Abstract: Methods and systems are provided for simulating chemical and biological processes in a distributed technical computing environment. A technical computing client may associate a job, comprising one or more tasks, with a chemical or biological process. The technical computing client can distribute these tasks to technical computing workers for execution of the task. The technical computing workers execute the task and may provide a result of the task for the technical computing client. As such, the present invention allows the use of multiple computing resources on a network to perform simulation to facilitate decreasing the computation time.

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: The present invention is directed to a method, apparatus, and computer program product for performing selective memory restoration of a simulation based on an indexing scheme. The present invention executes a block diagram model of a biological process to generate simulations results using a simulation engine. An indexing scheme is used for registering memory locations used by a simulation context for a subsystem in the block diagram model. Experimental data is gathered from an in situ experimental device. A simulation environment is used to compare expected simulation results with experimental data. The block diagram model is then updated based on the results of the comparison to create a modified block diagram model, which is then used to selectively restore the simulation to a steady-state.

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: 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. An analysis environment communicates with the simulation engine and displays the expected result.

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 the 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.

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.

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 the 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 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 the 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.

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.