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At least some parts of contemporary science could be characterized as “model-based” (P.Godfrey-Smith); at the same time the usage of computational methods in science has been increased rapidly over last decades. Crossing these two issues, we have computational modelling and computer simulation methods, which possibly requires special attention of philosophers of science. As far as bioinformatics (computational biology) consists of such methods, it could be used as a broad illustration of epistemological problems connected with simulations and models. Possibly it can provide a better understanding of what is it to be a model/simulation; which capacities do models have and which they don’t; how to make a distinction between modelling, simulating and experimenting and, most of all, do we really need such distinction. It has been claimed (P.Humphreys), that computer simulations require some new kind of epistemology (different from “old” model-talk in philosophy of science); we can show (by example of bioinformatics) in which exactly sense these claims should be discussed and then (partly) accepted or rejected.