Cell-based models and methods for simulating lymphocyte differentiation and other biological events

A computer program product for modeling lymphocyte differentiation comprising a computer usable medium including a computer readable program, wherein the computer readable program when executed by a computer causes a method to be performed, the method comprising:

• receiving configurable simulation information, the configurable simulation information including:
• configured physical and chemical parameters;
• configured environmental information;
• configured metabolic information;
• initializing an ontogeny engine to an initial step boundary in accordance with the configurable simulation information, wherein the initial step boundary defines at least one virtual early lymphoid progenitor (ELP) cell in a virtual environment;
• and
• advancing the ontogeny engine, until a halting condition is encountered, from a current step boundary to a next step boundary in accordance with the configurable simulation information and the current step boundary, the advancing comprising performing a stepCells function and a stepPhysics function.

A system for modeling lymphocyte differentiation, comprising:

• a processor;
• means for executing on the processor and receiving configurable simulation information, the configurable simulation information including:
• configured physical and chemical parameters;
• configured environmental information;
• and
• configured metabolic information, wherein configured metabolic information includes information for defining a lymphocyte virtual genome and a set of chemical-interaction rules;
• means for executing on the processor and initializing an ontogeny engine to an initial step boundary in accordance with the configurable simulation information, wherein the initial step boundary defines at least one virtual early lymphoid progenitor (ELP) cell in a virtual environment, the ELP cell having been assigned the lymphocyte virtual genome;
• means for executing on the processor and advancing the ontogeny engine from a current step boundary to a next step boundary in accordance with the configurable simulation information and the current step boundary, the advancing comprising performing a stepCells function and a stepPhysics function;
• and
• means for executing on the processor and continuing the advancing until a halting condition is encountered.