Systems and methods for generating automated software workflows for biological testing

Abstract

The workflow application integrates with a research software application associated with a laboratory instrument to provide a user with step-by-step instructions on how to follow the workflow steps of a laboratory experiment. The instructions are dynamically tailored, according to the nature of the workflow, the samples being experimented upon and/or the operating states of the instrument and/or the research software application. The workflow application significantly reduces the learning curve to operate sophisticated laboratory instruments. In a genetic testing instrument the workflow application can prescribe the need for control samples and can optimize the layout of samples within the instrument's sample receiving plate or fixture.

1 . A workflow application adapted to run on a computer system and having an interface for coupling to a research software application associated with a research instrument; 
 the workflow application having a predefined set of instructional story materials and being configured to present said story materials to a user according to a predefined research workflow and thereby assist the user in carrying out steps associated with said workflow;    the workflow application having manager system that dynamically tailors specific story materials based on at least one of the workflow being performed, the state of the research software application and the state of the research instrument.    
     
     
         2 . The workflow application of  claim 1  wherein said manager system is further configured to provide control instructions to said research instrument.  
     
     
         3 . The workflow application of  claim 1  wherein said manager system is further configured to provide control instructions to said research instrument by communicating information to said research software application.  
     
     
         4 . The workflow application of  claim 1  wherein said manager system is further configured to receive and interpret experiment results from said research instrument.  
     
     
         5 . The workflow application of  claim 1  wherein said manager system is further configured to receive and interpret experiment results from said research instrument by receiving information from said research software application.  
     
     
         6 . The workflow application of  claim 1  wherein said manager system is further configured to set parameters within said research software application.  
     
     
         7 . The workflow application of  claim 1  wherein said manager system includes a pipette manager that optimizes the physical layout of a laboratory experiment by providing tailored instructions to the user regarding said physical layout.  
     
     
         8 . The workflow application of  claim 1  wherein said laboratory instrument is a genetic testing instrument employing a multi-well plate to receive samples and wherein said manager system includes a pipette manager that optimizes the placement of samples within said plate by providing tailored instructions to the user on where to place the samples.  
     
     
         9 . The workflow application of  claim 1  wherein said manager system includes a setup manager that automatically determines the requirements for control samples to be included in a laboratory experiment and provides tailored instructions to the user regarding inclusion of such control samples within said experiment.  
     
     
         10 . A method of conducting laboratory experimentation, comprising: 
 ascertaining the nature of an experimental workflow by interacting with the user of a research instrument having an associated research software application;    automatically generating a set of instructional story materials to assist the user in carrying out steps associated with said workflow; and    dynamically tailoring specific story materials based on at least one of the workflow being performed, the state of the research software application and the state of the research instrument.    
     
     
         11 . The method of  claim 10  further comprising using a workflow application to generate said set of instructional story materials and additionally using said workflow application to control said research instrument.  
     
     
         12 . The method of  claim 10  further comprising using a workflow application to generate said set of instructional story materials and additionally using said workflow application to control said research instrument by communicating information to said research software application.  
     
     
         13 . The method of  claim 10  further comprising using a workflow application to generate said set of instructional story materials further using said workflow application to receive experimental results from said research instrument and display information indicative of said experimental results to the user of said workflow application.  
     
     
         14 . The method of  claim 10  wherein said laboratory instrument is a genetic testing instrument employing a multi-well plate to receive samples and wherein said method further comprises optimizing the placement of samples within said plate by providing tailored instructions to the user on where to place the samples.  
     
     
         15 . The method of  claim 14  wherein said optimizing step is performed based on a predefined set of rules that are enforced by a computer system.  
     
     
         16 . A computer program product encoded on a machine readable medium, comprising: 
 a setup manager adapted to ascertain the nature of an experimental workflow;    a pipette manager adapted to provide user instructions on how to physically deploy wet chemistry components within a test fixture;    a run manager adapted to control a laboratory instrument in performing an experimental workflow; and    a results manager adapted to process results obtained from a laboratory instrument used to perform an experimental workflow upon wet chemistry components within a test fixture.    
     
     
         17 . The computer program product of  claim 16  further comprising interface adapted to couple to a research software application associated with a research instrument.  
     
     
         18 . The computer program product of  claim 17  wherein said run manager controls said laboratory instrument by communicating information to said research software application via said interface.  
     
     
         19 . The computer program product of  claim 17  wherein said results manager receives said results obtained from a laboratory instrument via said interface.  
     
     
         20 . The computer program product of  claim 16  wherein said pipette manager is adapted to optimize the physical layout of a laboratory experiment by providing tailored instructions to the user regarding said physical layout.  
     
     
         21 . The computer program product of  claim 16  for use with a genetic testing instrument employing a multi-well plate to receive samples and wherein said pipette manager optimizes the placement of samples within said plate by providing tailored instructions to the user on where to place the samples.  
     
     
         22 . The computer program product of  claim 16  wherein said setup manager automatically determines the requirements for control samples to be included in a laboratory experiment and provides tailored instructions to the user regarding inclusion of such control samples within said experiment.