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Making an item public

Once you log into caNanoLab, you can create and save samples, publications, and protocols to caNanoLab and modify access to an item. If you are a curator, you can also make the saved item publicly-accessible. If you are not a curator, you must submit the item to a curator for review and approval for public release.

This chapter describes how to manage protocols in caNanoLab with the Protocols function. Topics in this chapter include:

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, 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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Creating a Protocol

To create a new protocol

  1. Click the Protocols menu.

    Manage Protocols displays.

  2. Click Create a New Protocol.

  3. From Create Protocol, fill in the following information as needed.

    NameDescription

    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

    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.

  4. Click Submit.

    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.

  5. Once you submit the protocol, the Edit Protocol page opens. With the appropriate security permissions you can

    1. Edit the protocol information.

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Editing a Protocol

The Edit Protocol page enables you to edit protocol information and edit access to the protocol.

Updating data after it is Public

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.

  1. From the Edit Protocol page, fill in the following information as needed.

    To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.

    Edit ProtocolDescription

    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 (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 TitleThe 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.

  2. Click Submit when you are done editing the Protocol.

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Sharing a Protocol with a User or Group

The following sections describe how to share an item with a user or collaboration group. To make it available to the public, you must be a curator OR submit it for review first.

Specifying User or Group Access

To share with a user or collaboration group

  1. From the Update page, the Access to the panel lists who initially has access to the item based on your user role.
    1. As a Public user, you have access, along with any Researcher or Curator.
    2. As a Researcher, you have access, along with any Curator.
    3. As a Curator, you have access, along with any other Curator.
  2. Next to Access to the..., click Add. The access information panel opens.
    The access information panel, listing groups and users.
  3. Select Collaboration Group or User. Click Search. A list appears next to that button. From the list, select a group or user.
    The Access By panel, for adding group or user.
  4. From the Access to the... list, specify READ (only) or READ WRITE DELETE access.

    Public Access to

    If you are a curator and select Public, Access to is pre-populated with READ (only) and cannot be changed.

     

  5. Click Save. The system updates the access information panel and updates the item in My Workspace.

Editing and Removing Access

To edit the access: From the Update page, in the Access to the ... panel, locate the access entry you want to edit. Next to that entry, click Edit. Make changes to the access and click Save. The system updates the access information panel. 

The access information panel, listing groups.

To delete a listing: From the Update page, click Edit next to the access entry. From the access information panel, click Delete and confirm the deletion. The system updates the access information panel and updates the item in My Workspace.

The Access By panel, for deleting a group or user.

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Making a Protocol Public

Submitting a Database Item for Review

If you are not a curator and want to make your sample, publication, or protocol, publicly-accessible, you must submit it for review once it is saved to the caNanoLab database.

  1. At the bottom of the Create or Update page, click Submit for Review.

    Submit for Review button

    The status of the database item on your My Workspace page changes to Pending.

    Once a curator reviews the item and is satisfied, the curator will change the access to Public. 

  2. The status of the database item on your My Workspace page will then change to Public.

    Updating a Public item

    If you update an item after it is Public, you must submit the item for review again for the changes to be reflected in the Public version.

Making a Database Item Publicly-Accessible (Curator Only)

To make an item public, you must be a curator and access the Curation menu. For more information, see  Review Data Pending Release.

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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

  1. Click the Protocols menu.
    Manage Protocols displays.

  2. Click Search Existing Protocols.

    Leaving all search criteria blank

    There are no required fields when you specify search criteria. If you leave all the fields blank, all items are returned.

  3. From Protocol Search, fill in the following search criteria as needed.

    NameDescription

    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.

  4. Click Search.
    Protocol Search Results opens.

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Protocol Search Results

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.

Protocol Search Results ColumnsDescription
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).


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 DateIndicates the date on which the protocol was added.

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Additional Protocol Tasks

The following table lists how to edit a protocol with the following techniques.

TaskHow to

Deleting a Protocol

Delete removes the protocol from the caNanoLab database, executed behind the scenes at a scheduled time.

To delete a protocol

  1. Perform a search.
  2. On the search results, click Edit in the Actions column.
  3. From the Edit Protocol page, click Delete in the lower-left corner of the window.
  4. 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

  1. Perform a search.
  2. On the search results, click + Add to Favorites in the Actions column.
    Bookmarking a protocol from search results

    The Added to Favorites message appears in the results row.
  3. Click the My Favorites menu, and the bookmarked protocol is listed under My Protocols.

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