By implementing a deterministic immature stage, additional information regarding population dynamics is incorporated without developing a completely stochastic model, which would be considerably more computationally-intensive.
The focus on individuals is considerably more computationally demanding than top down system-level simulation, but provides a natural and flexible environment for studying systems demonstrating emergent behavior.
Gapped local alignment is considerably more computationally expensive than ungapped alignment, especially for ABI SOLiD color space data, but improves our ability to find SNPs, insertions, deletions, and compensate for color errors simultaneously.
Codon-based substitution models are less frequently implemented, as they consider sequence change at the level of codons, rather than nucleotides or amino acid residues, and are considerably more computationally intensive.
Certain behaviors of the studied system (for example, the NFκB oscillations) can be captured only by using the logic-derived differential equations (a method that is considerably more computationally expensive, and which involves many additional arbitrary parameters).
This is considerably more demanding computationally, and is not likely to provide additional insight in most simple cases.
Both computationally designed proteins were considerably more stable than the naturally occurring protein, with midpoints of thermal denaturation greater than 99 °C.
Since searching a combinatorial landscape computationally (i.e. in silico) is considerably more rapid and efficient than is performing 'real' experiments at every point, it is clear that we need much more effective models of biology than we have today 54.
