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NOTE: the purpose of building a query is to obtain an exportable list of your container names, which will then have to be pasted into the container shipment in step (3)

Steps:

1. Access “queries” from your left-hand menu.

2. Click to ‘create’ new query.

   1. Select the collection protocol in which the specimens are stored that will be shipped to CTRC.

   2. Select Specimen section > type in ‘container name’ > select the ‘container name' under ‘container details’. (Note that there are multiple subsections where you can find Container Name, so ensure you select the one under 'Container Details’.)

      1. Click operator ‘ALL’.

      2. Select to ‘parameterize’.

   3. Click ‘Add’.

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3. Add any other filters that will help you to limit the number of boxes that you might want to display, such as ‘Specimen Type’.

4. Click ‘View Records’

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5. Click ‘Actions’ > ‘Columns’

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   1. De-select any unwanted fields. At a minimum, include ‘Specimen Labels’ and ‘Container Details’ > ‘Container Name’.

   2. In the ‘Aggregates’ step, click ‘Count’ under Aggregate Functions, Choose to count ‘Specimen Labels’ by clicking on the ‘0' to the right (it will become a '1’).

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   3. Click ‘Done'

6. This will display all containers that meet any criteria that you described.

7. Save Query by clicking ‘Actions’ > ‘Save’ > title your query accordingly.

8. View Records will display all of your Containers with the count of the number of specimens in each box.

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9. Select the boxes to be shipped using the Container Name filter and then choose ‘Export’ from the Actions button to produce a .csv file of the container names.

10. Proceed to Step 3 below to create your shipment!

1. Transfer to permanent freezer

   1. Navigate to the Box and choose ‘Transfer’ from the ‘More’ button.

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   2. In the pop-up menu, choose the ‘Site’ where the permanent freezer is located.

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   3. Then choose the Parent Container (This will be the rack or tower where the box will be placed.) Then use the magnifying glass to find available slots in the rack.

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   4. The pop-up shows that there are 4 available slots in Tower A. Choose ‘Select’ to manually choose a slot.

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   5. Available locations are shown as grey. Choose one and click ‘Done’.

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   6. This fills in the container details where the box will be placed. Enter a ‘Reason’ and Click ‘Transfer’.

For large shipments of multiple boxes, it is simpler to accept them directly into the freezer site where they will be stored. The requires that you communicate with the sender and provide the Site name to the shipper before the samples are shipped.

Follow the steps above to receive a shipment. But for Location, you can now directly choose the freezer location to store the boxes.

1. Navigate to ‘Shipments’ using the hamburger menu on the OpenSpecimen homepage.

2. Choose ‘Containers’ from the ‘Create’ button.

   

3. Complete the required fields and any optional fields if using a shipping company. If prompted, enter a Name for your shipment. This will be autogenerated in v10.3 (Feb 2024). See descriptions above for the values to enter in these fields.

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4. **If a Biorepository gives you a specific name to use for Receiving Site, use that instead of ‘Cellular Translational Research Core’. Whatever Site Name they provide must be added as a Site to your CP prior to shipping samples or specimens.

5. Choose ‘Next’ to navigate to the Containers tab where the boxes to be shipped will be entered.

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6. Paste a list of Container names or scan the container names, if barcoded, into the box. Click ‘Add’ when finished.

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7. Choose ‘Ship’ or ‘Save Draft’ to add additional boxes at a later time.

8. The shipment record is created. :

   1. Name, will auto populate

   2. Sending Site = (Site name for the applicable freezer)

      1. If you’re unsure of the freezer’s name, navigate to your container menu to verify

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      2. You will find the Site name associated with the freezers where your samples are stored. This is the ‘Sending Site’.

   3. Receiving Institute = ‘University of Utah Health’

   4. Receiving Site = 'Cellular Translational Research Core'

   5. Notify Users = your CTRC contact

      1. NOTE: while this field is not marked as ‘required’, if you do not input the appropriate notifying user, the CTRC will be unaware of your shipment!

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9. Click ‘Next’

   1. Paste/Input container names copied/exported from step 2 and click ‘Add’.

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   2. After clicking ‘Add’ the confirmation of shipments will appear for review. Confirm accuracy!

   3. Click ‘Ship’ to finalize shipment

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10. The shipment record is created! Proceed with sending the samples to the new location. The individuals specified in ‘Notify Users’ will receive an email with this information and they can then access and receive your containers when they arrive at the new location.

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1. Add the Protocols to the Allowed CPs in the freezer where the boxes will be placed and the CTRC Virtual Freezer.

   1. Navigate to the freezer

   2. Edit

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   3. Add the new CP to ‘Collection Protocols’ allowed in the freezer.

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