Abstract: Genetic sequence data occurring in genome sequences is represented for efficient access of the sequence information in a defined storage scheme. A described replet-sequence matrix data structure allows the compression and efficient access of sequence information. The data structure allows the dynamic change of ontology: the replet-information table can evolve by adding, updating, removing replets, and the set of replets present in the table represent the ontology at the moment. The data structure enables the sequence information to be processed in parallel, and also enables multiple views of the sequence data to exist along with replet specific information.

Abstract: A system, and associated article of manufacture, in which biochemical reactions of the system are modeled by using spatially heterogeneous stochastic Petri-net modeling. The biochemical reactions of the system to be modeled are defined. A spatial decomposition of the system is defined by defining regions of a space in which the system is to be modeled and by assigning each biochemical reaction to a region, such that the system is spatially heterogeneous. Relationships for inter-region movement of reactants of the biochemical reactions are defined as flux, advection, convection, and/or diffusion-based molecular movements. The system of the biochemical reactions is then modeled by modeling the biochemical reactions of each region as a spatially homogenous stochastic Petri-net and by modeling the inter-region movement of the reactants based on the relationships as defined.

Abstract: A system, and associated article of manufacture, in which biochemical reactions of the system are modeled by using spatially heterogeneous stochastic Petri-net modeling. The biochemical reactions of the system to be modeled are defined. A spatial decomposition of the system is defined by defining regions of a space in which the system is to be modeled and by assigning each biochemical reaction to a region, such that the system is spatially heterogeneous. Relationships for inter-region movement of reactants of the biochemical reactions are defined as flux, advection, convection, and/or diffusion-based molecular movements. The system of the biochemical reactions is then modeled by modeling the biochemical reactions of each region as a spatially homogenous stochastic Petri-net and by modeling the inter-region movement of the reactants based on the relationships as defined.

Abstract: Modeling of biochemical reactions of a system is accomplished using spatially heterogeneous stochastic Petri-net modeling. The biochemical reactions of the system to be modeled are defined. A spatial decomposition of the system is defined by defining regions of a space in which the system is to be modeled and by assigning each biochemical reaction to a region, such that the system is spatially heterogeneous. Relationships for inter-region movement of reactants of the biochemical reactions are defined as flux, advection, convection, and/or diffusion-based molecular movements. The system of the biochemical reactions is then modeled by modeling the biochemical reactions of each region as a spatially homogenous stochastic Petri-net and by modeling the inter-region movement of the reactants based on the relationships as defined.