In this talk we will present the foundation of a unified, object-oriented,
three-dimensional biomodelling environment, which allows us to integrate
multiple submodels at scales from subcellular to those of tissues and
organs [1]. Our current implementation combines a modified discrete model from
statistical mechanics, the Cellular Potts Model, with a continuum reaction
diffusion model [2] and a state automaton with well-defined conditions for
cell differentiation transitions to model genetic regulation. This
environment allows one to rapidly and compactly create computational models
of a class of complex-developmental phenomena. To illustrate model
development, we describe simulations of the simplified version of the
formation of the skeletal pattern in a growing embryonic vertebrate limb.

In the second half of the talk we will describe the first
three-dimensional
stochastic model [3,4] based on contact-mediated cell communication, for
studying myxobacteria fruiting body development. The myxobacteria under
starvation undergo several developmental stages including rippling,
streaming, jamming, aggregation, and, finally, developing mature fruiting
bodies. Combining contact signaling between cells and slime production
mechanisms, our model reproduces all different stages in a transition from
3D traffic jams to aggregates and demonstrates possible structure of cell
arrangement within the fruiting body.