Frequently Asked Questions

Hint

To view the entire answer to a question, collapse the answer by clicking the collapsible-item-arrow button below.

Dashboard

How can I view accessions after I have submitted samples, reads, or experiments in COPO?

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  • Click the accessions-dashboard-button button.

  • The accessions dashboard will be displayed.

  • Alternatively, navigate to the Accessions’ dashboard.


Is there a way to analyse metadata submissions?

Yes, the following are ways to analyse metadata submissions:
  1. Tree of Life dashboard

    • Alternatively, click the tol-dashboard-button button.

  2. Tree of Life inspection web page

    • Alternatively, click the tol-inspect-button button.

  3. Tree of Life inspection by Genome Acquisition Lab web page

    • Alternatively, click the tol-inspect-by-gal-button button.

  4. Statistics web page

Manifest Update

How can I update values for samples that I have submitted in COPO?

Reupload the amended manifest.

Note

  • The manifest must be reuploaded in the same profile that the samples were submitted in.

  • The desired value(s) will be updated once the field value is not a compliance field [1].

  • See the Updating Samples section for information about which field values can be updated.

Permits

Can I view or download permits that I have uploaded in COPO?

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Yes, permits can be retrieved and downloaded by selecting the desired sample record(s) on the Samples web page

Then, clicking the download-permits-button1 button on the web page.


Why am I unable to upload permit one after the other?

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Warning

  • If you have more than one permit file to upload, they must be uploaded at the same time i.e. after you have clicked the upload-permits-button button, navigate to the directory where the permits are stored and CTRL + click all of the permits so that all the permits are highlighted and uploaded at the same time.

  • All permit files have to be selected/opened from the directory and uploaded together not one after the other.

Profiles

How can I be added to a profile group?

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* Make a request to the :email:`COPO team ` indicating the type of profile group that you would like to be assigned to. * The desired profile type will be displayed in the **Profile Type** dropdown menu in the **Add Profile** form after the request has been approved.

How can I create a profile on COPO?

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* Click the |add-profile-button| button then, fill in and save the form displayed. .. figure:: /assets/images/profile/profile_add_form.png :alt: Profile types dropdown menu :align: center :target: https://raw.githubusercontent.com/collaborative-open-plant-omics/Documentation/main/assets/images/profile/profile_add_form.png :class: with-shadow with-border :width: 400px :height: 400px **Add Profile form: Choosing a Profile Type**

  • View the following video to see how to create a profile.


How can I upload/submit research objects to a profile owned by another user or how can I create a group or how can I share my profile with others?

See Sharing Profiles section for more information.


How can I add a subproject to a profile on COPO?

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  • In the Add Profile form, choose the desired subproject(s) from the list of associated projects as shown below.

  • See the Secondary Projects section for information about the available subprojects.

Associated profile types dropdown menu

Add Profile form: Selecting Associated Profile Type dropdown menu


How can I add a subproject or secondary project to a primary project in ENA/Biosamples?

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  • Contact the with the request providing the project accession of the child/subproject and the project accession of the parent/primary project.


How can I edit or delete a profile that I have created in COPO?

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  • Click the vertical-ellipsis-icon icon that is associated with the desired profile.

  • The option to edit or delete a profile record will be displayed once clicked.

  • The web page will refresh after the task has been completed successfully.


How many profiles can I have in COPO?

You can have as many profiles as needed to represent your research objects.

  • For instance, you can create a profile to represent work done as part of a grant, subproject within a project or a PhD project.


How can I view more profiles that I have created in COPO?

Scroll downwards on the web page.

  • More profiles that you have created will be loaded.


How can I view more information about a profile that I have created in COPO?

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Note

  • The profile-view-more-button button will only be associated with a profile if the profile has at least one of the following information.

  • Click the profile-view-more-button button associated with the profile.

  • After the button is clicked, a popup dialog will show at least one of the following information if it is available:

    • Release Status (if applicable)

    • Release Date (if applicable)

    • Associated Profile Type(s)

    • Sequencing Centre

Profile view more information popup dialog

Profile: View more information popup dialog


How can I navigate to the top of the web page after having loaded several work profiles?

Scroll upwards on the web page.

  • Alternatively, click the navigate-to-top-button button which automatically navigates to the top of the web page.


How can I create components for a profile?

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  1. Navigate to the work profile web page

  2. Click the add-profile-button button

  3. Fill in then, save the form that is displayed

  4. Click the profile-actions-button button associated with the created profile record to view a dropdown list of tasks that can be performed for that profile

  5. Complete the action/task

  6. Click the profile-components-button button associated with the profile record to view the component of the action that was performed

Samples

Can I delete samples that have submitted?

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No, samples cannot be deleted after the manifest have been submitted.


Can I retrieve samples or the manifest that have been submitted?

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Yes, see the How to Download Submitted Sample Manifest section for more information.


How can I view images that have been uploaded?

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See the View Submitted Images section for more information.


How can I download permits that have been uploaded?

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See the Download Submitted Permits section for more information.


What are the formats that I download samples in?

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The following are the formats that samples can be downloaded in:

Sample Managers

How can I be assigned as a sample manager?

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  • Make a request to the indicating the type of profile group that you would like to be assigned as a sample manager.

  • The permission will be granted after the request has been approved.


How can I know if I have been assigned as a sample manager?

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  • The accept-reject-samples-navigation-button button will be displayed on the web page.

  • The accept/reject samples web page will be displayed once the button is clicked.

  • Alternatively, if you can navigate to the Accept/Reject Samples’ web page with an Unauthorisation error web page being displayed then, you are a sample manager.


How can I accept or reject samples that users have submitted?

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Note

See Accessing the Accept or Reject Samples web page section for guidelines on accessing the Accept or Reject Samples web page.

See Accepting or Rejecting Samples section for more information.


Can I download permits that users have uploaded in COPO?

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Yes, on the Accept or Reject Samples web page, permits can be downloaded by selecting the desired sample record(s) then, clicking the download-permits-button2 button on the web page.

See Downloading permits section for more information.


Can I view images that users have uploaded in COPO?

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Yes, on the Accept or Reject Samples web page, images can be viewed by selecting the desired sample record(s) then, clicking the view-images-button2 button on the web page.

See Viewing images section for more information.


If I belong to more than one sample manager manifest group, how can I view or accept samples that belong to them?

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Note

  • The manifest dropdown menu will only be displayed on the Accept or Reject samples web page if you as a sample manager, belongs to more than one sample manager manifest group.

  • If the dtol sample manager group dropdown menu option is selected, both Aquatic Symbiosis Genomics (ASG) profiles and Darwin Tree of Life (DToL) profiles will be displayed in the All profiles tab and/or Profiles for My Sequencing Centre the Accept or Reject samples web page will be displayed (if any exists).

  • Choose desired sample manager group from the manifest group dropdown menu.

  • Click the accept-reject-samples-navigation-button button to accept or reject samples.

    Add email address dialogue

    Accept or Reject samples: Email address prompt shown when a user logs into COPO for the first time

See Viewing images section for more information.


Footnotes