Block diagram explorer in a method and apparatus for integrated modeling, simulation and analysis of chemical and biological systems

Abstract

A system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical system comprising a plurality of chemical reactions. The system also includes a simulation engine accepting as input said constructed model of the chemical or biochemical system and generating as output an expected result. The modeling environment includes a block diagram explorer for displaying a block diagram in a graphical user interface describing the system as a hierarchical network of interconnected blocks. Each block represents a species participating one of the chemical reactions or one of said chemical reactions in the system. The block diagram explorer allows for a user to manipulate and modify the graphical parameters of the block diagram representation to provide insight into the functionality and operation of the system being modeled.

1 . (canceled) 
     
     
         2 . A method comprising:
 providing, using a computing device, a connectivity matrix, the connectivity matrix including a plurality of species participating in a plurality of chemical reactions;   generating, using the computing device, an executable block diagram based on the connectivity matrix, the generating including:
 representing molecular interactions in the plurality of chemical reactions using the executable block diagram, 
 incorporating, into the executable block diagram:
 a first block and a second block, respectively, representing one or more of the plurality of species, 
 a third block representing one or more of the plurality of chemical reactions, 
 an input connector connecting the first block to the third block, and 
 an output connector connecting the third block to the second block; 
 
   processing the connectivity matrix to determine two-dimensional positions for the first block, the second block, and the third block on a graphical layout of the executable block diagram; and   displaying, on a display device, the graphical layout of the executable block diagram, where the first block, the second block, and the third block are displayed at the determined two-dimensional positions.   
     
     
         3 . The method of  claim 2 , further comprising:
 executing the executable block diagram, the executing including:
 simulating the plurality of chemical reactions, and 
 generating a simulation result based on the simulating; and 
   modifying, using the computing device, the graphical layout of the executable block diagram based on the simulation result, the modifying including:
 displaying at least one of the first block, the second block and the third block at a modified two-dimensional position. 
   
     
     
         4 . The method of  claim 3 , further comprising:
 modifying the graphical layout of the executable block diagram based on a user input.   
     
     
         5 . The method of  claim 4 , wherein the user input selects a block, the method further comprising:
 displaying the selected block, and   removing non-selected blocks from the graphical layout of the executable block diagram.   
     
     
         6 . The method of  claim 4 , the modifying further comprising:
 adding one or more additional blocks to the graphical layout of the executable block diagram, or   removing one or more of the first block, the second block and the third block from the graphical layout of the executable block diagram.   
     
     
         7 . The method of  claim 3 , wherein the modifying comprises:
 recalculating a position of the at least one of the first block, the second block and the third block based on the simulation result.   
     
     
         8 . The method of  claim 3 , wherein the modifying comprises:
 splitting one of the first block, the second block and the third block into a plurality of cloned blocks.   
     
     
         9 . The method of  claim 2 , wherein the processing further comprises:
 using a rule or an objective to determine the two-dimensional positions for the first block, the second block or the third block on the graphical layout of the executable block diagram.   
     
     
         10 . The method of  claim 2 , wherein:
 the first block represents a first species among the plurality of species,   the second block represents a second species among the plurality of species,   the third block represents a first chemical reaction among the plurality of chemical reactions,   the input connector indicates that the first chemical reaction uses the first species as an input, and   the output connector indicates that the first chemical reaction produces the second species as an output.   
     
     
         11 . A non-transitory computer-readable medium storing:
 one or more instructions that, when executed on a processing device, cause the processing device to:
 provide a connectivity matrix, the connectivity matrix including a plurality of species participating in a plurality of chemical reactions; 
 generate an executable block diagram based on the connectivity matrix, the generating including:
 representing molecular interactions in the plurality of chemical reactions using the executable block diagram, 
 incorporating, into the executable block diagram:
 a first block and a second block, respectively, representing one or more of the plurality of species, 
 a third block representing one or more of the plurality of chemical reactions, 
 an input connector connecting the first block to the third block, and 
 an output connector connecting the third block to the second block; 
 
 
 process the connectivity matrix to determine two-dimensional positions for the first block, the second block, and the third block on a graphical layout of the executable block diagram; and 
 display, on a display device, the graphical layout of the executable block diagram, where the first block, the second block, and the third block are displayed at the determined two-dimensional positions. 
   
     
     
         12 . The non-transitory medium of  claim 11 , further storing:
 one or more instructions that, when executed on the processing device, cause the processing device to:
 execute the executable block diagram, the executing including:
 simulating the plurality of chemical reactions, and 
 generating a simulation result based on the simulating; and 
 
 modify the graphical layout of the executable block diagram based on the simulation result, the modifying including:
 displaying at least one of the first block, the second block and the third block at a modified two-dimensional position. 
 
   
     
     
         13 . The non-transitory medium of  claim 12 , further storing:
 one or more instructions that, when executed on the processing device, cause the processing device to:
 modify the graphical layout of the executable block diagram based on a user input. 
   
     
     
         14 . The non-transitory medium of  claim 13 , wherein the user input selects a block, the medium further storing:
 one or more instructions that, when executed on the processing device, cause the processing device to:
 display the selected block, and 
 remove non-selected blocks from the graphical layout of the executable block diagram. 
   
     
     
         15 . The non-transitory medium of  claim 13 , further storing:
 one or more instructions that, when executed on the processing device, cause the processing device to:
 add one or more additional blocks to the graphical layout of the executable block diagram, or 
 remove one or more of the first block, the second block and the third block from the graphical layout of the executable block diagram. 
   
     
     
         16 . The non-transitory medium of  claim 12 , further storing:
 one or more instructions that, when executed on the processing device, cause the processing device to:
 recalculate a position of the at least one of the first block, the second block and the third block based on the simulation result. 
   
     
     
         17 . The non-transitory medium of  claim 11 , wherein:
 the first block represents a first species among the plurality of species,   the second block represents a second species among the plurality of species,   the third block represents a first chemical reaction among the plurality of chemical reactions,   the input connector indicates that the first chemical reaction uses the first species as an input, and   the output connector indicates that the first chemical reaction produces the second species as an output.   
     
     
         18 . A system comprising:
 a processor executing instructions for:
 providing a connectivity matrix, the connectivity matrix including a plurality of species participating in a plurality of chemical reactions; 
 generating an executable block diagram based on the connectivity matrix, the generating including:
 representing molecular interactions in the plurality of chemical reactions using the executable block diagram, 
 incorporating, into the executable block diagram:
 a first block and a second block, respectively, representing one or more of the plurality of species, 
 a third block representing one or more of the plurality of chemical reactions, 
 an input connector connecting the first block to the third block, and 
 an output connector connecting the third block to the second block; 
 
 
 processing the connectivity matrix to determine two-dimensional positions for the first block, the second block, and the third block on a graphical layout of the executable block diagram; and 
   a display device for:
 displaying the graphical layout of the executable block diagram, where the first block, the second block and the third block are displayed at the determined two-dimensional positions. 
   
     
     
         19 . The system of  claim 18 , wherein the processor further executes instructions for:
 executing the executable block diagram, the executing including:
 simulating the plurality of chemical reactions, and 
 generating a simulation result based on the simulating; and 
   modifying the graphical layout of the executable block diagram based on the simulation result, the modifying including:
 displaying, on the display device, at least one of the first block, the second block and the third block at a modified two-dimensional position. 
   
     
     
         20 . The system of  claim 19 , wherein the processor further executes instructions for:
 modifying the graphical layout of the executable block diagram based on a user input.   
     
     
         21 . The system of  claim 19 , wherein the processor further executes instructions for:
 recalculating a position of the at least one of the first block, the second block and the third block based on the simulation result.