2 - Managing Protocols in caNanoLab 2.1 DRAFT

 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 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.

Submitting a Protocol

To submit a new protocol:

1. 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.

2. 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.

   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	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 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 2 - Managing Protocols in caNanoLab 2.1 DRAFT.

   To clear the entries and start again, click the Reset button.

3. When you finish defining the protocol, click the Submit button.

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.

Changing Group Access to the Protocol

To change the group access to the protocol:

1. From the Access to the Protocol field, click Add.
   The Access Information dialog box opens.
2. 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.
3. For Access to This Protocol, specify whether the selected group or user can read, update, and delete the protocol or read (only).
4. 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

To delete a protocol, perform a search, 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 right of the window. Confirm the deletion.

Searching Existing Protocols

To launch a search for a specific protocol:

1. Click the Protocols caNanoLab menu option. On the Manage Protocols Home page, click the Search Existing Protocols link. This opens the Search Protocols form.

   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.

2. 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 that has been assigned to the protocol.
   Protocol File Title	Enter the name of the protocol file title

3. Click Search to launch the search.
   To clear the values and start again, click Reset to clear the search criteria.

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.

The following table lists and describes each column.

Adding a Protocol to My Favorites