Detailed assay protocol specification

Abstract

Techniques are disclosed relating to assay configuration. Assay devices are often used to determine characteristics of test samples, e.g., using polymerase chain reaction (PCR) or Deoxyribonucleic Acid (DNA) melt techniques. Various disclosed techniques allow detailed specification of assay parameters. This may allow user modification of assays and/or assay development by third parties. In embodiments in which assay parameters are specified using a separate device, these techniques may reduce validation requirements resulting from modified assays. In some embodiments, assay configuration information that may be added/removed/modified may include: a sequence of operations, parameters for the sequence of operations, data processing parameters, call logic rules/dependencies, and/or reporting rules.

What is claimed is: 
     
         1 . An assaying device comprising:
 a cassette receiver configured to receive a first cassette for a first type of assay and a second cassette for a second type of assay, each of which includes a biological sample;   assay instrumentation useable to perform assay steps corresponding to at least the first and second types of assays, wherein the assay instrumentation includes a light source and a detector;   a computer processor circuit;   a computer memory storing routines executable by the computer processor circuit, wherein the routines include:
 assay device control routines executable to control the assay instrumentation to perform the assay steps; 
 assay configuration loading routines executable to download a plurality of assay configuration routines executable to call the assay device control routines to perform assay steps for the first and second types of assays; and 
 interface routines executable to determine whether to perform the first type of assay or the second type of assay when a particular cassette is received via the cassette receiver. 
   
     
     
         2 . The assaying device of  claim 1 , wherein the routines further include:
 a first assay configuration routine executable to call the assay device control routines to perform assay steps corresponding to the first type of assay in order to generate a first assay report; and   a second assay configuration routine executable to call the assay device control routines to perform assay steps corresponding to the second type of assay in order to generate a second assay report.   
     
     
         3 . The assaying device of  claim 2 , wherein the first assay configuration routine includes:
 test operation configuration information executable by the assaying device to call assay device control routines to perform assay steps corresponding to the first type of assay based on a set of test operation parameters to generate first data for a first sample; and   result processing configuration information executable by the assaying device to determine an outcome for the first type of assay based on the first data and a set of outcome identification rules specified by the result processing configuration information.   
     
     
         4 . The assaying device of  claim 1 , wherein the first type of assay is for detecting a first pathogen and the second type of assay is for detecting a second, different pathogen. 
     
     
         5 . The assaying device of  claim 1 :
 wherein the cassette receiver includes an optical scanner; and   wherein the interface routines are further executable to cause the optical scanner to detect a code on the particular cassette to perform the first type of assay based on the detected code being indicative of the first type of assay.   
     
     
         6 . The assaying device of  claim 1 , wherein the cassette receiver is configured to move liquid within the first cassette and within the second cassette. 
     
     
         7 . The assaying device of  claim 1 , wherein one or more of the plurality of assay configuration routines were generated by computer systems remote from the assaying device. 
     
     
         8 . A method comprising:
 storing, at an assaying device including assay instrumentation, assay device control routines executable to control the assay instrumentation to perform assay steps corresponding to a plurality of different types of assays;   downloading, at the assaying device, one or more assay configuration routines, wherein each assay configuration routine corresponds to a different type of assay, and wherein each assay configuration routine is executable to call the assay device control routines to perform assay steps for the type of assay to which the assay configuration routine corresponds;   receiving, at the assaying device, a sample;   determining, with the assaying device, to perform a particular type of assay of the plurality of different types of assays on the sample;   based on the determining, controlling, with the assaying device, the assay instrumentation to perform the particular type of assay according to the corresponding assay configuration routine to generate data about the sample; and   generating, using the data about the sample and the corresponding assay configuration routine, a report.   
     
     
         9 . The method of  claim 8 , wherein downloading one or more assay configuration routines includes downloading one or more assay configuration routines from one or more physical storage media coupled to the assaying device. 
     
     
         10 . The method of  claim 8 , wherein each assay configuration routine includes:
 test operation configuration information executable by the assaying device to call assay device control routines to perform assay steps for the type of assay to which the assay configuration routine corresponds based on a set of test operation parameters to generate data for a sample; and   result processing configuration information executable by the assaying device to determine an outcome for the type of assay to which the assay configuration routine corresponds based on the data and a set of outcome identification rules specified by the result processing configuration information.   
     
     
         11 . The method of  claim 8 , wherein one or more assay configuration routines correspond to different types of assays for detecting respective different pathogens. 
     
     
         12 . The method of  claim 8 , wherein one or more assay configuration routines correspond to polymerase chain reaction assays. 
     
     
         13 . The method of  claim 8 , wherein determining to perform the particular type of assay on the sample includes the assaying device detecting a code on a cassette containing the sample and wherein the determining is based on the detected code being indicative of the particular type of assay. 
     
     
         14 . The method of  claim 8 ,
 wherein receiving the sample includes receiving a cassette containing the sample; and   wherein controlling the assay instrumentation to perform the particular type of assay includes moving a portion of the sample within the cassette during the assay.   
     
     
         15 . The method of  claim 8 , wherein the assay configuration routines were generated by one or more computer system that are remote from the assaying device by the one or more computer systems:
 causing a user configuration tool for the assaying device to be displayed;   receiving, from a user via the user configuration tool, test operation input that indicates an assay to be performed;   generating, based on the test operation input, test operation configuration information that specifies a sequence of test operations for the assay to be performed by the assaying device and specifies the set of test operation parameters for the sequence of test operations;   receiving, from the user, outcome identification input that specifies at least one rule for identification of an outcome from among a plurality of potential outcomes; and   generating, based on the outcome identification input, result processing configuration information that specifies a set of outcome identification rules for identification of an outcome from among a plurality of potential outcomes of the assay to be performed.   
     
     
         16 . The method of  claim 8 , wherein the assay device control routines are not modified as a result of the downloading of the assay configuration routines. 
     
     
         17 . A non-transitory, computer-readable medium storing routines executable by a computer processor circuit of an assaying device, the routines comprising:
 assay device control routines executable to control assay instrumentation of the assaying device to perform assay steps corresponding to a plurality of different types of assays;   assay configuration loading routines executable to download a plurality of respective assay configuration routines executable to call the assay device control routines to perform assay steps for their respective different types of assays; and   interface routines executable to determine which respective different type of assay to perform when the assaying device receives a particular cassette.   
     
     
         18 . The computer-readable medium of  claim 17 , the routines further comprising:
 a first assay configuration routine executable to call the assay device control routines to perform assay steps corresponding to a first type of assay in order to generate a first assay report; and   a second assay configuration routine executable to call the assay device control routines to perform assay steps corresponding to a second type of assay in order to generate a second assay report.   
     
     
         19 . The computer-readable medium of  claim 18 , wherein the first assay configuration routine includes:
 test operation configuration information executable by the assaying device to call assay device control routines to perform assay steps corresponding to the first type of assay based on a set of test operation parameters to generate first data for a first sample; and   result processing configuration information executable by the assaying device to determine an outcome for the first type of assay based on the first data and a set of outcome identification rules specified by the result processing configuration information.   
     
     
         20 . The computer-readable medium of  claim 17 , where the assay configuration loading routines are executable to download the plurality of respective assay configuration routines from one or more computer systems remote from the assaying device.