Step 1: Add Researchers

To add Researcher info, go to the Researchers link and click the New Researcher button. Enter information about each Researcher then click Add.

Step 2: Add Neighborhood

Homes are assigned to neighborhoods. To add a new Neighborhood go to the Neighborhoods link and click the New Neighborhood button. You must provide a unique name using a consistent naming scheme for the Neighborhood.

Step 3: Add Location

Each home is a location and is assigned to a neighborhood. To add a new Location, go to the Locations link and click the New Location button. Each new Location must be assigned to an existing Neighborhood. The list of all Locations can be downloaded as: PDF CSV Excel or copied to the clipboard Copy

Step 4: Create a Collection Event

A collection Event is scheduled for visiting a single Location. To create a new Event, go to the Events link and click the New Event button. Each Event must have a unique (and consistent) name, a Location selected and a range of collection dates. Researchers that will be present at the event may also be selected.

Step 5: Add Subject Information

Subjects are any named individual (human or animial) that we want to track consistently throughout the project. To add a new Subject, go to the Subjects link and click the New Subject button. Each new Subject must be assigned to an existing Location. The full detailed list of all Subject information can be downloaded as: PDF CSV Excel or copied to the clipboard Copy

Step 6: Create Samples

Once an Event is scheduled, Samples can be generated for the Event.
To do this, either 1. Select the Event from the Event List Events and click on Add Samples button
OR 2. go to the Samples link and click the Add Samples button.
On the next page, select the Event that you want to generate samples for if it is not already selected.
Note: You can only create samples for Events that are scheduled in the future, not for past Events.
Select the number of Samples that you want to create and click Add.
Note: If Subjects have already been added to the Location for the Event, samples will automatically be created for these Subjects in addition to the number of samples selected.
On the next page will be a list of Samples that have been generated with unique IDs and prefilled information.
The Download Form button will download an Excel/Google Sheets form for filling in information about the samples during collection.
The Upload Form button will allow you to upload the completed form to update the database.
Note: New Subjects in form must be added prior to uploading the form (see above).

Step 7: Print Sample Lables

Create a Label format by going to the go to the Subjects link and clicking the New Label Format button
. From here, enter a unique name for the label type and enter in all of the dimensions for the label sheet.
To print Sample labels, click the Print Sample Labels button from either a selected Event page or from the Samples link and select the Event from the dropdown. You will be provided with a list of the existing Samples and Subject information for that event with all of the samples pre-selected. If you do not want to print a lable for a sample, deselect that sample. Select the appropriate printing options. Change the start position to finish off a partially used label sheet (numbers increase along each column starting at 1). Select the label paper from the dropdown or add a new label sheet type by clicking the Add New Label Format button. Clicking the Print button will download a pdf that can be printed or saved.

Step 8: Mark Collected Samples

After a collection Event, the Sample labels should be scanned in, and marked with a status (e.g. Collected, Refused, Absent, etc.). One way to do this is by clicking on the QR scanner button on the top of the page. This will open up a window that will allow you to scan the QR code on the Sample label using your phone camera. Once the QR code is scanned, click the Search button and the Sample detail page will be loaded. Click the Edit button to change the status of the Sample. Alternatively, the Sample ID can be typed into the search bar at the top of the page or on the Samples page. Multiple samples can be marked as collected by going to the Samples link and locating the samples in the table. Sample status can be updated using a dropdown in the table, or multiple rows can be updated by selecting them and then clicking on the Edit button.

Step 9: Upload Sample Results

Once the samples have been collected and processed, their results need to be uploaded to the system.

Creating a Test

Before uploading sample results, a test must be created in the system. Each test should include:

• Test Name – A unique identifier for the test.
• Lab Name – The laboratory where the test is performed.
• Target – The specific target being tested.
• Detection Threshold - The threshold value for considering a positive result.
• Description of protocol - Notes that describe the protocol.

To create a new test:

1. Navigate to the Tests page.
2. Click on the New Test button.
3. Enter the information then click Add.

Uploading qPCR Sample Results from file

1. Navigate to the Sample Results page.
2. Click on the Upload Results button.
3. On the upload page:
   • Choose Excel file to upload by clicking on the "Browse" button.
   • Select the researcher(s) who performed the qPCR.
   • Ensure that the file is in the correct format as described on the page.
   • Click Submit to submit the results.
4. The system will process the file and display a summary of uploaded results.
5. If errors are found (e.g., missing sample IDs, missing tests, incorrect formatting), the system will report them. **No data will be uploaded until all issues are resolved.**
6. The data from a given file and run date can only be uploaded once to prevent duplicate entries.

How Results Are Processed

When the results file is uploaded, the system will:

• Match samples and tests with existing records in the database.
• Check if results for the same run date and file name already exist to prevent duplicate uploads.
• Automatically assign Positive, Negative, or Undetermined results based on the Cq value and the test threshold.
• Mark the upload as successful and display a summary of the added sample results.

Viewing Uploaded Results

After the upload is complete, the results will be displayed at the Sample Results pages where you can:

• View details of each uploaded sample result.
• Filter and search for specific results.
• Edit values inline if needed or by clicking on the sample result id link.

Troubleshooting Upload Issues

If the upload fails, check for the following:

• Ensure that **all sample IDs exist** in the system.
• Verify that the **test names match** an existing test in the database.
• Make sure that the **Cq values are correctly formatted**.
• Check for duplicate entries—sample results for the same **run date and file name** cannot be uploaded twice.