The Mathworks, Inc.

Ricardo E Paxson

Joseph F Hicklin

Ramamurthy Mani

Roy Lurie

Patrick L Edson

Edward Whittington Gulley

Melissa J Pike

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.

Methods and system for simulation of chemical and biological processes in a distributed technical computing environment

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.

Method, computer program product, and apparatus for selective memory restoration of a simulation

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.

Computer-implemented cellular modeling having parallel pathways

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.

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

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.

Method and apparatus for improved simulation of chemical and biochemical reactions

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.

Method and apparatus for integrated modeling, simulation and analysis of chemical and biochemical reactions

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.

Creation and maintenance of a history list in a method and apparatus for integrated modeling, simulation and analysis of chemical and biological systems

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.

Method and apparatus for integrated modeling, simulation and analysis of chemical and biological systems having a sequence of reactions, each simulated at a reaction time determined based on reaction kinetics

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Ricardo E Paxson