Method and apparatus for improved simulation of chemical and biochemical reactions

• US 8,296,070 B2
• Filed: 02/20/2004
• Issued: 10/23/2012
• Est. Priority Date: 02/20/2004
• Status: Expired due to Fees

• Current Assignee: The MathWorks, Inc.
• Original Assignee: The MathWorks, Inc.
• Inventors: Paxson, Ricardo E., Hicklin, Joseph F.
• Primary Examiner(s): SIMS, JASON M
• Application Number:
  US10/783,624
• Publication Number:
  US 20050187747A1
• Time in Patent Office: 3,168 Days
• Field of Search: None
• US Class Current: 702/19
• 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 5/20 Probabilistic models
• CPC Class Codes: G16B 5/30 Dynamic-time models
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

An integrated system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical reaction. The system also includes a simulation engine accepting as input said constructed model of the chemical or biochemical reaction and generating as output an expected result for a first chemical reaction using a first type of computational model and an expected result for a second chemical reaction using a second type of computational model. An analysis environment communicates with the simulation engine and displays the expected result.

Claims

1. A system for improved simulation of a biological system comprising a plurality of chemical reactions, the system comprising:

a storage; and

a processor for;

constructing a graphical model of a biological system, the graphical model of the biological system comprising at least one chemical reaction, the at least one chemical reaction represented using a wild card character that allows multiple instances of an expression to be identified using a single reaction, and a merge block having an input and an output, the output of the merge block at a time step during an execution of the graphical model being equal to a most recent input provided to the merge block,

accepting as input the constructed graphical model of the biological system, and

executing the graphical model to generate as output dynamic behavior of the biological system by using the merge block and the at least one chemical reaction to produce a set of reactions described by the multiple instances of the expression.

2. The system of claim 1 wherein the graphical model is a block diagram model of the biological system.

3. The system of claim 2 wherein the processor is further configured to provide at least one block identifying a set of related chemical reactions.

4. The system of claim 1 wherein the processor is further configured to provide a graphical user interface for accepting user commands and data.

5. The system of claim 1, wherein the processor is further configured to display the dynamic behavior of the biological system.

18. The system of claim 1, wherein the processor further stores the dynamic behavior of the biological system in the storage.

6. A method for simulation of a biological system, the method comprising:

constructing, using a computing device, a graphical model of the biological system, the graphical model of the biological system comprising at least one chemical reaction, the at least one chemical reaction represented using a wild card character that allows multiple instances of an expression to be identified using a single reaction, and a merge block having an input and an output, the output of the merge block at a time step during an execution of the graphical model being equal to a most recent input provided to the merge block;

executing, using the computing device, the graphical model to generate dynamic behavior of the modeled biological system by using the merge block and the at least one chemical reaction to produce a set of reactions described by the multiple instances of the expression.

7. The method of claim 6 wherein constructing further comprises:

constructing a block diagram model of the biological system.

8. The method of claim 7 wherein the block diagram model includes at least one block identifying a set of related chemical reactions.

9. The method of claim 6 wherein constructing further comprises:

accepting user commands and data; and

constructing the graphical model of the biological system using the user commands and data.

17. The method of claim 6, further comprising:

annotating the composite graphical model in response to a user requesting to add annotations to the model that are provided by the user.

19. The method of claim 6, further comprising storing the dynamic behavior of the modeled biological system in a storage device.

10. An article of manufacture having embodied thereon computer-readable instructions for improved simulation of a biological system comprising a plurality of chemical reactions, the article of manufacture comprising:

computer-readable instructions for constructing, using received user commands and data, a graphical model of a biological system, the graphical model of the biological system comprising at least one chemical reaction, the at least one chemical reaction represented using a wild card character that allows multiple instances of an expression to be identified using a single reaction, and a merge block having an input and an output, the output of the merge block at a time step during an execution of the graphical model being equal to a most recent input provided to the merge block;

computer-readable instructions for executing the constructed composite graphical model of the biological system to generate dynamic behavior of the modeled biological system by using the merge block and the at least one chemical reaction to produce a set of reactions described by the multiple instances of the expression.

11. The article of manufacture of claim 10 further comprising computer-readable instructions for displaying the dynamic behavior that is generated.

12. The article of manufacture of claim 10 wherein the computer-readable instructions for constructing a graphical model of the biological system comprises computer-readable instructions for constructing a block diagram model of the biological system.

13. The article of manufacture of claim 10 wherein the computer-readable instructions for constructing a block diagram model of the biological system includes computer-readable instructions for constructing at least one block identifying a set of related chemical reactions.

20. The article of manufacture of claim 10, further comprising computer-readable instructions for storing the dynamic behavior of the modeled biological system in a storage.

14. A system for simulation of a biological system, the system comprising:

means for constructing a graphical model of the biological system, the graphical model of the biological system comprising at least one chemical reaction, the at least one chemical reaction represented using a wild card character that allows multiple instances of an expression to be identified using a simple reaction, and a merge block having an input and an output, the output of the merge block at a time step during an execution of the graphical model being equal to a most recent input provided to the merge block;

means for executing the graphical model to generate dynamic behavior of the modeled biological system by using the merge block and the at least one chemical reaction to produce a set of reactions described by the multiple instances of the expression.

15. A computer-readable storage medium holding computer-executable instructions for simulation of a biological system, the medium comprising one or more instructions for:

constructing a graphical model of the biological system, the graphical model of the biological system comprising at least one chemical reaction, the at least one chemical reaction represented using a wild card character that allows multiple instances of an expression to be identified using a single reaction, and a merge block having an input and an output, the output of the merge block at a time step during an execution of the graphical model being equal to a most recent input provided to the merge block, the multiple instances of the expression representing at least a first chemical reaction and a second chemical reaction;

calculating putative reaction times for execution of the first chemical reaction and the second chemical reaction in the graphical model;

sorting the putative reaction times;

executing one of the first chemical reaction and the second chemical reaction identified by a first reaction, the first chemical reaction and the second chemical reaction being executed using the merge block and the at least one chemical reaction represented using a wild card character;

recalculating the putative reaction times for the first chemical reaction and the second chemical reaction after the executing of the first chemical reaction or the second chemical reaction; and

sorting the recalculated putative reaction times.

16. The medium of claim 15, further comprising:

instructions for iterating execution of the instructions for executing, the instructions for recalculating and the instructions for sorting the recalculated putative reaction times until a final simulation time has been reached to generate a dynamic behavior of the modeled biological system.