, Public appears in the Collaboration Group box and cannot be edited.
- For Access to This Protocol, specify whether the selected group or user can read, update, and delete the protocol or read (only).
- Click Cancel to remove the entries or click Save to add the access information.
The Update Protocol page appears with the group or user added to the Access to the Protocol panel.
Deleting a Protocol
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This action deletes the protocol from the caNanoLab database, executed behind the scenes at a scheduled time. |
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 2 - Managing Protocols in caNanoLab 2.1 DRAFT 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
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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:
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Click the Protocols caNanoLab menu option. On the Manage Protocols Home page, click the Search Existing Protocols link. This opens the Search Protocols form.
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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 following table lists and describes the fields. Enter text or select criteria as appropriate.
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Protocol Type
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Protocol Name
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Enter a partial or complete name of the protocol. Select Contains (for partial text) or Equals (for an exact search) from the dropdown list.
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Protocol Abbreviation
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Enter a partial or complete name of an abbreviation that has been assigned to the protocol.
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Protocol File Title
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Enter the name of the protocol file title
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Click Search to launch the search.
To clear the values and start again, click Reset to clear the search criteria.
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Protocol Search Results
Once you submit a search for a protocol (2 - Managing Protocols in caNanoLab 2.1 DRAFT), search results display in the caNanoLab screen. Results show pertinent protocol information defined which is defined in the 2 - Managing Protocols in caNanoLab 2.1 DRAFT section. Columns are sortable by page by clicking on the column heading.
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The number of items located in the search display appears in the the upper-left of the search results table. The bottom right of the search results table enables you to navigate to pages. To return to the Search page, click the Back ( |
The following table lists and describes each column.
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Click Edit in the first column to display the protocol on the 2 - Managing Protocols in caNanoLab 2.1 DRAFT.
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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 Favorites tab. Success appears in the column when the protocol is successfully added.
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If the protocol is already added as a Favorite, clicking Add to Favorites displays an error message. |
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Protocol Type
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Protocol Name
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Enter or select from the drop-down list the protocol name.
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Protocol Version
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Enter or select from the drop-down list the protocol version number.
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Protocol Abbreviation
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Shortened phrase used in place of the protocol name.
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Protocol File
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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.
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Adding a Protocol to My Favorites
Favorites displays samples, protocols, and publications that you choose to bookmarked for quick access. To add a protocol to My Favorites, perform a protocol search, find the protocol that you want to bookmark, and click the Add to Favorites link in the first column of the 2 - Managing Protocols in caNanoLab 2.1 DRAFT row. The Added to Favorites message appears in the results row.
Click the Favorites option in the menu bar, and the bookmarked protocol will be listed under My Protocols.
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