RDCRN Biospecimen Tracker User Guide
- Karen Lapthorn
The Biospecimen Tracker User Guide provides detailed instructions on the primary features and functionality of the Tracker application. (Prefer a video overview? You can find one here. )
Table of Contents:
Help and Resources
If you need additional help or training using the RDCRN Biospecimen Tracker, need to report an error, or have a question, use the RDCRN Service Desk to contact us.
How to access the Biospecimen Tracker
If your protocol has a REDCap sample collection form that connects to the Biospecimen Tracker, a link to the Tracker will appear on your consortium’s landing page along with any other resources associated with your protocol.
Sample Collection Forms in REDCap
To utilize the features of the RDCRN Biospecimen Tracker, information about a sample must be added to a sample collection form in REDCap. Your sample collection form will be customized to meet your needs. At minimum, this REDCap form must include:
An identifier for each sample which will be visible in the RDCRN Biospecimen Tracker.
A status for each sample indicating if it should be made available in the RDCRN Biospecimen Tracker.
Samples must be set to a status of Ready to Ship or Shipped but Can Ship Again in order to appear in the Tracker.
A read-only Sample Shipping Log field where both automated and manually added updates from the Tracker can be viewed. The Log will display:
Notes manually added by a user when a shipment is created containing the sample.
An automated notification that a shipment containing the sample has been created along with the shipment tracking number.
An automated notification that a shipment containing the sample has been successfully delivered by the shipping carrier.
Notes manually added by a user at the destination site once a shipment is received.
Received or Not Received status updates if samples are individually confirmed by a user at the destination site.
Optional Data
Additional data may be collected in REDCap and passed to the RDCRN Biospecimen Tracker. This data is not required but may be useful to view in the Tracker:
Sample Collection Date
Sample Collection Time
Sample Type
Sample Description
The Local ID (or Subject ID) associated a Sample may also be passed from REDCap into the Tracker. This is optional and can be configured protocol by protocol. Added June 2021
The RDCRN Biospecimen Tracker also supports the creation of flexible Sample Tag values in REDCap that can contain additional data values. For example, if you wish to indicate the test tube cap color, a Cap Color field can be created in REDCap and passed to the Tracker via the Sample Tags field. A REDCap form may have one or many Sample Tags.
Aliquots
The RDCRN Biospecimen Tracker supports samples that are aliquots. The Tracker will show the association between a parent sample and aliquot if that association is indicated in REDCap.
Each aliquot must have its own unique identifier. However, to ease the burden of data entry, the REDCap form can include an option to tell the Tracker to use the parent Sample Collection Date and Sample Collection Time for each associated aliquot:
REDCap RDCRN Biospecimen Tracker Configuration
The following values are set per Protocol in a special REDCap Configuration project:
A list of sites including origin site(s) and destination site(s)
All possible shipping routes that a user can select in the Tracker when creating a new shipment
A shipping route consists of an origin site and a destination site
An optional list of email addresses associated with a site that will receive email alerts from the RDCRN Biospecimen Tracker
A setting to indicate if the Local ID (or Subject ID) is shown in the Tracker. Added June 2021
Email Alerts (optional)
The Shipment Tracker sends email alerts when:
A new shipment is created.
A shipment is updated to a status of Delivered by the shipping carrier.
A Delivered shipment is updated with Confirmation of Receipt of each sample and/or Notes are added and the shipment is Saved.
Alert emails are sent from the email address ‘specimen-tracker-no-reply@rdcrn.org’ and sent to all recipients associated with the shipment Origin and Destination sites (configured in REDCap).
Added June 2021 If you wish to email all users who have received a Tracker email alert, you may Reply (or Replay All) to the Email alert. You will then see all recipients in the To line. This may be helpful if you wish to communicate with the personnel who either sent or received a specific shipment.
Recipients of email alerts are associated with a Site in REDCap:
Create Shipment
Locate the samples to be included in a shipment
All samples flagged as Ready to Ship in your Protocol’s REDCap sample collection form(s) will show in a list on the Create Shipment page. There are several features to help you locate a specific sample:
Use the search box to search for a sample.
Click a column heading (such as SampleID) to sort the list of samples.
Click the Filter by Projects dropdown to see all samples, or samples from a specific project.
Click the links at the bottom of the page to see additional pages of samples.
Expand a sample row to view more details about that sample, if available. Click the three dots on a sample row to view additional information that may have been collected in REDCap, such as:
Sample type (if indicated in REDCap)
Sample collection Date (if indicated in REDCap)
Sample collection Time (if indicated in REDCap)
Sample Description (if indicated in REDCap)
Sample Log (if the sample has been previously shipped but can be shipped again)
If a sample is not found, you can:
Use the Refresh Samples button on the Create Shipment page to ensure you are viewing the most up-to-dates list of samples from REDCap.
Confirm your user account has access to the Protocol in REDCap.
Confirm in REDCap the sample is marked with a status of Ready to Ship or Shipped but Can Ship Again.
Add one or more samples to a shipment
Position your cursor over the sample row you wish to include in the shipment and click the + (plus) symbol. You will see the sample listed in the New Shipment box. You can then add additional samples that will be included in the shipment.
To remove a sample from a shipment, click the – (minus) symbol. The sample will be removed from the New Shipment box and will reappear in the list of samples.
Enter shipment details
Once you have included all relevant samples in the New Shipment box, click Enter Shipment Information. You will be prompted to enter the following information:
Origin Site:
Use the dropdown to select the site from where the shipment is originating.
Destination Site:
Use the dropdown to select the site where the shipment is going next.
Final Destination:
If the samples are going to an intermediate location and will be shipped again within the RDCRN Biospecimen Tracker, set to No. This will ensure that the samples can be selected again on the Create Shipment page.
If the samples are going to their final destination or will not be shipped again within the RDCRN Biospecimen Tracker, set to Yes.
Shipping Carrier:
Select the correct shipping carrier from the available options.
Added June 2021 Users who are hand-delivering their ‘shipments' can select ‘No Carrier’. These special shipments will show immediately as ‘Delivered’ and do not require a Tracking Number.
Added June 2021 USPS has been added as a Carrier
Tracking Number:
Enter the tracking number that will be used with the shipment. The Tracking Number must be correct for the Biospecimen Tracker to receive updates from the carrier on the status of the shipment.
Added June 2021 If your shipment is set to ‘No Carrier’ the Tracking Number is optional. You may skip this, or if you have an internal number you wish to include here you can input your own value. It must be at least 5 characters long and contain only letters, numbers or underscores.
Shipment Notes (Optional):
Enter any notes or special instructions related to the shipment. The notes will appear on the Shipping Manifest PDF as well as the Sample Shipping Log field visible in both the Biospecimen Tracker and REDCap.
Once all values have been entered, click Confirm Shipment.
Confirm and submit shipment
A summary of the shipment will appear. Double-check the details and click BACK if you need to make any changes.
Click the Complete Shipment link to finalize the shipment. This will trigger the following actions:
A new shipment record with a unique shipment ID will be added to the Shipment Tracker portion of the site.
A shipping manifest PDF will be generated and automatically downloaded.
An email will be sent to designated users to alert of a new shipment.
A note will be added to the Sample Shipping Log field in REDCap.
A shipping manifest file (PDF) will automatically download to your computer. The manifest can be printed and included in the shipment package.
The manifest includes:
Shipment details, such as carrier, tracking number, and destination site
List of samples included in the shipment
Added June 2021 Shipment Collection Time (if populated) has been added to the Manifest.
Shipment Notes
Shipment Tracker
Locate a shipment to view shipment details
All previously created shipments will appear in a list on the Shipment Tracker page. By default, you will see shipments created within the past 30 days, but this timeframe can be adjusted using the Showing Shipments dropdown.
There are a number of features to help you locate a specific shipment:
Use the search box to search for a shipment.
Click a column heading (such as Shipment Date) to sort the list of shipment.
Use the shipment Status checkboxes to filter the list of shipments.
Click the links at the bottom of the page to see additional pages of shipments.
Each shipment row displays important details about that shipment, including:
Unique Shipment ID generated by the RDCRN Biospecimen Tracker
Number of samples included in the shipment
Date the shipment was created in the RDCRN Biospecimen Tracker
The shipment Tracking Number
A shipment status of:
PRE_TRANSIT: The label is created, but the package has not yet been dropped off or picked up by the carrier.
TRANSIT: The package has been scanned by the carrier and is in transit.
DELIVERED: The package has been successfully delivered.
Shipments with ‘No Carrier’ default to DELIVERED status.
RETURNED: The package is en route to be returned to the sender or has been returned successfully.
FAILURE: The carrier indicated that there has been an issue with the delivery. This can happen for various reasons and depends on the carrier.
UNKNOWN: The package has not been found via the carrier’s tracking system.
Indication if the shipment was manually confirmed at the destination site
Change a shipment status
Added JuLY 2021
Shipment status values are fed into the RDCRN Biospecimen Tracker from the associated carrier. Shipments with ‘No Carrier’ default to DELIVERED status. Status values can be manually changed by using the Status dropdown on the Shipment Tracker page. This feature may be helpful when the status from the carrier is incorrect or delayed.
Once updated, the shipment status can also be reset back to the status supplied by the shipping carrier. To reset a status, using the status dropdown and select the Reset Status option.
View shipment details
Expand a shipment row to view more details about that shipment. Click the three dots on a shipment row to view additional information, such as:
Origin and Destination
Carrier
List of samples included in the shipment
Export shipment details to csv file
Added June 2021
Shipment details may be exported from the Tracker as a csv file. Use the checkboxes located on the far left of each shipment row to individually select each shipment you wish to download. To quickly select ALL shipments shown in the list (including those on subsequent/previous pages) use the checkbox in the very top row.
Once at least one shipment has been selected, use the Download CSV button in the upper right to create the export file. The file contains key information about the shipment and the samples included, included all values found on the Shipment Manifest PDF. If shipment contains more than one sample, you will see a row for each sample. For example, if you export 2 shipments and each shipment contains 3 samples, the export file will contain a header row and 6 additional rows of data.
Shipment data can be downloaded as many times as you wish.
Manually confirm receipt of samples within a shipment (optional)
A user at the Destination site may manually confirm receipt of each sample within a shipment once the shipment has been updated with a status of DELIVERED.
To confirm receipt of each sample, locate the shipment from the list shown on the Shipment Tracker page. Click the three dots on the shipment row to expand.
A list of samples included in the shipment are shown. For each sample, a status of received (check mark) or not received (x) can be indicated.
Indicating the status of a sample will automatically add a notification of this change to the Sample Shipping Log field in REDCap.
Additional Notes can be added by the user as well. Any notes added will be added to the Sample Shipping Log field visible in both the Biospecimen Tracker and REDCap. Enter notes in the Add Notes box and click Add Note.
The shipment Save button must be clicked to save the indicated sample statuses and notes.