Apparatus and method for validating a computer model

• US 20020193979A1
• Filed: 05/16/2002
• Published: 12/19/2002
• Est. Priority Date: 05/17/2001
• Status: Abandoned Application

• Current Assignee: Entelos Holding Corp. (SilkRoad Inc.)
• Original Assignee: Entelos Holding Corp. (SilkRoad Inc.)
• Inventors: Paterson, Thomas S.
• Application Number:
  US10/151,581
• Publication Number:
  US 20020193979A1
• Time in Patent Office: Days
• US Class Current: 703/22
• CPC Class Codes: G06F 30/20 Design optimisation, verification or simulation optimisation, verification or simulation of circuit designs G06F30/30
• CPC Class Codes: G06F 9/44505 Configuring for program initiating, e.g. using registry, configuration files
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16H 50/50 for simulation or modelling of medical disorders

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.

Claims

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.

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.

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.

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.

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.

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.

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.

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.