1. A method comprising: providing, using a computing device, a matrix listing a plurality of species participating in one or more chemical reactions; generating, using the 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 input to modify the graphical layout of the executable block diagram; and modifying, using the computing device, the graphical layout of the executable block diagram based on the received input.