Modeling Biological Systems

Overview Why model biological systems? What to model? Types of models

Why model biological systems? May provide insight into a problem in experimentation (e.g. a genetic circuit oscillating at a frequency that inhibits bi-stable behavior). Increased inefficiency. Instead of conducting every experiment in the lab, some can be simulated to judge practicality and necessity. Selection of ideal biological parts for desired output.

Types of Models Continuous time simulation - assumes there are enough reactants for a continuous probability distribution of all reactions. Fast computationally, not as accurate in general. Stochastic simulation - takes into account the low concentration of reactants on the cellular level. Very slow computationally, considered far more accurate. Hybrid stochastic simulation - combination of continuous time and stochastic methods.

What to Model? Although it would be nice to model every parameter, in most cases it is impractical or impossible to do so due to computational limitations.