When I said that software engineers add in the speed and reliability, I didn't mean they _only_ add in the speed and reliability: just that these two tenants of good software engineering where accounted for in this "correct" way of doing things (as opposed to the state of most genomics software that I described above).
However, I can see how my phrasing can give the wrong impression about the contributions an engineer makes when the biologist and engineer sit down to do create the real thing together. In a positive environment, both sides (biologists and software engineers) share enough information with one another that the either can make contributions to the scientific/software engineering domain.