Abstract: Systems and methods are provided herein that enable computer-implemented modeling of a biological event. Cell-based models produced from such systems and methods are also disclosed. In some embodiments, systems and methods are provided for cell-centric simulation with accommodating environment feedback. In one embodiment, a computer-implemented method of modeling a biological event can include receiving configurable simulation information and initializing an ontogeny engine to an initial step boundary in accordance with the configurable simulation information. The method can also include 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 can include performing a stepCells function. The method can further include continuing the advancing until a halting condition is encountered.

Abstract: Systems and methods are provided herein that enable computer-implemented modeling of a biological event. Cell-based models produced from such systems and methods are also disclosed. In some embodiments, systems and methods are provided for cell-centric simulation with accommodating environment feedback. In one embodiment, a computer-implemented method of modeling a biological event can include receiving configurable simulation information and initializing an ontogeny engine to an initial step boundary in accordance with the configurable simulation information. The method can also include 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 can include performing a stepCells function. The method can further include continuing the advancing until a halting condition is encountered.

Abstract: Systems and methods are provided herein that enable computer-implemented modeling of a biological event. Cell-based models produced from such systems and methods are also disclosed. In some embodiments, systems and methods are provided for cell-centric simulation with accommodating environment feedback. In one embodiment, a computer-implemented method of modeling a biological event can include receiving configurable simulation information and initializing an ontogeny engine to an initial step boundary in accordance with the configurable simulation information. The method can also include 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 can include performing a metabolizeCell function. The method can further include continuing the advancing until a halting condition is encountered.

Abstract: A method system, and apparatus for virtual modeling of biological tissue yields virtual multicellular individuals that exhibit adaptive emergent functionality in response to environmental stimuli. Virtual environmental parameters and cells with genomes are generated, and modified by genetic operations. Cells are developed into generations of multicellular individuals, which are evaluated and selected via evolutionary search according to fitness criteria, and individuals exhibiting adaptive emergent functionality, such as self-repair, are developed and identified.

Abstract: Systems and methods are disclosed herein that enable computer-implemented modeling of lymphocyte differentiation and developmental processes. Cell-based models and methods for simulating natural and transgenic lymphocyte differentiation are also disclosed. In some embodiments, systems and methods are provided for cell-centric simulation of lymphocyte differentiation with accommodating virtual thymic and/or bone marrow environment feedback. In one embodiment, a computer-implemented method of modeling lymphocyte differentiation can include receiving configurable simulation information and initializing an ontogeny engine to an initial step boundary in accordance with the configurable simulation information. The method can also include 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.

Abstract: A multi-cellular virtual tissue having the emergent properties of self-repair, adaptive response to an altered environment, or tissue differentiation, and a method of generating the tissue by computer modeling are disclosed. The tissue is formed of a plurality of virtual cells, each having a heritable virtual genome containing a set of virtual genes relating to each of (a1) intercellular adhesion, (a2) cell division, (a3) cell growth, (a4) intercellular signaling, and (a5) the state of one cell relative to an adjacent cell.

Abstract: A method system, and apparatus for virtual modeling of biological tissue yields virtual multicellular individuals that exhibit adaptive emergent functionality in response to environmental stimuli. Virtual environmental parameters and cells with genomes are generated, and modified by genetic operations. Cells are developed into generations of multicellular individuals, which are evaluated and selected via evolutionary search according to fitness criteria, and individuals exhibiting adaptive emergent functionality, such as self-repair, are developed and identified.