System and method for simulating cellular biochemical pathways
First Claim
1. A system for demonstrating signal cascades that occur in certain cells when certain stimuli are introduced, comprising:
- (a) a database of known cellular components and reactions; and
(b) an inference engine for generating signal cascades, wherein the inference engine is linked to the database.
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Abstract
The present invention relates to a system and method for examining pathways. In particular, the present invention provides a system and method for examining pathways that underlie cellular functions, specifically signal transduction pathways. One aspect of the invention relates to the prediction of (a) functional properties of a protein, (b) potential interaction partners of the protein, and/or (c) potential target biochemical pathways within which the protein may interact. Thus, according to the invention, the influence of a given stimulus on a biochemical pathway can be assessed.
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Citations
56 Claims
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1. A system for demonstrating signal cascades that occur in certain cells when certain stimuli are introduced, comprising:
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(a) a database of known cellular components and reactions; and
(b) an inference engine for generating signal cascades, wherein the inference engine is linked to the database. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13)
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12. The system of 11, wherein said information comprises signal transduction information on plant cellular environments or animal cellular environments.
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14. A computer-implemented method for a reverse pathway comprising:
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(a) providing information regarding a target cellular environment and an endpoint;
(b) simulating at least one aspect of a reverse pathway based on the information provided regarding the target cellular environment and the endpoint; and
(c) displaying at least one aspect of the reverse pathway.
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15. A computer-implemented method of predicting pathways comprising:
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(a) simulating signal cascades of pathways that occur when stimuli are introduced;
(b) dynamically generating results using a simulation module, the simulation module comprising an inference engine linked to at least one dynamic database, the at least one dynamic database containing definitions relating to cellular concepts, components and reactions.
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16. A computer-implemented method for simulating at least one aspect of a cellular biochemical pathway comprising:
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(a) providing information regarding a target cellular environment and a stimulus event;
(b) simulating at least one aspect of a cellular biochemical pathway based on the information provided regarding the target cellular environment and the stimulus event; and
(c) displaying at least one aspect of the cellular biochemical pathway. - View Dependent Claims (17, 18, 19)
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20. A system for simulating at least one aspect of a cellular biochemical pathway comprising:
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(a) a data input interface for receiving cellular environment information and stimuli information;
(b) a simulation module that generates at least one simulated pathway for at least one aspect of a cellular pathway by determining an order of cellular events that occur within a defined cellular environment, wherein the simulation is based on the cellular environment and stimuli information received by the data input interface; and
(c) a display module that displays a representation of the at least one simulated pathway. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27, 28)
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29. A method for generating a representation of a biochemical pathway, comprising:
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providing as inputs;
(a) a set of separately defined concepts and events, (b) a physiological context of the biochemcial pathway, (c) at least one stimulus, and (d) an event corresponding to the at least one stimulus; and
dynamically determining substances available to the biochemical pathway and an order in which events occur in the biochemical pathway. - View Dependent Claims (30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47)
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48. A method for generating a representation of an event of a biochemical pathway comprising, providing as inputs:
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(a) a set of separately defined reactants of the event, (b) a physiological context of the event, and (c) at least one defined substance that is a stimulus of the event; and
dynamically determining an event of the biochemical pathway, comprising a process that is an immediate result of the stimulus. - View Dependent Claims (49, 50)
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51. A method of determining an effect that modulating one or more reactions in a biochemical pathway has on an operation of the biochemical pathway, comprising:
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(a) generating and displaying a representation of a first biochemical pathway by dynamically determining substances and processes that form the first biochemical pathway, and an order in which the substances appear and the processes occur in the first biochemical pathway;
(b) generating and displaying a representation of a second biochemical pathway, wherein a definition of at least one substance or process of the first biochemical pathway is changed so as to modulate at least one reaction of the first biochemical pathway; and
(c) comparing the representations of the first and second biochemical pathways and determining an effect of modulating the at least one reaction of the first biochemical pathway.
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52. A method of identifying a potential pharmacological target in a biochemical pathway that affects a physiological condition of an organism, comprising:
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(a) generating and displaying a representation of a first biochemical pathway by dynamically determining substances and processes that form the first biochemical pathway, and an order in which the substances appear and the processes occur in the first biochemical pathway;
(b) generating and displaying a representation of a second biochemical pathway wherein a definition of at least one substance or process of the first biochemical pathway is changed so as to modulate at least one reaction of the first biochemical pathway; and
(c) comparing the representations of the first and second biochemical pathways and determining an effect of modulating the at least one reaction of the first biochemical pathway;
wherein a substance of the first biochemical pathway is a potential target for a drug that modulates the reactivity when the substance participates in a reaction which, when modulated, alters the biochemical pathway in a desired manner.
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53. A device for generating a representation of a biochemical pathway, comprising:
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(a) means for entering data;
(b) an electronic storage media that stores definitions of substances and processes of the biochemical pathway;
(c) a data processing unit that generates a representation of the biochemical pathway; and
(d) means for displaying a representation of at least one substance or process of the biochemical pathway;
wherein the definitions of each substance and process comprises at least one attribute of the substance or process.
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54. A device for generating a representation of a biochemical pathway event, comprising:
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(a) a device for entering input data;
(b) an electronic storage media that stores definitions of substances and processes from which the biochemical pathway is formed;
(c) a data processing unit that, in response to inputs comprising at least one defined substance or process that is a stimulus of the biochemical pathway event, dynamically determines the biochemical pathway event by determining a process that is an immediate result of the stimulus substance or process; and
(d) a display device that displays a representation of at least one substance or process of the biochemical pathway;
wherein the definitions of each substance and process comprises at least one attribute of the substance or process. - View Dependent Claims (55)
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56. A device for generating a representation of a pathway, comprising:
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(a) means for entering data;
(b) means for storing definitions of concepts and events of the pathway;
(c) means for generating a representation of the pathway; and
(d) means for displaying a representation of at least one concept or event of the pathway;
wherein the definitions of each concept and event comprises at least one attribute of the concept or event.
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Specification