TITLE: INSPECT sample tracking system
AUTHORS: Shashank Sathe, Clarence Mah, Noorsher Ahmed, Michelle Franc Ragsac, John Williams

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A specimen to data tracking tool for SEARCH SARS-CoV-2 tests. The  application is used by SEARCH technicians to track samples as they  proceed through each step within the RT-qPCR testing workflow. The app is  currently hosted here: </span><a href="http://inspect-covid.com/qpcr_records" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">http://inspect-covid.com/qpcr_records/</span></a></div></div>

[STEPS]
?. [Before Starting]
Before starting ensure that the INSPECT system is publicly accessible and that you are registered on the INSPECT user list.
?. [Sample Extraction and Plating]
Freshly received samples can be registered into INSPECT by scanning the 2D sample tube barcode into the system. This is performed in conjunction to the sample extraction and plating step.
?. [Sample Extraction and Plating]
Enter the Lot # of the RNA Lysis buffer being used. The Lot # can also be scanned into the app.Enter the name of the assisting technician (if any).
?. [Sample Extraction and Plating]
Start sample plating by using the platemap guides provided by INSPECT.
?. [Sample Extraction and Plating]
Load control samples first. INSPECT assumes that the control samples are being loaded in well A1 and H1.
?. [Sample Extraction and Plating]
Scan sample barcode into the provided text area and load sample into the assigned well.
?. [Sample Extraction and Plating]
Once all samples have been plated, end the sample plating step and proceed to the plate barcode scanning step. INSPECT requires the user to enter the Sample Extraction Plate (SEP) barcode. Additionally, if present, users can enter the Sample Storage Plate (SSP) and Sample Storage Bag (SSB) barcodes as well.
?. [Sample Extraction and Plating]
?. [Sample Extraction and Plating]
?. [RNA Extraction]
INSPECT assumes that the RNA extraction from SEPs is an automated process, performed using Kingfisher or similar robotic machines. Thus, sample barcode scanning is not required. Users must enter the origin SEP and the destination RNA Extraction Plate (REP) barcodes. Only upon entering both will the samples be successfully linked between sample extraction and RNA extraction steps.
?. [RNA Extraction]
Enter Lot #s of the reagents being used in the RNA Extraction step
?. [RNA Extraction]
Enter the barcode of the SEP and the barcode of the new REP and proceed with extracting RNA from the samples.
?. [RNA Extraction]
?. [RNA Extraction]
INSPECT assumes that the RT-qPCR test is performed on a 384-well plate format. For this purpose,  4x 96-well plates are compressed into a single 384-well plate. Thus, each 384-well RNA Working Plate (RWP) must be linked with 4x 96-well REPs, and the well ID for each sample must be transformed into a 384-well plate format. This process is automated by INSPECT and can be acheived by simply scanning the new RWP and the associated REPs
?. [RNA Extraction]
?. [Viral Gene Expression Test]
Similar to previous steps, each qPCR Reaction Plate (QRP) must be linked to an existing RWP. Since the RWP and the QRP have the same platemap format, the well ID for each sample is carried over from the previous assignment.
?. [Viral Gene Expression Test]
Enter a valid RWP barcode and the new QRP barcode
?. [Viral Gene Expression Test]
?. [Viral Gene Expression Test]
After the qPCR reaction has completed, the technician is required to upload the qPCR results file. This can be done using the results submission page. The filename for the results file must be the same as the QRP barcode.
?. [Viral Gene Expression Test]
Once the results are successfully uploaded, INSPECT will make decision calls on each sample (during file upload). These decisions have to be reviewed by a qialified technician. On the Review Results page, enter the barcode of the QRP for which you would like to review thh results.
?. [Result Reporting]
Once the results for a QRP have been reviewed, the RT-qPCR testing workflow is complete. Users can search for samples and corresponding results through the SEARCH tab.