Apparatus and method for validating a computer model

Abstract

An apparatus and method for validating a computer model is described. In one embodiment, a computer-readable medium comprises instructions to associate a set of configurations of a computer model with a stimulus-response test, each configuration of the set of configurations representing a different model scenario, the stimulus-response test defining a modification to each configuration of the set of configurations. The computer-readable medium also comprises instructions to apply the stimulus-response test to the set of configurations to produce a simulated response for each configuration of the set of configurations and instructions to compare the simulated responses for the set of configurations with an expected response to the stimulus-response test.

What is claimed is:  
     
         1 . A computer-readable medium comprising: 
 instructions to associate a plurality of configurations of a computer model with a stimulus-response test, each configuration of the plurality of configurations representing a different model scenario, the stimulus-response test defining a modification to each configuration of the plurality of configurations;    instructions to apply the stimulus-response test to the plurality of configurations to produce a simulated response for each configuration of the plurality of configurations; and    instructions to compare the simulated responses for the plurality of configurations with an expected response to the stimulus-response test.    
     
     
         2 . The computer-readable medium of  claim 1 , further comprising: 
 instructions to create the stimulus-response test.    
     
     
         3 . The computer-readable medium of  claim 1 , further comprising: 
 instructions to display the simulated responses for the plurality of configurations.    
     
     
         4 . A computer-readable medium comprising: 
 instructions to receive a user-specified selection of a first configuration of a plurality of configurations of a computer model, each configuration of the plurality of configurations representing a different model scenario, the first configuration representing a first model scenario;    instructions to associate the first configuration with a plurality of stimulus-response tests, each stimulus-response test of the plurality of stimulus-response tests defining a different modification to the first configuration, the plurality of stimulus-response tests being associated with a plurality of expected responses to the plurality of stimulus-response tests;    instructions to apply the plurality of stimulus-response tests to the first configuration to produce a plurality of simulated responses for the first configuration; and    instructions to display the plurality of simulated responses for the first configuration.    
     
     
         5 . The computer-readable medium of  claim 4 , further comprising: 
 instructions to create the plurality of stimulus-response tests.    
     
     
         6 . The computer-readable medium of  claim 4 , further comprising: 
 instructions to compare the plurality of simulated responses for the first configuration with the plurality of expected responses to the plurality of stimulus-response tests.    
     
     
         7 . The computer-readable medium of  claim 4 , further comprising: 
 instructions to receive a user-specified selection of a second configuration of the plurality of configurations, the second configuration representing a second model scenario;    instructions to associate the second configuration with the plurality of stimulus-response tests, each stimulus-response test of the plurality of stimulus-response tests further defining a different modification to the second configuration;    instructions to apply the plurality of stimulus-response tests to the second configuration to produce a plurality of simulated responses for the second configuration; and    instructions to display the plurality of simulated responses for the second configuration.    
     
     
         8 . A computer-readable medium comprising: 
 instructions to define a plurality of stimulus-response tests, a first stimulus-response test of the plurality of stimulus-response tests defining a modification to a first biological process of a plurality of biological processes represented by a computer model of a biological system, a second stimulus-response test of the plurality of stimulus-response tests defining a modification to at least one from the first biological process and a second biological process of the plurality of biological processes;    instructions to automatically apply the plurality of stimulus-response tests to the computer model to produce simulated responses to the first and second stimulus-response tests; and    instructions to compare the simulated responses to the first and second stimulus-response tests with expected responses to the first and second stimulus-response tests, respectively.    
     
     
         9 . The computer-readable medium of  claim 8 , wherein the computer model represents the first biological process using a first mathematical relation and the second biological process using a second mathematical relation, and the instructions to define the plurality of stimulus-response tests include: 
 instructions to define the first stimulus-response test as a parametric change in the first mathematical relation; and    instructions to define the second stimulus-response test as a parametric change in at least one from the first mathematical relation and the second mathematical relation.    
     
     
         10 . The computer-readable medium of  claim 8 , further comprising: 
 instructions to display the simulated responses to the first and second stimulus-response tests and the expected responses to the first and second stimulus-response tests.    
     
     
         11 . The computer-readable medium of  claim 8 , further comprising: 
 instructions to provide an indication if the simulated response to the first stimulus-response test is substantially consistent with the expected response to the first stimulus-response test.    
     
     
         12 . The computer-readable medium of  claim 8 , further comprising: 
 instructions to define a virtual therapy to simulate a therapy for the biological system, the virtual therapy defining a modification to at least one biological process of the plurality of biological processes; and    instructions to apply the virtual therapy to the computer model to produce a simulated response to the virtual therapy, the simulated response to the virtual therapy predicting effectiveness of the therapy for the biological system.    
     
     
         13 . A computer-readable medium comprising: 
 instructions to define a computer model that represents a plurality of biological processes of a biological system;    instructions to define a plurality of stimulus-response tests, a first stimulus-response test of the plurality of stimulus-response tests defining a modification to a first biological process of the plurality of biological processes, a second stimulus-response test of the plurality of stimulus-response tests defining a modification to at least one from the first biological process and a second biological process of the plurality of biological processes;    instructions to define expected responses to the first and second stimulus-response tests;    instructions to automatically execute the computer model based on the plurality of stimulus-response tests to produce simulated responses to the first and second stimulus-response tests; and    instructions to compare the simulated responses to the first and second stimulus-response tests with the expected responses to the first and second stimulus-response tests, respectively.    
     
     
         14 . The computer-readable medium of  claim 13 , wherein the instructions to define the computer model include: 
 instructions to define the first biological process using a first mathematical relation and the second biological process using a second mathematical relation.    
     
     
         15 . The computer-readable medium of  claim 14 , wherein the instructions to define the plurality of stimulus-response tests include: 
 instructions to define the first stimulus-response test as a parametric change in the first mathematical relation; and    instructions to define the second stimulus-response test as a parametric change in at least one from the first mathematical relation and the second mathematical relation.    
     
     
         16 . The computer-readable medium of  claim 13 , further comprising: 
 instructions to define a virtual therapy to simulate a therapy for the biological system, the virtual therapy defining a modification to at least one biological process of the plurality of biological processes; and    instructions to execute the computer model based on the virtual therapy to produce a simulated response to the virtual therapy, the simulated response to the virtual therapy predicting effectiveness of the therapy for the biological system.    
     
     
         17 . A computer-implemented method of validating a computer model of a biological system, comprising: 
 defining a plurality of configurations of the computer model, each configuration of the plurality of configurations representing a different combination of genetic and environmental factors for the biological system;    associating the plurality of configurations with a stimulus-response test, the stimulus-response test defining a modification to each configuration of the plurality of configurations;    associating the stimulus-response test with an expected response for a given phenotype of the biological system;    automatically applying the stimulus-response test to the plurality of configurations to produce a simulated response for each configuration of the plurality of configurations; and    comparing the simulated responses for the plurality of configurations with the expected response for the given phenotype to produce a validity indication associated with a configuration of the plurality of configurations with respect to the given phenotype.    
     
     
         18 . The computer-implemented method of  claim 17 , wherein comparing the simulated responses for the plurality of configurations with the expected response for the given phenotype includes: 
 identifying the simulated response for the validated configuration as being substantially consistent with the expected response for the given phenotype.    
     
     
         19 . The computer-implemented method of  claim 17 , wherein automatically applying the stimulus-response test to the plurality of configurations includes: 
 sequentially applying the stimulus-response test to each configuration of the plurality of configurations.    
     
     
         20 . The computer-implemented method of  claim 17 , wherein automatically applying the stimulus-response test to the plurality of configurations includes: 
 simultaneously applying the stimulus-response test to at least two configurations of the plurality of configurations.    
     
     
         21 . The computer-implemented method of  claim 17 , wherein the stimulus-response test simulates a test applied to the biological system of the given phenotype to produce the expected response for the given phenotype.  
     
     
         22 . For a computer model that represents a plurality of biological processes of a biological system, a computer-implemented method of predicting effectiveness of a therapy for the biological system, comprising: 
 validating the computer model by: 
 associating the computer model with a plurality of stimulus-response tests, each stimulus response test of the plurality of stimulus-response tests defining a modification to at least one biological process of the plurality of biological processes;  
 automatically applying the plurality of stimulus-response tests to the computer model to produce a simulated response to each stimulus-response test of the plurality of stimulus-response tests; and  
 for each stimulus-response test of the plurality of stimulus-response tests, comparing the simulated response to the stimulus-response test with an expected response to the stimulus-response test;  
   defining a virtual therapy to simulate the therapy, the virtual therapy defining a modification to at least one biological process of the plurality of biological processes; and    applying the virtual therapy to the validated computer model to produce a simulated response to the virtual therapy, the simulated response to the virtual therapy predicting effectiveness of the therapy for the biological system.    
     
     
         23 . The computer-implemented method of  claim 22 , wherein comparing the simulated response to the stimulus-response test with the expected response to the stimulus-response test includes: 
 identifying the simulated response to the stimulus-response test as being substantially consistent with the expected response to the stimulus-response test.    
     
     
         24 . A computer-implemented method of validating a computer model, comprising: 
 receiving a user-specified selection of a first configuration of a plurality of configurations of the computer model, each configuration of the plurality of configurations representing a different model scenario, the first configuration representing a first model scenario;    associating the first configuration with a plurality of stimulus-response tests, each stimulus-response test of the plurality of stimulus-response tests defining a modification to the first configuration, the plurality of stimulus-response tests being associated with a plurality of expected responses to the plurality of stimulus-response tests;    applying the plurality of stimulus-response tests to the first configuration to produce a plurality of simulated responses for the first configuration; and    comparing the plurality of simulated responses for the first configuration with the plurality of expected responses to the plurality of stimulus-response tests to produce a validity indication associated with the first configuration.    
     
     
         25 . The computer-implemented method of  claim 24 , further comprising: 
 receiving a user-specified selection of a second configuration of the plurality of configurations, the second configuration representing a second model scenario;    associating the second configuration with the plurality of stimulus-response tests, each stimulus-response test of the plurality of stimulus-response tests further defining a modification to the second configuration;    applying the plurality of stimulus-response tests to the second configuration to produce a plurality of simulated responses for the second configuration; and    comparing the plurality of simulated responses for the second configuration with the plurality of expected responses to the plurality of stimulus-response tests to produce a validity indication associated with the second configuration.