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. When you click the Protocols option on the caNanoLab menu bar, the Manage Protocol 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.
My Workspace
Once you submit a protocol, the protocol is added to My Workspace for quick access.
Searching Existing Protocols displays the page to perform a search of an existing protocol.
Search Tips
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 Performing a caNanoLab Keyword Search.
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.
Visibility option
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.
To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.
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*
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 URLClick 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 Reset.
When you finish defining the protocol, click Submit.
My Workspace
Once you submit 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. For more information, see Using My Workspace.
Editing a Protocol
You can edit a protocol using the following techniques:
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 (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* | 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 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 and Changing Access to a Protocol. |
Sharing and Changing Access to a Protocol
Deleting a Protocol
Note
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 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.
Searching Existing Protocols
You can access this page after logging into caNanoLab or you can access publicly-available sample protocols from the Login page.
Keyword Search
To launch a search for a specific protocol
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.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 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.
Click Search to launch the search.
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.
Note
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 ( ) button, not the Browser button.
The following table lists and describes each column.
| Sample Search Results Columns | Description |
|---|---|
| Action | Click View in the first column to display the protocol in a PDF file. Note: 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. Note 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 | 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 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
The caNanoLab My Favorites menu option displays samples, protocols, and publications that you bookmark for quick access.
To add a protocol to My Favorites:
- Perform a protocol search.
- Find the protocol that you want to bookmark and click + Add to Favorites in the first column of the Protocol Search Results row.
The Added to Favorites message appears in the results row. - Click the My Favorites option in the caNanoLab menu bar, and the bookmarked protocol is listed under My Protocols.
