Method and apparatus for improved simulation of chemical and biochemical reactions
First Claim
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, andexecuting 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.
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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.
12 Citations
20 Claims
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1. A system for improved simulation of a biological system comprising a plurality of chemical reactions, the system comprising:
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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. - View Dependent Claims (2, 3, 4, 5, 18)
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6. A method for simulation of a biological system, the method comprising:
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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. - View Dependent Claims (7, 8, 9, 17, 19)
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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:
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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. - View Dependent Claims (11, 12, 13, 20)
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14. A system for simulation of a biological system, the system comprising:
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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.
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15. A computer-readable storage medium holding computer-executable instructions for simulation of a biological system, the medium comprising one or more instructions for:
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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. - View Dependent Claims (16)
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Specification