Method, computer program product, and apparatus for selective memory restoration of a simulation

• US 8,554,486 B2
• Filed: 02/20/2004
• Issued: 10/08/2013
• Est. Priority Date: 02/20/2004
• Status: Active Grant

• Current Assignee: The MathWorks, Inc.
• Original Assignee: The MathWorks, Inc.
• Inventors: Lurie, Roy, Hicklin, Joseph F., Paxson, Ricardo E.
• Primary Examiner(s): Whaley, Pablo S
• Application Number:
  US10/783,522
• Publication Number:
  US 20050187745A1
• Time in Patent Office: 3,518 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• 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: G16B 5/30 Dynamic-time models
• CPC Class Codes: G16C 20/10 Analysis or design of chemical reactions, syntheses or processes

Abstract

The present invention is directed to a method, apparatus, and computer program product for performing selective memory restoration of a simulation based on an indexing scheme. The present invention executes a block diagram model of a biological process to generate simulations results using a simulation engine. An indexing scheme is used for registering memory locations used by a simulation context for a subsystem in the block diagram model. Experimental data is gathered from an in situ experimental device. A simulation environment is used to compare expected simulation results with experimental data. The block diagram model is then updated based on the results of the comparison to create a modified block diagram model, which is then used to selectively restore the simulation to a steady-state.

Claims

1. A computer-program product for selective memory restoration of a simulation comprising:

a non-transitory computer-readable medium encoded with computer-executable instructions that, as a result of being executed by a computer, control the computer to perform a method for selective memory restoration of a simulation based on an indexing scheme, the method comprising;

(a) generating an expected simulation result of a biological process by executing a block diagram model of the biological process with a simulation engine, wherein the simulation engine provides one or more states or parameters associated with the block diagram model and the block diagram model is associated with a first memory layout;

(b) registering memory locations in the computer based on an indexing scheme that identifies a specific memory location used by a simulation context, and assigning a unique identifier to the memory location, wherein the memory location constitutes the simulation context for a subsystem in the block diagram model, wherein the simulation context comprises one or more values associated with the one or more states or parameters established during the simulation

(c) gathering experimental data directly from an in situ experimental device conducting an ongoing in situ experiment of the biological process;

(d) comparing the expected simulation result to the experimental data using an analysis environment that is in communication with the simulation engine;

(e) updating the block diagram model based on the comparison to generate a modified block diagram model comprising one or more states and parameters, the modified block diagram model associated with a second memory layout; and

(f) selectively restoring the simulation to a steady-state by re-initializing the simulation using the modified block diagram model comprising the one or more states or parameters and associated with the second memory layout.

2. The computer-program product of claim 1, wherein the analysis environment outputs results of an analysis performed by the analysis environment.

3. The computer-program product of claim 1, wherein the instructions, when executed, further cause the computer to:

display at least one of the expected simulation result generated by the simulation engine or the experimental data gathered from the experimental device.

4. The computer-program product of claim 1, wherein the instructions, when executed, further cause the computer to:

determine a difference between the expected simulation result and the experimental data gathered from the experimental device; and

generate an event signal when the difference between the expected simulation result and the experimental data gathered from the experimental device exceeds a predetermined threshold.

5. The computer-program product of claim 1, wherein the computer-readable medium is further encoded with computer-executable instructions for constructing the model of the biological process with a modeling environment.

6. The computer-program product of claim 1, wherein the modeling environment includes a graphical user interface for accepting at least one of user commands or data to construct the model of the biological process.

7. The computer-program product of claim 6, wherein the modeling environment is in communication with the analysis environment.

8. The computer-program product of claim 7, wherein the analysis environment transmits to the modeling environment the experimental data gathered from the experimental device.

9. The computer-program product of claim 8, wherein the modeling environment uses the transmitted data to refine the model of the biological process.

10. The computer-program product of claim 1, wherein the analysis environment gathers data from a microarray.

11. The computer-program product of claim 1, wherein the computer-readable medium is further encoded with computer-executable instructions for gathering data from a gene chip.

12. A method for selective memory restoration of a simulation based on an indexing scheme, the method comprising:

(a) generating, using a computer, an expected simulation result of a biological process by executing a block diagram model of the biological process with a simulation engine, wherein the simulation engine provides one or more states or parameters and the block diagram model is associated with a first memory layout;

(b) registering memory locations in the computer based on an indexing scheme that identifies a specific memory location used by a simulation context, and assigning a unique identifier to the memory location, wherein the memory location constitutes the simulation context for a subsystem in the block diagram model, wherein the simulation context comprises one or more values associated with the one or more states or parameters established during the simulation;

(c) gathering, using the computer, experimental data directly from an in situ experimental device conducting an ongoing in situ experiment of the biological process;

(d) comparing, using the computer, the expected simulation result to the experimental data using an analysis environment that is in communication with the simulation engine;

(e) updating the block diagram model based on the comparison to generate a modified block diagram model comprising one or more states and parameters, the modified block diagram model associated with a second memory layout; and

(f) selectively restoring the simulation to a steady-state by re-initializing the simulation using the modified block diagram model comprising the one or more states or parameters and associated with the second memory layout.

13. The method of claim 12 further comprising displaying, using the computer, at least one of the expected simulation result or the experimental data gathered from the experimental device.

14. The method of claim 13 wherein displaying comprises graphically displaying, using the computer, the at least one of the expected simulation result or the experimental data gathered from the experimental device.

15. The method of claim 13 further comprising:

determining, using the computer, a difference between the expected simulation result and the experimental data gathered from the experimental device; and

generating, using the computer, an event signal when the difference between the expected simulation result and the experimental data exceeds a predetermined threshold.

16. The method of claim 12 further comprising accepting, using the computer, at least one of user commands or data to construct the model of the biological process.

17. The method of claim 16 wherein the at least one of user commands or data is accepted via a graphical user interface.

18. The method of claim 16 further comprising transmitting, using the computer, the experimental data to a modeling environment configured to model the biological process.

19. The method of claim 18 further comprising generating, using the computer, a refined model of the biological process using the transmitted data.

20. The method of claim 12 wherein the conducting further comprises conducting the in situ experiment using a microarray.

21. The method of claim 12 wherein the conducting further comprises conducting the in situ experiment using a gene chip.

22. An apparatus for selective memory restoration of a simulation based on an indexing scheme, the apparatus comprising a processor and a non-transitory computer-readable storage medium encoded with computer-executable instructions which, when executed by said processor, cause the processor to execute a method for:

(a) generating an expected simulation result of a biological process by executing a block diagram model of the biological process with a simulation engine, wherein the simulation engine provides one or more states or parameters associated with the block diagram model and the block diagram model is associated with a first memory layout;

(b) registering memory locations in the computer based on an indexing scheme that identifies a specific memory location used by a simulation context, and assigning a unique identifier to the memory location, wherein the memory location constitutes the simulation context for a subsystem in the block diagram model, wherein the simulation context comprises one or more values associated with the one or more states or parameters established during the simulation;

(c) gathering experimental data directly from an in situ experimental device conducting an ongoing in situ experiment of the biological process;

(d) comparing the expected simulation result to the experimental data using an analysis environment that is in communication with the simulation engine;

(e) updating the block diagram model based on the comparison to generate a modified block diagram model comprising one or more states and parameters, the modified block diagram model associated with a second memory layout; and

(f) selectively restoring the simulation to a steady-state by re-initializing the simulation using the modified block diagram model comprising the one or more states or parameters and associated with the second memory layout.

23. The apparatus of claim 22 further comprising computer-executable instructions for displaying at least one of the expected simulation result or the experimental data gathered from the experimental device.

24. The apparatus of claim 22 further computer-executable instructions for determining a difference between the expected simulation result and the experimental data gathered from the experimental device;

and

means for triggering an alarm when the difference between the expected simulation result and the experimental data exceeds a predetermined threshold.

25. The apparatus of claim 22 further comprising computer-executable instructions for accepting at least one of user commands or data to construct the model of the biological process.

26. The apparatus of claim 22, wherein the at least one of user commands or data is accepted via a graphical user interface.

27. The apparatus of claim 22 further comprising computer-executable instructions for generating a refined model of the biological process using the experimental data gathered from the experimental device.

28. A method for selective memory restoration of a simulation based on an indexing scheme, the method comprising:

(a) generating, using a computer, an expected simulation result of a chemical reaction by executing a block diagram model of the chemical reaction with a simulation engine, wherein the simulation engine provides one or more states or parameters and the block diagram model is associated with a first memory layout;

(b) registering memory locations in the computer based on an indexing scheme that identifies a specific memory location used by a simulation context, and assigning a unique identifier to the memory location, wherein the memory location constitutes the simulation context for a subsystem in the block diagram model, wherein the simulation context comprises one or more values associated with the one or more parameters established during the simulation;

(c) gathering experimental data directly from an in situ experimental device conducting an in situ experiment;

(d) comparing the expected simulation result to the experimental data using an analysis environment that is in communication with the simulation engine;

(e) updating the block diagram model based on the comparison to generate a modified block diagram model comprising one or more states and parameters, the modified block diagram model associated with a second memory layout; and

(f) selectively restoring the simulation to a steady-state by re-initializing the simulation using the modified block diagram model comprising the one or more states or parameters and associated with the second memory layout.

29. The method of claim 28, further comprising:

displaying, by the analysis environment, at least one expected simulation result generated by the simulation engine or the experimental data gathered from the experimental device.

30. The method of claim 29, wherein displaying comprises graphically displaying at least one of the expected simulation result generated by the simulation engine or the experimental data gathered from the experimental device.

31. The method of claim 28, further comprising:

determining a difference between the expected simulation result and the experimental data gathered from the experimental device; and

triggering an alarm when the difference between the expected simulation result and the experimental data exceeds a predetermined threshold.

32. The method of claim 28 further comprising accepting, via a modeling environment, at least one of user commands or data to construct the model of the chemical reaction.

33. The method of claim 32, wherein the modeling environment accepts the at least one of user commands or data via a graphical user interface.

34. The method of claim 32, further comprising transmitting the experimental data to the modeling environment.

35. The method of claim 34, further comprising generating, by the modeling environment, a refined model of the chemical reaction using the transmitted data.

36. A computer-program product for selective memory restoration of a simulation comprising:

a non-transitory computer-readable medium encoded with computer-executable instructions that, as a result of being executed by a computer, control the computer to perform a method for selective memory restoration of a simulation based on an indexing scheme, the method comprising;

(a) generating, using a computer, an expected simulation result of a chemical reaction by executing a block diagram model of the chemical reaction with a simulation engine, wherein the simulation engine provides one or more states or parameters and the block diagram model is associated with a first memory layout;

(b) registering memory locations in the computer based on an indexing scheme that identifies a specific memory location used by a simulation context, and assigning a unique identifier to the memory location, wherein the memory location constitutes the simulation context for a subsystem in the block diagram model, wherein the simulation context comprises one or more values associated with the one or more parameters established during the simulation;

(c) gathering experimental data directly from an in situ experimental device conducting an in situ experiment;

(d) comparing the expected simulation result to the experimental data using an analysis environment that is in communication with the simulation engine;

(e) updating the block diagram model based on the comparison to generate a modified block diagram model comprising one or more states and parameters, the modified block diagram model associated with a second memory layout; and

(f) selectively restoring the simulation to a steady-state by re-initializing the simulation using the modified block diagram model comprising the one or more states or parameters and associated with the second memory layout.

37. The computer-program product of claim 36, wherein the computer-readable medium is further encoded with computer-executable instructions for displaying at least one of the expected simulation result or the experimental data gathered from the experimental device.

38. The computer-program product of claim 36, wherein the computer-readable medium is further encoded with computer-executable instructions for:

determining a difference between the expected simulation result and the experimental data gathered from the experimental device; and

triggering an alarm when the difference between the expected simulation result and the experimental data exceeds a predetermined threshold.

39. The computer-program product of claim 36, wherein the computer-readable medium is further encoded with computer-executable instructions for accepting at least one of user commands or data to construct the model of the chemical reaction.

40. The computer-program product of claim 36, wherein the computer-readable medium is further encoded with computer-executable instructions for accepting at least one of user commands or data via a graphical user interface to construct the model of the chemical reaction.

41. The computer-program product of claim 36, wherein the computer-readable medium is further encoded with computer-executable instructions for generating a refined model of the chemical reaction using the experimental data gathered from the experimental device.