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
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.
When you click the Protocols menu, the Manage Protocol page appears with the following options.
You can also perform the following functions with a protocol.
Creating a Protocol
Making an item public
To create a new protocol
Click the Protocols caNanoLab menu option.
On the Manage Protocols page, click Create a New Protocol.
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).To enter an alternative to an option, select other if available and enter a value. The value is added to the list of 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 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 about sharing, see Sharing a Protocol with a User or Group or Making the Protocol Public.
If you do not add access
If you do not add access, this item remains private and only you, the owner, can view and/or modify it.
To clear the entries and start again, click Reset
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.
Once you save the protocol, the Update Protocol page opens. With the appropriate security permissions you can
Update the protocol information.
Updating a Protocol
The Update Protocol page enables you to update protocol information and update access to the protocol.
Updating data after it is Public
Once data is made Public, you can update the data, but it will be retracted from Public, and you will need to resubmit it to the curator again for review.
The following table lists and describes the fields. An asterisk indicates a required field.
| Update Sample | Description |
|---|---|
Protocol Type* | Enter or select from the drop-down list the protocol type (required). To enter an alternative to an option, select other if available and enter a value. The value is added to the list of 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 | 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. If you do not add access If you do not add access, this item remains private and only you, the owner, can view and/or modify it. |
Click Update when you are done editing the Protocol. To disregard the changes, click Reset.
Sharing a Protocol with a User or Group
Making a Protocol Public
Searching Existing Protocols
If you are not logged in or are browsing caNanoLab
If you are not logged into caNanoLab and perform a search or you are browsing caNanoLab from the public home page, only publicly-accessible items will be returned in the search results. This also applies to Performing a caNanoLab Keyword Search.
To launch a search for a specific protocol
Click the Protocols menu.
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 Protocol Search page displays.
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).To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.
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, search results show pertinent protocol information defined in Creating 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 of the search results.
| 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. |
Protocol Type | Enter or select from the drop-down list the protocol type (required). To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options. |
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. |
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.
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
- Perform a protocol search.
- 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. - Click the My Favorites menu, and the bookmarked protocol is listed under My Protocols.
