The madness is stemming from the complexity of the challenge. Trying to visualize and model all of the inter-related concepts of simulating a biological network in my mind. I've been jumping all over the place studying and reading white papers, books, journals, thesises, etc on microbiology, informatics, MD, genetics, pathways, chemiformatics, modeling, threading, game theory, genetic algorithms, complexity theory, baysian networks, chaos theory, design patterns, gerontology, agent based programming, GROMACs, E-Cell, RDBMSs, MMRPGs, protein folding, distributed computing, super-computing, blah, blah, blah. I've been turning this all over and over in my head and attempting to view it from many angles to see if a clear path will iluminate itself. I start putting it on paper, whiteboards and in graph paper and i just keep sketching out models and meta-models but none of them feel right. Grrr. I had to take a couple of weeks off to clear my head b/c I was going bonkers.
The biggest problem for this kind of simulations as I see it is the lack of quantitative biological parameters.
True. The combinatorial explosion that occurs when you overlay the various models upon one another are staggering but it has to be done. Dismissing it as intractable = death for us all.
