Modeling biological systems
First Claim
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1. A method comprising:
- generating a model of a biological system, the model comprising rules that express a substitution of at least one symbol by at least another symbol, the symbols representing a biological element, and at least some of the rules being expressed in a manner that enables an inference engine to infer alternative results from the system based on an initial hypothetical state.
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Abstract
Biological systems are modeled using formal languages and theorem provers and model checkers and term rewriting systems. The models include rules that express a substitution of at least one symbol by at least another symbol. The symbols represent elements of the biological system, and the rules are expressed in a manner that, for example, enables an inference engine to infer alternative results from the system based on an initial hypothetical state.
Inference engines are also applied to symbolically simulate, test properties, and explore the biological system. Abstractions and algorithms can be employed to enable symbolic calculation of state sets for the biological system.
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Citations
109 Claims
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1. A method comprising:
generating a model of a biological system, the model comprising rules that express a substitution of at least one symbol by at least another symbol, the symbols representing a biological element, and at least some of the rules being expressed in a manner that enables an inference engine to infer alternative results from the system based on an initial hypothetical state. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
- 18. An article comprising machine-readable media having encoded thereon a model of a biological system, the model comprising rules that express a substitution of at least one symbol by at least another symbol, the symbols representing a biological element, and at least one of the rules being expressed in a manner that enables an inference engine to infer alternative results from the system based on an initial hypothetical state.
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34. A method comprising:
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receiving a set of symbols in an inference engine, the set representing a hypothetical initial state of a biological system, the symbols representing elements of the biological system; and
processing the initial state using rules that express a substitution of at least one of the symbols by at least another symbol representing a biological element to infer alternative resultant states of the system. - View Dependent Claims (35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65)
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66. A method comprising:
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receiving a set of symbols in an inference engine, the set of symbols representing a hypothetical initial state of a biological system, the symbols representing biological elements of the system; and
iteratively substituting at least one of the symbols by at least another symbol representing a biological element using rules that represent interactions between the biological elements until a terminal state is detected or until alternative resultant states are detected. - View Dependent Claims (67, 68, 69, 70, 71, 72, 73, 74, 75, 76)
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77. A method comprising:
receiving into an inference engine a rule set comprising rules that express a substitution of one or more of the symbols representing biological elements by at least another symbol representing a biological element; and
determining a property of the rule set.- View Dependent Claims (78, 79, 80, 81)
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82. A method comprising:
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receiving into an inference engine (1) at least a first and a second set of symbols wherein the first set of symbols represents a hypothetical first state of a biological system, and the second set of symbols represents a hypothetical second state of the biological system, and the symbols represent biological elements of the biological system, and (2) rules that express a substitution of one or more of the symbols representing biological elements by at least another symbol representing a biological element; and
determining if one or more of the rules must be true or false for the first state to reach the second state by processing the first state using the rules. - View Dependent Claims (83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95)
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96. An article comprising machine-readable media having encoded thereon software configured to cause the processor to:
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receive a set of symbols, the set representing a hypothetical initial state of a biological system, the symbols representing biological elements of the system; and
iteratively substitute one or more of the symbols representing biological elements by at least another symbol representing a biological element using rules that represent interactions between the biological elements until a terminal state or until alternative resultant states are detected. - View Dependent Claims (97, 98, 99, 100, 101, 102, 103, 104, 105)
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106. An article comprising machine-readable media having encoded thereon software configured to cause the processor to:
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receive information for a first state of a biological system;
generate symbols representing biological elements of the system; and
iteratively substitute one or more of the symbols representing biological elements by at least another symbol representing a biological element using rules that represent interactions between the biological elements until a terminal state or until alternative resultant states are detected. - View Dependent Claims (107, 108, 109)
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Specification