Abstract: A computer-implemented method for cellular modeling is provided. The computer-implemented method for cellular modeling may include generating a cellular model, the model comprising a plurality of compartments, each compartment comprising at least one reaction, at least one species, or a combination of at least one reaction and at least one species; receiving a selection of at least one compartment for simulation to obtain at least one selected compartment; simulating the at least one selected compartment to obtain a result; and providing an output of the result from simulating the compartment; wherein at least two of the compartments comprise parallel pathways through the cellular model.

Abstract: A computer-implemented method for cellular modeling is provided. The computer-implemented method for cellular modeling may include generating a cellular model, the model comprising a plurality of compartments, each compartment comprising at least one reaction, at least one species, or a combination of at least one reaction and at least one species; receiving a selection of at least one compartment for simulation to obtain at least one selected compartment; simulating the at least one selected compartment to obtain a result; and providing an output of the result from simulating the compartment; wherein at least two of the compartments comprise parallel pathways through the cellular model.

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.

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. Each chemical reaction has a probability distribution associated therewith based on the kinetics of the particular chemical reaction. The probability distribution may be set by a user, determined automatically, or experimentally determined. 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 simulation engine calculates a reaction time for each chemical reaction based on the probability distribution associated with the particular chemical reaction. An analysis environment communicates with the simulation engine and displays the expected result.

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. Each time a chemical reaction executes during a simulation of the chemical or biochemical system, the simulation engine stores the reaction time and an identifier for the reaction that executes at that reaction time to produce a time-ordered history list. The history list can be replayed by simulating the reactions as the reactions occur in the history list to produce the same state sequence as the original simulation.

Abstract: An system for improved modeling of chemical and biological systems includes a graphical user interface accepting user commands and input for constructing a model of a biological system or a chemical reaction. The system also includes a simulation engine accepting as input said constructed model of the chemical reaction or biological system and generating as output dynamic behavior of the modeled biological system or chemical reaction. An analysis environment communicates with the simulation engine and displays the dynamic behavior.

Abstract: An integrated system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical reaction. The system also includes a simulation engine accepting as input said constructed model of the chemical or biochemical reaction and generating as output an expected result for a first chemical reaction using a first type of computational model and an expected result for a second chemical reaction using a second type of computational model.

Abstract: A system for modifying a model of a chemical reaction or biochemical process responsive to experimental results generated by an in situ experiment conducted on an experimental platform includes a simulation engine and an analysis environment. The simulation engine generates an expected result from a model of the chemical reaction or biochemical process. The analysis environment communicates with the simulation engine, gathers data from an experimental platform, and compares the expected result to data gathered from the platform.

Abstract: An integrated system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical reaction. The system also includes a simulation engine accepting as input said constructed model of the chemical or biochemical reaction and generating as output an expected result. An analysis environment communicates with the simulation engine and displays the expected result.