X Development LLC

Nicholas Casavant

Jason Donald Thompson

Frank D Russo

Yu Tanouchi

A system is described for constructing a biological simulation using inputs from a knowledge base data structure and one or more templates. The knowledge base data structure comprises a set of entries representing distinct molecules and chemical reactions specific within the cell. Each template defines a sub-model program specification and a set of sub-model parameters to further characterize the sub-model specification. A graphical user interface is presented on a display for a user to view and select a templates and to assign information from the knowledge base to the selected template. From the graphical user interface, the user selects multiple templates to be included in the simulation and information from the knowledge base generally describing the cell. Based on the information selected from the graphical user interface, a compiler generates a simulation configuration data file comprising computer code capable of being executed by a simulation engine.

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

Techniques are described for determining the strain on a cell wall using two models: 1) a short timescale model, describing the relationship between physical properties assumed to be fixed and 2) a long timescale model, describing the dynamic chemical composition of a cell wall. Short term modeling of the physical properties in a cell wall is used to properly understand how physical factors such as osmotic pressure affects the strain on the cell wall, which is in turn used to identify conditions under which a cell wall will cease to function properly or lyse entirely. Although temporally the physical properties which cause cell walls to underperform/lyse can be evaluated under a short time frame, the chemical properties that lead to the physical properties which cause that behavior themselves change over much longer timescales, in a relative sense.

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Palo Alto, CA, United States of America

Nicholas Casavant