Data structure, compilation service, and graphical user interface for rapid simulation generation

A non-transitory computer readable storage medium storing instructions encoded thereon that, when executed by a processor, cause the processor to perform the steps comprising:

• accessing, with a computer, a knowledge base data structure comprising a plurality of entries, the entries representing distinct molecules and entries representing distinct chemical reactions;
• accessing, with the computer, a set of templates, each template including a sub-model program specification and a set of sub-model parameters corresponding to a set of sub-model parameter fields, wherein the accessed set of templates includes a shared sub-model program specification, each template of the accessed set receiving different parameter values for assignment to the sub-model parameter fields;
• providing, through the computer, a graphical user interface for display on a computer screen, the graphical user interface providing for viewing and selection of at least one of:
• one or more of the templates, and one or more of the entries of the knowledge base data structure;
• receiving, at the computer, a set of input selections specifying a plurality of the templates of the set for inclusion in a simulation and assignment for a plurality of entries from the knowledge base data structure to the specified templates, wherein the knowledge base data structure comprises a representation of a reaction network containing the plurality of entries for assignment to the selected templates;
• and
• executing, by the computer, a compiler to generate a simulation configuration data file based on the set of input selections, the simulation configuration data file comprising computer code that is executed by a simulation engine.

A system comprising:

• a processor;
• and
• a non-transitory computer readable storage medium storing instructions encoded thereon that, when executed by a processor, cause the processor to perform the steps comprising:
• accessing, with a computer, a knowledge base data structure comprising a plurality of entries, the entries representing distinct molecules and entries representing distinct chemical reactions;
• accessing, with the computer, a set of templates, each template including a sub-model program specification and a set of sub-model parameters for the sub-model program corresponding to a set of sub-model parameter fields, wherein the accessed set of templates includes a shared sub-model program specification, each template of the accessed set receiving different parameter values for assignment to the sub-model parameter fields;
• providing, through the computer, a graphical user interface for display on a computer screen, the graphical user interface providing for viewing and selection of at least one of:
• one or more of the templates, and one or more of the entries of the knowledge base data structure;
• receiving, at the computer, a set of input selections specifying a plurality of the templates of the set for inclusion in a simulation and assignment for a plurality of entries from the knowledge base data structure to the specified templates, wherein the knowledge base data structure comprises a representation of a reaction network containing the plurality of entries for assignment to the selected templates;
• and
• executing, by the computer, a compiler to generate a simulation configuration data file based on the set of input selections, the simulation configuration data file comprising computer code that is executed by a simulation engine.