Biological systems can be modeled beneficially as reactive systems, using languages and tools developed for the construction of man-made systems. Our long-term aim is to model a full multi-cellular animal as a reactive system —- specifically, the C. elegans nematode worm, which is complex, but very well-defined in terms of anatomy and genetics. The challenge is to construct a full, true-to-all-known-facts, 4-dimensional, fully animated model of the development and behavior of this worm (or of a comparable multi-cellular animal), which is easily extendable as new biological facts are discovered.
I share this goal (although I may or may not constrain myself to C. elegans).
To start, I'm curious about embryogenesis and how a single egg cell can develop into an adult worm. I've found a paper entitled "Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans" that contains a simple model that I'd like to try and replicate.
One of the initial stumbling blocks is how to render the model for visualization. I've started looking at Direct3D, as well as a couple of C# graphics engines, including Axiom. I'm not sure yet where the project will lead, but wherever it takes me, it should be an interesting journey.
I'm going to give the project the highly creative name elegans2007a.
Once I have this relatively simple model working, I'll begin extending it (or throw it out an create a better model).
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