GRAPHICAL RULE BASED MODELING OF BIOCHEMICAL NETWORKS
First Claim
1. A method for generating a biochemical reaction network, comprising:
- identifying the components and states of molecular entities within a system;
generating molecular entity graphs representing the components and states of said molecular entities;
formulating graph transformation rules representing the potential reactions and products of said molecular entities; and
applying said graph transformation rules iteratively to said molecular entity graphs until no new graphs are generated or a termination condition is satisfied to provide a network of biochemical reactions.
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Abstract
Formalized graphical reaction rules and conventions accounting for chemical states and binding or reaction states are provided for modeling complex biological systems such as signal transduction pathways. A system model is derived by defining typed attributed graphs which delimit molecular entities and their possible states. Graph transformation rules defining a class of potential reactions are defined and applied to the graphs and all new graphs that subsequently arise as a result of graph transformation. In one embodiment, a model is generated through the use of graph-rewriting rules which are associated with rate laws and applied iteratively to a seed set of chemical species graphs until a termination condition occurs.
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Citations
23 Claims
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1. A method for generating a biochemical reaction network, comprising:
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identifying the components and states of molecular entities within a system;
generating molecular entity graphs representing the components and states of said molecular entities;
formulating graph transformation rules representing the potential reactions and products of said molecular entities; and
applying said graph transformation rules iteratively to said molecular entity graphs until no new graphs are generated or a termination condition is satisfied to provide a network of biochemical reactions. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
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9. A method for generating a model of complex biochemical networks, comprising:
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specifying an initial set of molecular entities within a system;
identifying possible physical and chemical states of molecules, components and complexes of said molecular entities to provide a set of chemical species;
representing graphically said molecules, components, complexes and states of said chemical species;
specifying graph transformation rules for classes of products and reactions of said chemical species;
applying said graph transformation rules on an initial set of graphs of said chemical species to produce a first generation set of graphs; and
applying iteratively said graph transformation rules on said first generation set and upon on all subsequent generations of sets of graphs produced by the subsequent application of said graph transformation rules on the subsequent generations of sets of graphs to produce a model. - View Dependent Claims (10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)
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21. A computer system for modeling biochemical networks, comprising:
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a computation device configured for receiving data input;
a software program to operate said computation device, said program performing the operations of;
graphically representing molecules, components and chemical states of an initial set of molecular entities within a system;
applying specified graph transformation rules for classes of products and reactants of molecular entities within said system upon a seed set of graphs to produce a first generation set of graphs;
iteratively applying graph transformation rules to subsequent generations of graphs until a termination condition occurs; and
forming a model of molecular entities within said system; and
a user interface allowing the user to view computed model results and provide graphical and text input to said computation device. - View Dependent Claims (22, 23)
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Specification