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

A non-transitory computer readable medium storing instructions that, when executed by a processor, cause the processor to:

• provide a matrix listing a plurality of species participating in one or more chemical reactions;
• generate an executable block diagram based on the matrix, where:
• the executable block diagram represents a system including the one or more chemical reactions,
• the executable block diagram includes:
• a plurality of blocks representing the plurality of species, and
• a plurality of lines representing a relationship among the plurality of species,
• executing the executable block diagram simulates the one or more chemical reactions,
• the generating includes:
• processing the matrix to determine an optimized two-dimensional position for the plurality blocks on a graphical layout of the executable block diagram based on the relationship among the plurality of species;
• dynamically display the graphical layout of the executable block diagram in a graphical user interface, where the plurality of blocks are displayed at the determined optimized two-dimensional position;
• receive an input to modify the graphical layout of the executable block diagram;
• and
• modify the graphical layout of the executable block diagram based on the received input.

A method comprising:

• providing, using a computing device, a matrix listing a plurality of species participating in one or more chemical reactions;
• generating, using a computing device, an executable block diagram based on the matrix, where:
• the executable block diagram represents a system including the one or more chemical reactions,
• the executable block diagram includes:
• a plurality of blocks representing the plurality of species, and
• a plurality of lines representing a relationship among the plurality of species,
• executing the executable block diagram simulates the one or more chemical reactions;
• the generating includes:
• processing, using the computing device, the matrix to determine an optimized two-dimensional position for the plurality of blocks on a graphical layout of the executable block diagram based on the relationship among the plurality of species;
• dynamically displaying, on a display device, the graphical layout of the executable block diagram in a graphical user interface, where the plurality of blocks are displayed at the determined optimized two-dimensional position;
• receiving, using the computing device, an instruction from a user regarding a graphical parameter of the graphical layout of the executable block diagram;
• and
• modifying, using the computing device, the graphical layout of the executable block diagram according to the instruction.

A non-transitory computer readable medium storing instructions that, when executed by a processor, cause the processor to:

• provide a matrix listing a plurality of species participating in one or more chemical reactions;
• generate an executable block diagram based on the matrix, where:
• the executable block diagram represents a system including the one or more chemical reactions,
• the executable block diagram includes:
• a plurality of blocks representing the plurality of species, and
• a plurality of lines representing a relationship among the plurality of species,
• executing the executable block diagram simulates the one or more chemical reactions,
• the generating includes:
• processing the matrix to determine an optimized two-dimensional position for the plurality of blocks on a graphical layout of the executable block diagram based on the relationship among the plurality of species;
• dynamically display the graphical layout of the executable block diagram in a graphical user interface, where the plurality of blocks are displayed at the determined optimized two-dimensional position;
• receive an instruction from a user regarding a graphical parameter of the graphical layout of the executable block diagram;
• and
• modify the graphical layout of the executable block diagram according to the instruction.

A system comprising:

• a processor for executing instructions to provide:
• a block diagram explorer for:
• providing a matrix listing a plurality of species participating in one or more chemical reactions,
• a modeling component comprising:
• a modeling environment for generating an executable block diagram using the matrix, where:
• the executable block diagram represents a system including the one or more chemical reactions,
• the executable block diagram includes:
• a plurality of blocks representing the plurality of species, and
• a plurality of lines representing a relationship among the plurality of species,
• executing the executable block diagram simulates the one or more chemical reactions,
• the generating includes:
• processing the matrix to determine an optimized two-dimensional position for the plurality of blocks on a graphical layout of the executable block diagram based on the relationship among the plurality of species,
• a display device dynamically displaying the graphical layout in a graphical user interface, where the plurality of blocks are displayed at the determined optimized two-dimensional position;
• and
• a simulation engine accepting as input the executable block diagram and generating as output dynamic behavior of the system represented by the executable block diagram.